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Biomanus/experiments/bioagent-bench-runs/alzheimer-mouse_20260522_134022/task_query.txt

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+You are running a bioagent-bench task with local files already prepared.
+
+Task ID: alzheimer-mouse
+Task name: Alzheimer Mouse Models: Comparative Pathway Analysis
+Benchmark prompt:
+Perform a comparative differential expression analysis of three different Alzheimer's Disease mouse models (5xFAD, 3xTG-AD, and PS3O1S) to identify shared molecular KEGG pathways. The output should be a CSV file with the following columns: 'pathway','5xFAD_pvalue','3xTG_AD_pvalue','PS3O1S_pvalue'. Example csv <example>Pathway,5xFAD_pvalue,3xTG_AD_pvalue,PS3O1S_pvalue
+Phagosome Homo sapiens hsa04145,1.5045916403148935e-09,0.3102788532065793,0.4443015705596512
+</example> 
+Data background:
+Analyze 5xFAD, 3xTG-AD, and PS301S mouse models: normalize counts, perform differential expression, run KEGG pathway enrichment, and compare shared pathways across models.
+Constraints:
+1. Use only the benchmark inputs and references explicitly listed below.
+2. Do not inspect or use any files under benchmark truth/results directories, sibling task directories, generated biomni_data caches, or previous run outputs.
+3. Save the required final deliverables exactly to the paths listed below.
+4. Save any intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Biomanus/experiments/bioagent-bench-runs/alzheimer-mouse_20260522_134022
+5. Keep final deliverables in the same schema/format requested by the benchmark prompt.
+6. Return a concise final summary after writing the required files.
+7. The runner, Python REPL, MCP servers, Rscript, and CLI subprocesses are bound to this conda environment: /225040511/miniconda3/envs/biomni_e1. Do not switch to another conda environment.
+
+Benchmark data policy:
+- Allowed input data directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data
+- Allowed reference directory: <none>
+- Allowed scratch/output directory: /225040511/project/Biomanus/experiments/bioagent-bench-runs/alzheimer-mouse_20260522_134022
+- Forbidden truth/results directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/results
+- Forbidden sibling benchmark task directories: /225040511/project/bioagent-bench/dataset/<any task other than alzheimer-mouse>
+- Forbidden generated Biomni cache/runtime directories inside benchmark inputs: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/biomni_data and /225040511/project/bioagent-bench/dataset/alzheimer-mouse/reference/biomni_data
+- Do not inspect previous bioagent-bench-runs as data sources.
+- Do not download external databases or install new packages during the benchmark run.
+- You may use installed command-line tools, Python/R packages, and MCP servers as executors, but their inputs must come from the allowed paths above.
+
+Input data directory:
+/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data
+Visible input files:
+- 3xtgad_counts_clean.csv
+- 5xfad_counts_clean.csv
+- 5xfad_counts_integer.csv
+- DEA_3xTGAD.csv
+- DEA_5xFAD.csv
+- DEA_PS3O1S.csv
+- GSE161904_Raw_gene_counts_cortex.txt
+- GSE168137_countList.txt
+- entrez_3xtgad.txt
+- entrez_5xfad.txt
+- entrez_ps301s.txt
+- run_deseq2_5xfad.R
+
+Reference data directory:
+<none>
+Visible reference files:
+- <none>
+
+Required final output paths:
+- pathway_comparison.csv: /225040511/project/Biomanus/experiments/bioagent-bench-runs/alzheimer-mouse_20260522_134022/pathway_comparison.csv

Biomanus/experiments/bioagent-bench-runs/comparative-genomics_20260514_055459/agent_runtime/biomni_data/runtime_mcp_configs/runtime_mcp_20260514_055600_472734.yaml

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+mcp_servers:
+  diamond:
+    enabled: true
+    description: 'Installs packages: diamond. Copies scripts: diamond_server.py. Default
+      command: ["python", "/app/diamond_server.py"] | Resolved source server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_help_txt/mcp_diamond/app/diamond_server.py'
+    command:
+    - /225040511/miniconda3/envs/biomni_e1/bin/python
+    - /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_diamond/app/diamond_shim_server.py
+    command_available: true
+    dockerfile: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_diamond/Dockerfile
+    source_server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_help_txt/mcp_diamond/app/diamond_server.py
+    packages:
+    - diamond
+    help_file: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/merged_prefer_help_txt/diamond.txt
+    help_summary: ''
+    help_description: ''
+    execution_environment: ''
+    dependencies: []
+    env:
+      PATH: /225040511/miniconda3/envs/biomni_e1/bin:/225040511/miniconda3/envs/biomni_e1/bin:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/debugCommand:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/copilotCli:/root/.vscode-server/cli/servers/Stable-8b640eef5a6c6089c029249d48efa5c99adf7d51/server/bin/remote-cli:/225040511/miniconda3/condabin:/usr/local/nvm/versions/node/v18.20.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/root/.vscode-server/extensions/ms-python.debugpy-2026.6.0-linux-x64/bundled/scripts/noConfigScripts
+      CONDA_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      CONDA_DEFAULT_ENV: biomni_e1
+      CONDA_SHLVL: '1'
+      PYTHONNOUSERSITE: '1'
+      BIOMNI_EXECUTION_ENV_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      BIOMNI_EXECUTION_PYTHON: /225040511/miniconda3/envs/biomni_e1/bin/python
+    tools:
+    - name: makedb
+      description: Build a DIAMOND database from a FASTA file.
+      inputSchema:
+        properties:
+          in_file:
+            type: string
+            description: ''
+          db_file:
+            type: string
+            description: ''
+          threads:
+            type: number
+            description: ''
+          verbose:
+            type: boolean
+            description: ''
+          log:
+            type: boolean
+            description: ''
+          quiet:
+            type: boolean
+            description: ''
+          taxonmap:
+            type: string
+            description: ''
+          taxonnodes:
+            type: string
+            description: ''
+          taxonnames:
+            type: string
+            description: ''
+          taxon_exclude:
+            type: string
+            description: ''
+          block_size:
+            type: number
+            description: ''
+          bucket:
+            type: number
+            description: ''
+          no_parse_seqids:
+            type: boolean
+            description: ''
+          long_reads:
+            type: boolean
+            description: ''
+          orf_filter:
+            type: number
+            description: ''
+          in_format:
+            type: string
+            description: ''
+          file_buffer_size:
+            type: number
+            description: ''
+          ignore_warnings:
+            type: boolean
+            description: ''
+        required:
+        - in_file
+        - db_file
+    - name: cluster
+      description: Cluster protein sequences.
+      inputSchema:
+        properties:
+          in_file:
+            type: string
+            description: ''
+          db_file:
+            type: string
+            description: ''
+          out_file:
+            type: string
+            description: ''
+          daa_file:
+            type: string
+            description: ''
+          threads:
+            type: number
+            description: ''
+          verbose:
+            type: boolean
+            description: ''
+          sensitive:
+            type: boolean
+            description: ''
+          more_sensitive:
+            type: boolean
+            description: ''
+          identity:
+            type: number
+            description: ''
+          query_cover:
+            type: number
+            description: ''
+          cluster_mode:
+            type: number
+            description: ''
+          approx_id:
+            type: number
+            description: ''
+          cluster_cover:
+            type: number
+            description: ''
+          cluster_algo:
+            type: number
+            description: ''
+          member_cover:
+            type: number
+            description: ''
+          centroid_cover:
+            type: number
+            description: ''
+          evalue:
+            type: number
+            description: ''
+          tmpdir:
+            type: string
+            description: ''
+        required:
+        - in_file
+        - db_file
+        - out_file
+    - name: blastp
+      description: Align amino acid query sequences against a protein reference database.
+      inputSchema:
+        properties:
+          db:
+            type: string
+            description: ''
+          query:
+            type: string
+            description: ''
+          out:
+            type: string
+            description: ''
+          daa:
+            type: string
+            description: ''
+          threads:
+            type: number
+            description: ''
+          verbose:
+            type: boolean
+            description: ''
+          log:
+            type: boolean
+            description: ''
+          quiet:
+            type: boolean
+            description: ''
+          outfmt:
+            type: string
+            description: ''
+          matrix:
+            type: string
+            description: ''
+          gapopen:
+            type: number
+            description: ''
+          gapextend:
+            type: number
+            description: ''
+          unal:
+            type: number
+            description: ''
+          max_target_seqs:
+            type: number
+            description: ''
+          top:
+            type: number
+            description: ''
+          compress:
+            type: number
+            description: ''
+          evalue:
+            type: number
+            description: ''
+          min_score:
+            type: number
+            description: ''
+          identity:
+            type: number
+            description: ''
+          query_cover:
+            type: number
+            description: ''
+          subject_cover:
+            type: number
+            description: ''
+          sensitive:
+            type: boolean
+            description: ''
+          more_sensitive:
+            type: boolean
+            description: ''
+          block_size:
+            type: number
+            description: ''
+          index_chunks:
+            type: number
+            description: ''
+          tmpdir:
+            type: string
+            description: ''
+          dbsize:
+            type: number
+            description: ''
+          no_self_hits:
+            type: boolean
+            description: ''
+          salltitles:
+            type: boolean
+            description: ''
+          taxonlist:
+            type: string
+            description: ''
+          sorthits:
+            type: number
+            description: ''
+          max_hsps:
+            type: number
+            description: ''
+          comp_based_stats:
+            type: number
+            description: ''
+          masking:
+            type: string
+            description: ''
+          header:
+            type: boolean
+            description: ''
+          no_header:
+            type: boolean
+            description: ''
+        required:
+        - db
+        - query
+    - name: linclust
+      description: Cluster protein sequences in linear time.
+      inputSchema:
+        properties:
+          in_file:
+            type: string
+            description: ''
+          out_file:
+            type: string
+            description: ''
+          threads:
+            type: number
+            description: ''
+          min_seq_id:
+            type: number
+            description: ''
+          kmer_size:
+            type: number
+            description: ''
+          min_kmer_score:
+            type: number
+            description: ''
+          coverage:
+            type: number
+            description: ''
+          rescore:
+            type: string
+            description: ''
+          tmpdir:
+            type: string
+            description: ''
+          max_memory:
+            type: number
+            description: ''
+          verbose:
+            type: boolean
+            description: ''
+        required:
+        - in_file
+        - out_file
+    - name: getseq
+      description: Retrieve sequences from a DIAMOND database file.
+      inputSchema:
+        properties:
+          db_file:
+            type: string
+            description: ''
+          seq:
+            type: string
+            description: ''
+          seq_file:
+            type: string
+            description: ''
+          out_file:
+            type: string
+            description: ''
+          threads:
+            type: number
+            description: ''
+        required:
+        - db_file
+    - name: view
+      description: View a DIAMOND alignment archive (DAA) formatted file.
+      inputSchema:
+        properties:
+          daa_file:
+            type: string
+            description: ''
+          out_file:
+            type: string
+            description: ''
+          threads:
+            type: number
+            description: ''
+          outfmt:
+            type: string
+            description: ''
+          forwardonly:
+            type: boolean
+            description: ''
+          header:
+            type: boolean
+            description: ''
+          no_header:
+            type: boolean
+            description: ''
+        required:
+        - daa_file
+        - out_file
+    - name: makeidx
+      description: Make a database index.
+      inputSchema:
+        properties:
+          db_file:
+            type: string
+            description: ''
+          threads:
+            type: number
+            description: ''
+          block_size:
+            type: number
+            description: ''
+          index_chunks:
+            type: number
+            description: ''
+        required:
+        - db_file
+    - name: merge_daa
+      description: Merge multiple DAA files into a single file.
+      inputSchema:
+        properties:
+          daa_files:
+            type: array
+            description: ''
+          out_file:
+            type: string
+            description: ''
+        required:
+        - daa_files
+        - out_file
+    - name: dbinfo
+      description: Print information about a DIAMOND database file.
+      inputSchema:
+        properties:
+          db_file:
+            type: string
+            description: ''
+        required:
+        - db_file
+  orthofinder:
+    enabled: true
+    description: 'Installs packages: orthofinder. Copies scripts: orthofinder_server.py.
+      Default command: ["python", "/app/orthofinder_server.py"] | Resolved source
+      server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_orthofinder/app/orthofinder_server.py'
+    command:
+    - /225040511/miniconda3/envs/biomni_e1/bin/python
+    - /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_orthofinder/app/orthofinder_shim_server.py
+    command_available: true
+    dockerfile: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_orthofinder/Dockerfile
+    source_server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_orthofinder/app/orthofinder_server.py
+    packages:
+    - orthofinder
+    help_file: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/merged_prefer_help_txt/orthofinder.txt
+    help_summary: ''
+    help_description: ''
+    execution_environment: ''
+    dependencies: []
+    env:
+      PATH: /225040511/miniconda3/envs/biomni_e1/bin:/225040511/miniconda3/envs/biomni_e1/bin:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/debugCommand:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/copilotCli:/root/.vscode-server/cli/servers/Stable-8b640eef5a6c6089c029249d48efa5c99adf7d51/server/bin/remote-cli:/225040511/miniconda3/condabin:/usr/local/nvm/versions/node/v18.20.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/root/.vscode-server/extensions/ms-python.debugpy-2026.6.0-linux-x64/bundled/scripts/noConfigScripts
+      CONDA_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      CONDA_DEFAULT_ENV: biomni_e1
+      CONDA_SHLVL: '1'
+      PYTHONNOUSERSITE: '1'
+      BIOMNI_EXECUTION_ENV_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      BIOMNI_EXECUTION_PYTHON: /225040511/miniconda3/envs/biomni_e1/bin/python
+    tools:
+    - name: run_orthofinder
+      description: Runs OrthoFinder, a tool for comparative genomics.
+      inputSchema:
+        properties:
+          fasta_dir:
+            type: string
+            description: ''
+          output_dir:
+            type: string
+            description: ''
+          species_tree:
+            type: string
+            description: ''
+          mcl_inflation:
+            type: number
+            description: ''
+          threads:
+            type: number
+            description: ''
+          analysis_threads:
+            type: number
+            description: ''
+          is_dna:
+            type: boolean
+            description: ''
+          search_program:
+            type: string
+            description: ''
+          msa_program:
+            type: string
+            description: ''
+          tree_inference_program:
+            type: string
+            description: ''
+          no_species_names:
+            type: boolean
+            description: ''
+          previous_results_dir:
+            type: string
+            description: ''
+          orthogroup_inference_only:
+            type: boolean
+            description: ''
+          resume:
+            type: boolean
+            description: ''
+          species_tree_inference_program:
+            type: string
+            description: ''
+          citations_file:
+            type: string
+            description: ''
+          run_name:
+            type: string
+            description: ''
+          clean_intermediate:
+            type: boolean
+            description: ''
+          help_flag:
+            type: boolean
+            description: ''
+          version_flag:
+            type: boolean
+            description: ''
+        required:
+        - fasta_dir
+  gffutils:
+    enabled: true
+    description: 'Work with GFF and GTF files in a flexible database framework | Work
+      with GFF and GTF files in a flexible database framework | Installs packages:
+      gffutils. Copies scripts: gffutils_server.py. Default command: ["python", "/app/gffutils_server.py"]
+      | Execution environment: Python | Resolved source server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_gffutils/app/gffutils_server.py'
+    command:
+    - /225040511/miniconda3/envs/biomni_e1/bin/python
+    - /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_gffutils/app/gffutils_shim_server.py
+    command_available: true
+    dockerfile: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_gffutils/Dockerfile
+    source_server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_gffutils/app/gffutils_server.py
+    packages:
+    - gffutils
+    help_file: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/merged_prefer_help_txt/gffutils.txt
+    help_summary: Work with GFF and GTF files in a flexible database framework
+    help_description: Work with GFF and GTF files in a flexible database framework
+    execution_environment: Python
+    dependencies:
+    - argcomplete >=1.9.4
+    - argh >=0.26.2
+    - pyfaidx >=0.5.5.2
+    - python
+    - simplejson
+    env:
+      PATH: /225040511/miniconda3/envs/biomni_e1/bin:/225040511/miniconda3/envs/biomni_e1/bin:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/debugCommand:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/copilotCli:/root/.vscode-server/cli/servers/Stable-8b640eef5a6c6089c029249d48efa5c99adf7d51/server/bin/remote-cli:/225040511/miniconda3/condabin:/usr/local/nvm/versions/node/v18.20.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/root/.vscode-server/extensions/ms-python.debugpy-2026.6.0-linux-x64/bundled/scripts/noConfigScripts
+      CONDA_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      CONDA_DEFAULT_ENV: biomni_e1
+      CONDA_SHLVL: '1'
+      PYTHONNOUSERSITE: '1'
+      BIOMNI_EXECUTION_ENV_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      BIOMNI_EXECUTION_PYTHON: /225040511/miniconda3/envs/biomni_e1/bin/python
+    tools:
+    - name: gffutils_create
+      description: Creates a new gffutils database from GFF/GTF files.
+      inputSchema:
+        properties:
+          db:
+            type: string
+            description: ''
+          gff_files:
+            type: array
+            description: ''
+          gff_dialect:
+            type: string
+            description: ''
+          id_spec:
+            type: string
+            description: ''
+          merge_strategy:
+            type: string
+            description: ''
+          transform:
+            type: string
+            description: ''
+          force:
+            type: boolean
+            description: ''
+          verbose:
+            type: boolean
+            description: ''
+          disable_infer_transcripts:
+            type: boolean
+            description: ''
+          disable_infer_genes:
+            type: boolean
+            description: ''
+          disable_infer_extents:
+            type: boolean
+            description: ''
+          disable_infer_cds_extent:
+            type: boolean
+            description: ''
+          disable_infer_exon_extent:
+            type: boolean
+            description: ''
+          disable_infer_transcript_extent:
+            type: boolean
+            description: ''
+          disable_infer_gene_extent:
+            type: boolean
+            description: ''
+          disable_create_introns:
+            type: boolean
+            description: ''
+          disable_fix_strand:
+            type: boolean
+            description: ''
+          disable_fix_parent_child:
+            type: boolean
+            description: ''
+          disable_fix_start_stop:
+            type: boolean
+            description: ''
+          disable_fix_attributes:
+            type: boolean
+            description: ''
+          disable_fix_gff3_dialect:
+            type: boolean
+            description: ''
+          disable_fix_gtf_dialect:
+            type: boolean
+            description: ''
+          disable_dialect_check:
+            type: boolean
+            description: ''
+          disable_pragma_check:
+            type: boolean
+            description: ''
+          disable_order_check:
+            type: boolean
+            description: ''
+          disable_id_check:
+            type: boolean
+            description: ''
+          disable_feature_check:
+            type: boolean
+            description: ''
+          disable_relationship_check:
+            type: boolean
+            description: ''
+          disable_format_check:
+            type: boolean
+            description: ''
+          disable_all_fixes:
+            type: boolean
+            description: ''
+          disable_all_checks:
+            type: boolean
+            description: ''
+        required:
+        - db
+        - gff_files
+    - name: gffutils_update
+      description: Updates an existing gffutils database with new GFF/GTF files.
+      inputSchema:
+        properties:
+          db:
+            type: string
+            description: ''
+          gff_files:
+            type: array
+            description: ''
+          gff_dialect:
+            type: string
+            description: ''
+          id_spec:
+            type: string
+            description: ''
+          merge_strategy:
+            type: string
+            description: ''
+          transform:
+            type: string
+            description: ''
+          verbose:
+            type: boolean
+            description: ''
+          disable_infer_transcripts:
+            type: boolean
+            description: ''
+          disable_infer_genes:
+            type: boolean
+            description: ''
+          disable_infer_extents:
+            type: boolean
+            description: ''
+          disable_infer_cds_extent:
+            type: boolean
+            description: ''
+          disable_infer_exon_extent:
+            type: boolean
+            description: ''
+          disable_infer_transcript_extent:
+            type: boolean
+            description: ''
+          disable_infer_gene_extent:
+            type: boolean
+            description: ''
+          disable_create_introns:
+            type: boolean
+            description: ''
+          disable_fix_strand:
+            type: boolean
+            description: ''
+          disable_fix_parent_child:
+            type: boolean
+            description: ''
+          disable_fix_start_stop:
+            type: boolean
+            description: ''
+          disable_fix_attributes:
+            type: boolean
+            description: ''
+          disable_fix_gff3_dialect:
+            type: boolean
+            description: ''
+          disable_fix_gtf_dialect:
+            type: boolean
+            description: ''
+          disable_dialect_check:
+            type: boolean
+            description: ''
+          disable_pragma_check:
+            type: boolean
+            description: ''
+          disable_order_check:
+            type: boolean
+            description: ''
+          disable_id_check:
+            type: boolean
+            description: ''
+          disable_feature_check:
+            type: boolean
+            description: ''
+          disable_relationship_check:
+            type: boolean
+            description: ''
+          disable_format_check:
+            type: boolean
+            description: ''
+          disable_all_fixes:
+            type: boolean
+            description: ''
+          disable_all_checks:
+            type: boolean
+            description: ''
+        required:
+        - db
+        - gff_files
+    - name: gffutils_dump
+      description: Dumps data from a gffutils database to various formats.
+      inputSchema:
+        properties:
+          db:
+            type: string
+            description: ''
+          output:
+            type: string
+            description: ''
+          dialect:
+            type: string
+            description: ''
+          featuretype:
+            type: string
+            description: ''
+          id:
+            type: string
+            description: ''
+          seqid:
+            type: string
+            description: ''
+          start:
+            type: number
+            description: ''
+          end:
+            type: number
+            description: ''
+          strand:
+            type: string
+            description: ''
+          revcomp:
+            type: boolean
+            description: ''
+          limit:
+            type: number
+            description: ''
+          offset:
+            type: number
+            description: ''
+          attribute_split_char:
+            type: string
+            description: ''
+          attributes:
+            type: string
+            description: ''
+          extra_attributes:
+            type: string
+            description: ''
+          no_attributes:
+            type: boolean
+            description: ''
+          raw:
+            type: boolean
+            description: ''
+          table:
+            type: string
+            description: ''
+          fasta:
+            type: string
+            description: ''
+          chrom_lookup:
+            type: string
+            description: ''
+        required:
+        - db
+    - name: gffutils_sort
+      description: Sorts a GFF/GTF file.
+      inputSchema:
+        properties:
+          gff_file:
+            type: string
+            description: ''
+          output:
+            type: string
+            description: ''
+          force:
+            type: boolean
+            description: ''
+          disable_infer_transcripts:
+            type: boolean
+            description: ''
+          disable_infer_genes:
+            type: boolean
+            description: ''
+          disable_infer_extents:
+            type: boolean
+            description: ''
+          disable_infer_cds_extent:
+            type: boolean
+            description: ''
+          disable_infer_exon_extent:
+            type: boolean
+            description: ''
+          disable_infer_transcript_extent:
+            type: boolean
+            description: ''
+          disable_infer_gene_extent:
+            type: boolean
+            description: ''
+          disable_create_introns:
+            type: boolean
+            description: ''
+          disable_fix_strand:
+            type: boolean
+            description: ''
+          disable_fix_parent_child:
+            type: boolean
+            description: ''
+          disable_fix_start_stop:
+            type: boolean
+            description: ''
+          disable_fix_attributes:
+            type: boolean
+            description: ''
+          disable_fix_gff3_dialect:
+            type: boolean
+            description: ''
+          disable_fix_gtf_dialect:
+            type: boolean
+            description: ''
+          disable_dialect_check:
+            type: boolean
+            description: ''
+          disable_pragma_check:
+            type: boolean
+            description: ''
+          disable_order_check:
+            type: boolean
+            description: ''
+          disable_id_check:
+            type: boolean
+            description: ''
+          disable_feature_check:
+            type: boolean
+            description: ''
+          disable_relationship_check:
+            type: boolean
+            description: ''
+          disable_format_check:
+            type: boolean
+            description: ''
+          disable_all_fixes:
+            type: boolean
+            description: ''
+          disable_all_checks:
+            type: boolean
+            description: ''
+        required:
+        - gff_file
+    - name: gffutils_clean
+      description: Cleans a gffutils database by removing orphaned features.
+      inputSchema:
+        properties:
+          db:
+            type: string
+            description: ''
+          output:
+            type: string
+            description: ''
+          force:
+            type: boolean
+            description: ''
+        required:
+        - db
+    - name: gffutils_fasta
+      description: Retrieves sequences for features from a database.
+      inputSchema:
+        properties:
+          db:
+            type: string
+            description: ''
+          fasta:
+            type: string
+            description: ''
+          ids:
+            type: array
+            description: ''
+          output:
+            type: string
+            description: ''
+          featuretype:
+            type: string
+            description: ''
+          attribute:
+            type: string
+            description: ''
+          use_strand:
+            type: boolean
+            description: ''
+          prefix:
+            type: string
+            description: ''
+        required:
+        - db
+        - fasta
+        - ids
+    - name: gffutils_gff
+      description: Retrieves features and their relatives from a database in GFF format.
+      inputSchema:
+        properties:
+          db:
+            type: string
+            description: ''
+          ids:
+            type: array
+            description: ''
+          output:
+            type: string
+            description: ''
+          parents:
+            type: boolean
+            description: ''
+          children:
+            type: boolean
+            description: ''
+          ancestors:
+            type: boolean
+            description: ''
+          descendants:
+            type: boolean
+            description: ''
+          level:
+            type: number
+            description: ''
+          featuretype:
+            type: string
+            description: ''
+          reverse:
+            type: boolean
+            description: ''
+          limit:
+            type: number
+            description: ''
+        required:
+        - db
+        - ids
+    - name: gffutils_merge
+      description: Merges multiple gffutils databases into a single database.
+      inputSchema:
+        properties:
+          dbs:
+            type: array
+            description: ''
+          output:
+            type: string
+            description: ''
+          force:
+            type: boolean
+            description: ''
+        required:
+        - dbs
+    - name: gffutils_bed
+      description: Converts features from a gffutils database to BED format.
+      inputSchema:
+        properties:
+          db:
+            type: string
+            description: ''
+          output:
+            type: string
+            description: ''
+          featuretype:
+            type: string
+            description: ''
+          name_attribute:
+            type: string
+            description: ''
+          score_attribute:
+            type: string
+            description: ''
+          thick_attribute:
+            type: string
+            description: ''
+          block_attribute:
+            type: string
+            description: ''
+          track_line:
+            type: string
+            description: ''
+        required:
+        - db
+    - name: gffutils_stats
+      description: Prints statistics about a gffutils database.
+      inputSchema:
+        properties:
+          db:
+            type: string
+            description: ''
+          output:
+            type: string
+            description: ''
+          feature_counts:
+            type: boolean
+            description: ''
+          attribute_counts:
+            type: string
+            description: ''
+        required:
+        - db
+    - name: gffutils_validate
+      description: Validates a GFF/GTF file, reporting any errors found.
+      inputSchema:
+        properties:
+          gff_file:
+            type: string
+            description: ''
+          limit:
+            type: number
+            description: ''
+        required:
+        - gff_file
+  csvtk:
+    enabled: true
+    description: 'Installs packages: csvtk. Copies scripts: csvtk_server.py. Default
+      command: ["python", "/app/csvtk_server.py"] | Resolved source server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_help_txt/mcp_csvtk/app/csvtk_server.py'
+    command:
+    - /225040511/miniconda3/envs/biomni_e1/bin/python
+    - /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_csvtk/app/csvtk_shim_server.py
+    command_available: true
+    dockerfile: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_csvtk/Dockerfile
+    source_server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_help_txt/mcp_csvtk/app/csvtk_server.py
+    packages:
+    - csvtk
+    help_file: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/merged_prefer_help_txt/csvtk.txt
+    help_summary: ''
+    help_description: ''
+    execution_environment: ''
+    dependencies: []
+    env:
+      PATH: /225040511/miniconda3/envs/biomni_e1/bin:/225040511/miniconda3/envs/biomni_e1/bin:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/debugCommand:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/copilotCli:/root/.vscode-server/cli/servers/Stable-8b640eef5a6c6089c029249d48efa5c99adf7d51/server/bin/remote-cli:/225040511/miniconda3/condabin:/usr/local/nvm/versions/node/v18.20.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/root/.vscode-server/extensions/ms-python.debugpy-2026.6.0-linux-x64/bundled/scripts/noConfigScripts
+      CONDA_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      CONDA_DEFAULT_ENV: biomni_e1
+      CONDA_SHLVL: '1'
+      PYTHONNOUSERSITE: '1'
+      BIOMNI_EXECUTION_ENV_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      BIOMNI_EXECUTION_PYTHON: /225040511/miniconda3/envs/biomni_e1/bin/python
+    tools:
+    - name: csvtk_filter
+      description: Filter rows by values of selected fields with arithmetic expression
+        (e.g., "col1 > 10").
+      inputSchema:
+        properties:
+          in_file:
+            type: string
+            description: ''
+          filter_expr:
+            type: string
+            description: ''
+          tabs:
+            type: boolean
+            description: ''
+          no_header_row:
+            type: boolean
+            description: ''
+          out_file:
+            type: string
+            description: ''
+        required:
+        - in_file
+        - filter_expr
+    - name: csvtk_filter2
+      description: Filter rows by awk-like arithmetic/string expressions (e.g., '$1
+        > 10 && $2 == "A"').
+      inputSchema:
+        properties:
+          in_file:
+            type: string
+            description: ''
+          expression:
+            type: string
+            description: ''
+          tabs:
+            type: boolean
+            description: ''
+          no_header_row:
+            type: boolean
+            description: ''
+          out_file:
+            type: string
+            description: ''
+        required:
+        - in_file
+        - expression
+    - name: csvtk_pretty
+      description: Convert CSV to a readable aligned table.
+      inputSchema:
+        properties:
+          in_file:
+            type: string
+            description: ''
+          tabs:
+            type: boolean
+            description: ''
+          no_header_row:
+            type: boolean
+            description: ''
+        required:
+        - in_file
+    - name: csvtk_summary
+      description: Summary statistics of selected numeric or text fields (groupby
+        group fields).
+      inputSchema:
+        properties:
+          in_file:
+            type: string
+            description: ''
+          fields:
+            type: string
+            description: ''
+          groups:
+            type: string
+            description: ''
+          tabs:
+            type: boolean
+            description: ''
+          no_header_row:
+            type: boolean
+            description: ''
+        required:
+        - in_file
+        - fields
+    - name: csvtk_fix
+      description: Fix CSV/TSV with different numbers of columns in rows.
+      inputSchema:
+        properties:
+          in_file:
+            type: string
+            description: ''
+          tabs:
+            type: boolean
+            description: ''
+          out_file:
+            type: string
+            description: ''
+        required:
+        - in_file
+    - name: csvtk_dim
+      description: Dimensions of CSV file (rows and columns).
+      inputSchema:
+        properties:
+          in_file:
+            type: string
+            description: ''
+          tabs:
+            type: boolean
+            description: ''
+          no_header_row:
+            type: boolean
+            description: ''
+        required:
+        - in_file
+    - name: csvtk_headers
+      description: Print headers of a CSV/TSV file.
+      inputSchema:
+        properties:
+          in_file:
+            type: string
+            description: ''
+          tabs:
+            type: boolean
+            description: ''
+          no_header_row:
+            type: boolean
+            description: ''
+        required:
+        - in_file
+    - name: csvtk_ncol
+      description: Print number of columns.
+      inputSchema:
+        properties:
+          in_file:
+            type: string
+            description: ''
+          tabs:
+            type: boolean
+            description: ''
+        required:
+        - in_file
+    - name: csvtk_nrow
+      description: Print number of records (rows).
+      inputSchema:
+        properties:
+          in_file:
+            type: string
+            description: ''
+          tabs:
+            type: boolean
+            description: ''
+          no_header_row:
+            type: boolean
+            description: ''
+        required:
+        - in_file
+    - name: csvtk_concat
+      description: Concatenate CSV/TSV files by rows.
+      inputSchema:
+        properties:
+          files:
+            type: array
+            description: ''
+          tabs:
+            type: boolean
+            description: ''
+          no_header_row:
+            type: boolean
+            description: ''
+          out_file:
+            type: string
+            description: ''
+        required:
+        - files
+    - name: csvtk_freq
+      description: Frequencies of selected fields.
+      inputSchema:
+        properties:
+          in_file:
+            type: string
+            description: ''
+          fields:
+            type: string
+            description: ''
+          sort_by_freq:
+            type: boolean
+            description: ''
+          tabs:
+            type: boolean
+            description: ''
+          no_header_row:
+            type: boolean
+            description: ''
+          out_file:
+            type: string
+            description: ''
+        required:
+        - in_file
+        - fields
+    - name: csvtk_replace
+      description: Replace data of selected fields by regular expression.
+      inputSchema:
+        properties:
+          in_file:
+            type: string
+            description: ''
+          fields:
+            type: string
+            description: ''
+          pattern:
+            type: string
+            description: ''
+          replacement:
+            type: string
+            description: ''
+          tabs:
+            type: boolean
+            description: ''
+          no_header_row:
+            type: boolean
+            description: ''
+          out_file:
+            type: string
+            description: ''
+        required:
+        - in_file
+        - fields
+        - pattern
+        - replacement
+  mafft:
+    enabled: true
+    description: 'Installs packages: mafft. Copies scripts: mafft_server.py. Default
+      command: ["python", "/app/mafft_server.py"] | Resolved source server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_mafft/app/mafft_server.py'
+    command:
+    - /225040511/miniconda3/envs/biomni_e1/bin/python
+    - /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_mafft/app/mafft_shim_server.py
+    command_available: true
+    dockerfile: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_mafft/Dockerfile
+    source_server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_mafft/app/mafft_server.py
+    packages:
+    - mafft
+    help_file: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/merged_prefer_help_txt/mafft.txt
+    help_summary: ''
+    help_description: ''
+    execution_environment: ''
+    dependencies: []
+    env:
+      PATH: /225040511/miniconda3/envs/biomni_e1/bin:/225040511/miniconda3/envs/biomni_e1/bin:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/debugCommand:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/copilotCli:/root/.vscode-server/cli/servers/Stable-8b640eef5a6c6089c029249d48efa5c99adf7d51/server/bin/remote-cli:/225040511/miniconda3/condabin:/usr/local/nvm/versions/node/v18.20.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/root/.vscode-server/extensions/ms-python.debugpy-2026.6.0-linux-x64/bundled/scripts/noConfigScripts
+      CONDA_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      CONDA_DEFAULT_ENV: biomni_e1
+      CONDA_SHLVL: '1'
+      PYTHONNOUSERSITE: '1'
+      BIOMNI_EXECUTION_ENV_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      BIOMNI_EXECUTION_PYTHON: /225040511/miniconda3/envs/biomni_e1/bin/python
+    tools:
+    - name: mafft_align
+      description: Performs de novo multiple sequence alignment on a set of sequences
+        using MAFFT.
+      inputSchema:
+        properties:
+          input_file:
+            type: string
+            description: ''
+          output_file:
+            type: string
+            description: ''
+          strategy:
+            type: string
+            description: ''
+          sequence_type:
+            type: string
+            description: ''
+          retree:
+            type: number
+            description: ''
+          maxiterate:
+            type: number
+            description: ''
+          scoring_matrix:
+            type: string
+            description: ''
+          op:
+            type: number
+            description: ''
+          ep:
+            type: number
+            description: ''
+          threads:
+            type: number
+            description: ''
+          output_format:
+            type: string
+            description: ''
+          reorder:
+            type: boolean
+            description: ''
+          quiet:
+            type: boolean
+            description: ''
+        required:
+        - input_file
+    - name: mafft_adjust_direction
+      description: Adjusts the direction of nucleotide sequences in a FASTA file.
+      inputSchema:
+        properties:
+          input_file:
+            type: string
+            description: ''
+          output_file:
+            type: string
+            description: ''
+          accurate:
+            type: boolean
+            description: ''
+          threads:
+            type: number
+            description: ''
+          quiet:
+            type: boolean
+            description: ''
+        required:
+        - input_file
+    - name: mafft_add
+      description: Adds new sequences or fragments to an existing MAFFT alignment.
+      inputSchema:
+        properties:
+          existing_alignment:
+            type: string
+            description: ''
+          new_sequences:
+            type: string
+            description: ''
+          output_file:
+            type: string
+            description: ''
+          mode:
+            type: string
+            description: ''
+          threads:
+            type: number
+            description: ''
+          reorder:
+            type: boolean
+            description: ''
+          keeplength:
+            type: boolean
+            description: ''
+          quiet:
+            type: boolean
+            description: ''
+        required:
+        - existing_alignment
+        - new_sequences
+  hisat2:
+    enabled: true
+    description: 'Installs packages: hisat2. Copies scripts: hisat2_server.py. Default
+      command: ["python", "/app/hisat2_server.py"] | Resolved source server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_hisat2/app/hisat2_server.py'
+    command:
+    - /225040511/miniconda3/envs/biomni_e1/bin/python
+    - /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_hisat2/app/hisat2_shim_server.py
+    command_available: true
+    dockerfile: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_hisat2/Dockerfile
+    source_server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_hisat2/app/hisat2_server.py
+    packages:
+    - hisat2
+    help_file: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/merged_prefer_help_txt/hisat2.txt
+    help_summary: ''
+    help_description: ''
+    execution_environment: ''
+    dependencies: []
+    env:
+      PATH: /225040511/miniconda3/envs/biomni_e1/bin:/225040511/miniconda3/envs/biomni_e1/bin:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/debugCommand:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/copilotCli:/root/.vscode-server/cli/servers/Stable-8b640eef5a6c6089c029249d48efa5c99adf7d51/server/bin/remote-cli:/225040511/miniconda3/condabin:/usr/local/nvm/versions/node/v18.20.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/root/.vscode-server/extensions/ms-python.debugpy-2026.6.0-linux-x64/bundled/scripts/noConfigScripts
+      CONDA_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      CONDA_DEFAULT_ENV: biomni_e1
+      CONDA_SHLVL: '1'
+      PYTHONNOUSERSITE: '1'
+      BIOMNI_EXECUTION_ENV_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      BIOMNI_EXECUTION_PYTHON: /225040511/miniconda3/envs/biomni_e1/bin/python
+    tools:
+    - name: hisat2_align
+      description: Aligns sequencing reads to a reference genome using HISAT2.
+      inputSchema:
+        properties:
+          index_prefix:
+            type: string
+            description: ''
+          sam_output:
+            type: string
+            description: ''
+          mate1_files:
+            type: string
+            description: ''
+          mate2_files:
+            type: string
+            description: ''
+          unpaired_reads:
+            type: string
+            description: ''
+          input_format:
+            type: string
+            description: ''
+          skip:
+            type: number
+            description: ''
+          upto:
+            type: number
+            description: ''
+          trim5:
+            type: number
+            description: ''
+          trim3:
+            type: number
+            description: ''
+          quality_encoding:
+            type: string
+            description: ''
+          max_seed_mismatches:
+            type: number
+            description: ''
+          seed_length:
+            type: number
+            description: ''
+          seed_interval:
+            type: string
+            description: ''
+          n_ceil:
+            type: string
+            description: ''
+          pen_cansplice:
+            type: number
+            description: ''
+          pen_noncansplice:
+            type: number
+            description: ''
+          pen_canintronlen:
+            type: string
+            description: ''
+          pen_noncanintronlen:
+            type: string
+            description: ''
+          min_intronlen:
+            type: number
+            description: ''
+          max_intronlen:
+            type: number
+            description: ''
+          known_splicesite_infile:
+            type: string
+            description: ''
+          novel_splicesite_outfile:
+            type: string
+            description: ''
+          novel_splicesite_infile:
+            type: string
+            description: ''
+          no_temp_splicesite:
+            type: boolean
+            description: ''
+          no_softclip:
+            type: boolean
+            description: ''
+          sp:
+            type: string
+            description: ''
+          mismatch_penalty:
+            type: string
+            description: ''
+          np:
+            type: number
+            description: ''
+          read_gap_penalty:
+            type: string
+            description: ''
+          ref_gap_penalty:
+            type: string
+            description: ''
+          score_min:
+            type: string
+            description: ''
+          k:
+            type: number
+            description: ''
+          report_all:
+            type: boolean
+            description: ''
+          secondary:
+            type: boolean
+            description: ''
+          min_frag_len:
+            type: number
+            description: ''
+          max_frag_len:
+            type: number
+            description: ''
+          mate_orientation:
+            type: string
+            description: ''
+          no_mixed:
+            type: boolean
+            description: ''
+          no_discordant:
+            type: boolean
+            description: ''
+          summary_file:
+            type: string
+            description: ''
+          new_summary:
+            type: boolean
+            description: ''
+          met_file:
+            type: string
+            description: ''
+          met_stderr:
+            type: boolean
+            description: ''
+          met_interval:
+            type: number
+            description: ''
+          unaligned_reads_file:
+            type: string
+            description: ''
+          aligned_reads_file:
+            type: string
+            description: ''
+          unaligned_concordant_reads_file:
+            type: string
+            description: ''
+          aligned_concordant_reads_file:
+            type: string
+            description: ''
+          quiet:
+            type: boolean
+            description: ''
+          no_head:
+            type: boolean
+            description: ''
+          no_sq:
+            type: boolean
+            description: ''
+          rg_id:
+            type: string
+            description: ''
+          rg:
+            type: array
+            description: ''
+          remove_chrname:
+            type: boolean
+            description: ''
+          add_chrname:
+            type: boolean
+            description: ''
+          dta:
+            type: boolean
+            description: ''
+          dta_cufflinks:
+            type: boolean
+            description: ''
+          no_spliced_alignment:
+            type: boolean
+            description: ''
+          rna_strandness:
+            type: string
+            description: ''
+          transcriptome_mapping_only:
+            type: boolean
+            description: ''
+          bwa_mem:
+            type: boolean
+            description: ''
+          threads:
+            type: number
+            description: ''
+          reorder:
+            type: boolean
+            description: ''
+          mm:
+            type: boolean
+            description: ''
+          qc_filter:
+            type: boolean
+            description: ''
+          seed:
+            type: number
+            description: ''
+          non_deterministic:
+            type: boolean
+            description: ''
+        required:
+        - index_prefix
+        - sam_output
+    - name: hisat2_inspect
+      description: Inspects a HISAT2 index to extract information.
+      inputSchema:
+        properties:
+          index_basename:
+            type: string
+            description: ''
+          names:
+            type: boolean
+            description: ''
+          summary:
+            type: boolean
+            description: ''
+          snp:
+            type: boolean
+            description: ''
+          ss:
+            type: boolean
+            description: ''
+          haplotype:
+            type: boolean
+            description: ''
+          extract:
+            type: string
+            description: ''
+          across:
+            type: number
+            description: ''
+          verbose:
+            type: boolean
+            description: ''
+        required:
+        - index_basename
+    - name: hisat2_simulate_reads
+      description: Simulates sequencing reads from a reference genome.
+      inputSchema:
+        properties:
+          reference_fasta:
+            type: string
+            description: ''
+          num_reads:
+            type: number
+            description: ''
+          output_prefix:
+            type: string
+            description: ''
+          read_len:
+            type: number
+            description: ''
+          error_rate:
+            type: number
+            description: ''
+          max_mismatches:
+            type: number
+            description: ''
+          insert_size:
+            type: number
+            description: ''
+          insert_stdev:
+            type: number
+            description: ''
+          paired_end:
+            type: boolean
+            description: ''
+          quiet:
+            type: boolean
+            description: ''
+        required:
+        - reference_fasta
+        - num_reads
+        - output_prefix
+    - name: hisat2_build
+      description: Builds a HISAT2 index from a set of reference sequences.
+      inputSchema:
+        properties:
+          reference_in:
+            type: string
+            description: ''
+          index_basename:
+            type: string
+            description: ''
+          large_index:
+            type: boolean
+            description: ''
+          no_auto:
+            type: boolean
+            description: ''
+          packed:
+            type: boolean
+            description: ''
+          bmax:
+            type: number
+            description: ''
+          bmaxdivn:
+            type: number
+            description: ''
+          dcv:
+            type: number
+            description: ''
+          no_dc:
+            type: boolean
+            description: ''
+          no_ref:
+            type: boolean
+            description: ''
+          just_ac:
+            type: boolean
+            description: ''
+          offrate:
+            type: number
+            description: ''
+          ftabchars:
+            type: number
+            description: ''
+          local_offrate:
+            type: number
+            description: ''
+          local_ftabchars:
+            type: number
+            description: ''
+          snp_file:
+            type: string
+            description: ''
+          haplotype_file:
+            type: string
+            description: ''
+          ss_file:
+            type: string
+            description: ''
+          exon_file:
+            type: string
+            description: ''
+          threads:
+            type: number
+            description: ''
+          seed:
+            type: number
+            description: ''
+          quiet:
+            type: boolean
+            description: ''
+        required:
+        - reference_in
+        - index_basename
+    - name: tool
+      description: MCP tool tool from hisat2
+      inputSchema:
+        properties: {}
+        required: []
+    - name: hisat2_extract_splice_sites
+      description: Extracts splice sites from a GTF file for use with hisat2-build.
+      inputSchema:
+        properties:
+          gtf_file:
+            type: string
+            description: ''
+          output_file:
+            type: string
+            description: ''
+        required:
+        - gtf_file
+        - output_file
+    - name: hisat2_extract_exons
+      description: Extracts exons from a GTF file for use with hisat2-build.
+      inputSchema:
+        properties:
+          gtf_file:
+            type: string
+            description: ''
+          output_file:
+            type: string
+            description: ''
+        required:
+        - gtf_file
+        - output_file
+  star:
+    enabled: true
+    description: 'An RNA-seq read aligner. | An RNA-seq read aligner. | Installs packages:
+      star. Copies scripts: star_server.py. Default command: ["python", "/app/star_server.py"]
+      | Execution environment: Compiled | Resolved source server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_star/app/star_server.py'
+    command:
+    - /225040511/miniconda3/envs/biomni_e1/bin/python
+    - /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_star/app/star_shim_server.py
+    command_available: true
+    dockerfile: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_star/Dockerfile
+    source_server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_manual_txt/mcp_star/app/star_server.py
+    packages:
+    - star
+    help_file: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/merged_prefer_help_txt/star.txt
+    help_summary: An RNA-seq read aligner.
+    help_description: An RNA-seq read aligner.
+    execution_environment: Compiled
+    dependencies:
+    - _openmp_mutex >=4.5
+    - htslib >=1.21
+    - htslib >=1.22.1
+    - <1.24.0a0
+    - libgcc >=13
+    - libgomp
+    - libstdcxx >=13
+    - libzlib >=1.3.1
+    - <2.0a0
+    env:
+      PATH: /225040511/miniconda3/envs/biomni_e1/bin:/225040511/miniconda3/envs/biomni_e1/bin:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/debugCommand:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/copilotCli:/root/.vscode-server/cli/servers/Stable-8b640eef5a6c6089c029249d48efa5c99adf7d51/server/bin/remote-cli:/225040511/miniconda3/condabin:/usr/local/nvm/versions/node/v18.20.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/root/.vscode-server/extensions/ms-python.debugpy-2026.6.0-linux-x64/bundled/scripts/noConfigScripts
+      CONDA_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      CONDA_DEFAULT_ENV: biomni_e1
+      CONDA_SHLVL: '1'
+      PYTHONNOUSERSITE: '1'
+      BIOMNI_EXECUTION_ENV_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      BIOMNI_EXECUTION_PYTHON: /225040511/miniconda3/envs/biomni_e1/bin/python
+    tools:
+    - name: star_align_reads
+      description: Aligns RNA-seq reads to a reference genome using STAR.
+      inputSchema:
+        properties:
+          genome_dir:
+            type: string
+            description: ''
+          read_files_in:
+            type: array
+            description: ''
+          out_file_name_prefix:
+            type: string
+            description: ''
+          run_thread_n:
+            type: number
+            description: ''
+          read_files_command:
+            type: string
+            description: ''
+          out_sam_type:
+            type: array
+            description: ''
+          out_sam_unmapped:
+            type: string
+            description: ''
+          quant_mode:
+            type: string
+            description: ''
+          twopass_mode:
+            type: string
+            description: ''
+          out_filter_multimap_n_max:
+            type: number
+            description: ''
+          out_filter_mismatch_n_max:
+            type: number
+            description: ''
+          align_intron_min:
+            type: number
+            description: ''
+          align_intron_max:
+            type: number
+            description: ''
+          align_mates_gap_max:
+            type: number
+            description: ''
+        required:
+        - genome_dir
+        - read_files_in
+    - name: star_genome_generate
+      description: Generates genome indices for STAR alignment.
+      inputSchema:
+        properties:
+          genome_dir:
+            type: string
+            description: ''
+          genome_fasta_files:
+            type: array
+            description: ''
+          sjdb_gtf_file:
+            type: string
+            description: ''
+          sjdb_overhang:
+            type: number
+            description: ''
+          run_thread_n:
+            type: number
+            description: ''
+          genome_sa_index_nbases:
+            type: number
+            description: ''
+        required:
+        - genome_dir
+        - genome_fasta_files
+    - name: star_lift_over
+      description: STAR internal tool for lifting over splice junctions.
+      inputSchema:
+        properties:
+          genome_dir:
+            type: string
+            description: ''
+          sjdb_file_chrs:
+            type: array
+            description: ''
+          sjdb_gtf_file:
+            type: string
+            description: ''
+          run_thread_n:
+            type: number
+            description: ''
+        required:
+        - genome_dir
+        - sjdb_file_chrs
+        - sjdb_gtf_file
+    - name: star_generic_command
+      description: 'Execute a STAR command with arbitrary arguments. '
+      inputSchema:
+        properties:
+          args:
+            type: array
+            description: ''
+        required:
+        - args
+  blast:
+    enabled: true
+    description: 'Installs packages: blast. Copies scripts: blast_server.py. Default
+      command: ["python", "/app/blast_server.py"] | Resolved source server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_help_txt/mcp_blast/app/blast_server.py'
+    command:
+    - /225040511/miniconda3/envs/biomni_e1/bin/python
+    - /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_blast/app/blast_shim_server.py
+    command_available: true
+    dockerfile: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_blast/Dockerfile
+    source_server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_help_txt/mcp_blast/app/blast_server.py
+    packages:
+    - blast
+    help_file: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/merged_prefer_help_txt/blast.txt
+    help_summary: ''
+    help_description: ''
+    execution_environment: ''
+    dependencies: []
+    env:
+      PATH: /225040511/miniconda3/envs/biomni_e1/bin:/225040511/miniconda3/envs/biomni_e1/bin:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/debugCommand:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/copilotCli:/root/.vscode-server/cli/servers/Stable-8b640eef5a6c6089c029249d48efa5c99adf7d51/server/bin/remote-cli:/225040511/miniconda3/condabin:/usr/local/nvm/versions/node/v18.20.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/root/.vscode-server/extensions/ms-python.debugpy-2026.6.0-linux-x64/bundled/scripts/noConfigScripts
+      CONDA_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      CONDA_DEFAULT_ENV: biomni_e1
+      CONDA_SHLVL: '1'
+      PYTHONNOUSERSITE: '1'
+      BIOMNI_EXECUTION_ENV_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      BIOMNI_EXECUTION_PYTHON: /225040511/miniconda3/envs/biomni_e1/bin/python
+    tools:
+    - name: run_perl_script
+      description: Executes a Perl script with a comprehensive set of interpreter
+        switches.
+      inputSchema:
+        properties:
+          programfile:
+            type: string
+            description: ''
+          script_args:
+            type: array
+            description: ''
+          record_separator:
+            type: string
+            description: ''
+          autosplit:
+            type: boolean
+            description: ''
+          unicode_features:
+            type: string
+            description: ''
+          run_debugger:
+            type: boolean
+            description: ''
+          debugger_name:
+            type: string
+            description: ''
+          debugging_flags:
+            type: string
+            description: ''
+          no_sitecustomize:
+            type: boolean
+            description: ''
+          split_pattern:
+            type: string
+            description: ''
+          in_place_edit_backup_ext:
+            type: string
+            description: ''
+          include_dirs:
+            type: array
+            description: ''
+          line_ending:
+            type: string
+            description: ''
+          use_modules:
+            type: array
+            description: ''
+          no_modules:
+            type: array
+            description: ''
+          loop_around_program:
+            type: boolean
+            description: ''
+          loop_and_print:
+            type: boolean
+            description: ''
+          parse_switches:
+            type: boolean
+            description: ''
+          search_path:
+            type: boolean
+            description: ''
+          tainting_warnings:
+            type: boolean
+            description: ''
+          tainting_checks:
+            type: boolean
+            description: ''
+          dump_core:
+            type: boolean
+            description: ''
+          unsafe_operations:
+            type: boolean
+            description: ''
+          enable_warnings:
+            type: boolean
+            description: ''
+          enable_all_warnings:
+            type: boolean
+            description: ''
+          extract_from_text:
+            type: boolean
+            description: ''
+          extract_from_text_dir:
+            type: string
+            description: ''
+          disable_all_warnings:
+            type: boolean
+            description: ''
+        required:
+        - programfile
+    - name: check_perl_syntax
+      description: Checks the syntax of a Perl script without executing it.
+      inputSchema:
+        properties:
+          programfile:
+            type: string
+            description: ''
+          include_dirs:
+            type: array
+            description: ''
+          use_modules:
+            type: array
+            description: ''
+          no_modules:
+            type: array
+            description: ''
+          tainting_checks:
+            type: boolean
+            description: ''
+          unsafe_operations:
+            type: boolean
+            description: ''
+          enable_warnings:
+            type: boolean
+            description: ''
+          enable_all_warnings:
+            type: boolean
+            description: ''
+          disable_all_warnings:
+            type: boolean
+            description: ''
+        required:
+        - programfile
+    - name: get_perl_version
+      description: Prints the version, patchlevel, and license of the Perl interpreter.
+      inputSchema:
+        properties: {}
+        required: []
+    - name: run_perl_oneliner
+      description: Executes a one-line Perl program from a string.
+      inputSchema:
+        properties:
+          program:
+            type: string
+            description: ''
+          enable_all_features:
+            type: boolean
+            description: ''
+          script_args:
+            type: array
+            description: ''
+          record_separator:
+            type: string
+            description: ''
+          autosplit:
+            type: boolean
+            description: ''
+          unicode_features:
+            type: string
+            description: ''
+          debugging_flags:
+            type: string
+            description: ''
+          split_pattern:
+            type: string
+            description: ''
+          include_dirs:
+            type: array
+            description: ''
+          line_ending:
+            type: string
+            description: ''
+          use_modules:
+            type: array
+            description: ''
+          no_modules:
+            type: array
+            description: ''
+          loop_around_program:
+            type: boolean
+            description: ''
+          loop_and_print:
+            type: boolean
+            description: ''
+          tainting_warnings:
+            type: boolean
+            description: ''
+          tainting_checks:
+            type: boolean
+            description: ''
+          unsafe_operations:
+            type: boolean
+            description: ''
+          enable_warnings:
+            type: boolean
+            description: ''
+          enable_all_warnings:
+            type: boolean
+            description: ''
+          disable_all_warnings:
+            type: boolean
+            description: ''
+        required:
+        - program
+    - name: get_perl_config
+      description: Prints the configuration summary or a single Config.pm variable.
+      inputSchema:
+        properties:
+          variable:
+            type: string
+            description: ''
+        required: []
+  bioconductor-tximport:
+    enabled: true
+    description: 'Installs packages: bioconductor-tximport. Copies scripts: bioconductor-tximport_server.py.
+      Default command: ["python", "/app/bioconductor-tximport_server.py"] | Resolved
+      source server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_help_txt/mcp_bioconductor-tximport/app/bioconductor-tximport_server.py'
+    command:
+    - /225040511/miniconda3/envs/biomni_e1/bin/python
+    - /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_bioconductor-tximport/app/bioconductor-tximport_shim_server.py
+    command_available: true
+    dockerfile: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/mcp_generated/mcp_bioconductor-tximport/Dockerfile
+    source_server: /225040511/project/BioScientist/agent_system/toolbase/mcp_batch_from_help_txt/mcp_bioconductor-tximport/app/bioconductor-tximport_server.py
+    packages:
+    - bioconductor-tximport
+    help_file: /225040511/project/Hypo_Bio_OS/biomni_web/backend/data/merged_prefer_help_txt/bioconductor-tximport.txt
+    help_summary: ''
+    help_description: ''
+    execution_environment: ''
+    dependencies: []
+    env:
+      PATH: /225040511/miniconda3/envs/biomni_e1/bin:/225040511/miniconda3/envs/biomni_e1/bin:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/debugCommand:/Users/macbook/Library/Application
+        Support/Code/User/globalStorage/github.copilot-chat/copilotCli:/root/.vscode-server/cli/servers/Stable-8b640eef5a6c6089c029249d48efa5c99adf7d51/server/bin/remote-cli:/225040511/miniconda3/condabin:/usr/local/nvm/versions/node/v18.20.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/root/.vscode-server/extensions/ms-python.debugpy-2026.6.0-linux-x64/bundled/scripts/noConfigScripts
+      CONDA_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      CONDA_DEFAULT_ENV: biomni_e1
+      CONDA_SHLVL: '1'
+      PYTHONNOUSERSITE: '1'
+      BIOMNI_EXECUTION_ENV_PREFIX: /225040511/miniconda3/envs/biomni_e1
+      BIOMNI_EXECUTION_PYTHON: /225040511/miniconda3/envs/biomni_e1/bin/python
+    tools:
+    - name: make_tx2gene_from_gtf
+      description: Helper tool to create a tx2gene mapping file from a GTF file using
+        GenomicFeatures.
+      inputSchema:
+        properties:
+          gtf_file:
+            type: string
+            description: ''
+          output_csv:
+            type: string
+            description: ''
+          tx_id_type:
+            type: string
+            description: ''
+          gene_id_type:
+            type: string
+            description: ''
+        required:
+        - gtf_file
+    - name: summarize_to_gene
+      description: 'Summarize transcript-level tximport list to gene-level. '
+      inputSchema:
+        properties:
+          txi_rds_input:
+            type: string
+            description: ''
+          tx2gene:
+            type: string
+            description: ''
+          ignore_tx_version:
+            type: boolean
+            description: ''
+          ignore_after_bar:
+            type: boolean
+            description: ''
+          counts_from_abundance:
+            type: string
+            description: ''
+          output_rds:
+            type: string
+            description: ''
+        required:
+        - txi_rds_input
+        - tx2gene
+    - name: tximport
+      description: 'Import transcript-level abundance, count, and length estimates
+        from various '
+      inputSchema:
+        properties:
+          files:
+            type: array
+            description: ''
+          type:
+            type: string
+            description: ''
+          tx_in:
+            type: boolean
+            description: ''
+          tx_out:
+            type: boolean
+            description: ''
+          counts_from_abundance:
+            type: string
+            description: ''
+          tx2gene:
+            type: string
+            description: ''
+          var_reduce:
+            type: boolean
+            description: ''
+          drop_inf_reps:
+            type: boolean
+            description: ''
+          ignore_tx_version:
+            type: boolean
+            description: ''
+          ignore_after_bar:
+            type: boolean
+            description: ''
+          gene_id_col:
+            type: string
+            description: ''
+          tx_id_col:
+            type: string
+            description: ''
+          abundance_col:
+            type: string
+            description: ''
+          counts_col:
+            type: string
+            description: ''
+          length_col:
+            type: string
+            description: ''
+          output_rds:
+            type: string
+            description: ''
+        required:
+        - files
+        - type

Biomanus/experiments/bioagent-bench-runs/comparative-genomics_20260514_055459/blast_db/all_proteins.pjs

@@ -0,0 +1,24 @@
+{
+  "version": "1.2",
+  "dbname": "all_proteins",
+  "dbtype": "Protein",
+  "db-version": 5,
+  "description": "Micrococcus_all",
+  "number-of-letters": 3874170,
+  "number-of-sequences": 11758,
+  "last-updated": "2026-05-14T06:15:00",
+  "number-of-volumes": 1,
+  "bytes-total": 6118723,
+  "bytes-to-cache": 3980097,
+  "files": [
+    "all_proteins.pdb",
+    "all_proteins.phr",
+    "all_proteins.pin",
+    "all_proteins.pog",
+    "all_proteins.pos",
+    "all_proteins.pot",
+    "all_proteins.psq",
+    "all_proteins.ptf",
+    "all_proteins.pto"
+  ]
+}

Biomanus/experiments/bioagent-bench-runs/comparative-genomics_20260514_055459/classify_kos.R

@@ -0,0 +1,32 @@
+
+library(microclass)
+
+# Load the reference
+load("/225040511/project/bioagent-bench/dataset/comparative-genomics/reference/Actinobacteria.RData")
+
+# Load the combined protein sequences
+library(Biostrings)
+seqs <- readAAStringSet("/225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/blast_db/all_proteins.faa")
+
+cat("Loaded", length(seqs), "sequences\n")
+cat("First few names:\n")
+print(head(names(seqs), 5))
+
+# Try to classify with the training set
+# Using microclass::classify function
+cat("\nAttempting classification...\n")
+tryCatch({
+  # The trainingSet is a TaxaTrain object trained on Actinobacteria KOs
+  # Classify first 10 sequences as a test
+  result <- classify(trainingSet, seqs[1:10], threshold=0.5)
+  cat("Classification result class:", class(result), "\n")
+  print(result)
+}, error=function(e) {
+  cat("Classification error:", e$message, "\n")
+  cat("\nTrying alternative approach...\n")
+  # Check available functions
+  cat("Functions in microclass:\n")
+  for(fn in ls("package:microclass")) {
+    cat("  ", fn, "\n")
+  }
+})

Biomanus/experiments/bioagent-bench-runs/comparative-genomics_20260514_055459/cluster_annotation_mapping.csv

@@ -0,0 +1,1587 @@
+cluster_number,consensus_annotation
+1,"K00001  E1.1.1.1, adh, alcohol dehydrogenase [EC:1.1.1.1]"
+2,"K00003  hom, homoserine dehydrogenase [EC:1.1.1.3]"
+3,"K00013  hisD, histidinol dehydrogenase [EC:1.1.1.23]"
+4,"K00014  aroE, shikimate dehydrogenase [EC:1.1.1.25]"
+5,"K00018  hprA, glycerate dehydrogenase [EC:1.1.1.29]"
+6,"K00021  HMGCR, hydroxymethylglutaryl-CoA reductase (NADPH) [EC:1.1.1.34]"
+7,"K00024  mdh, malate dehydrogenase [EC:1.1.1.37]"
+8,"K00029  E1.1.1.40, maeB, malate dehydrogenase (oxaloacetate-decarboxylating)(NADP+) [EC:1.1.1.40]"
+9,"K00031  IDH1, IDH2, icd, isocitrate dehydrogenase [EC:1.1.1.42]"
+10,"K00034  gdh, glucose 1-dehydrogenase [EC:1.1.1.47]"
+11,"K00036  G6PD, zwf, glucose-6-phosphate 1-dehydrogenase [EC:1.1.1.49 1.1.1.363]"
+12,"K00052  leuB, IMDH, 3-isopropylmalate dehydrogenase [EC:1.1.1.85]"
+13,"K00053  ilvC, ketol-acid reductoisomerase [EC:1.1.1.86]"
+14,"K00057  gpsA, glycerol-3-phosphate dehydrogenase (NAD(P)+) [EC:1.1.1.94]"
+15,"K00057  gpsA, glycerol-3-phosphate dehydrogenase (NAD(P)+) [EC:1.1.1.94]"
+16,"K00057  gpsA, glycerol-3-phosphate dehydrogenase (NAD(P)+) [EC:1.1.1.94]"
+17,"K00058  serA, PHGDH, D-3-phosphoglycerate dehydrogenase / 2-oxoglutarate reductase [EC:1.1.1.95 1.1.1.399]"
+18,"K00058  serA, PHGDH, D-3-phosphoglycerate dehydrogenase / 2-oxoglutarate reductase [EC:1.1.1.95 1.1.1.399]"
+19,"K00059  fabG, OAR1, 3-oxoacyl-[acyl-carrier protein] reductase [EC:1.1.1.100]"
+20,"K00074  paaH, hbd, fadB, mmgB, 3-hydroxybutyryl-CoA dehydrogenase [EC:1.1.1.157]"
+21,"K00074  paaH, hbd, fadB, mmgB, 3-hydroxybutyryl-CoA dehydrogenase [EC:1.1.1.157]"
+22,"K00075  murB, UDP-N-acetylmuramate dehydrogenase [EC:1.3.1.98]"
+23,"K00088  IMPDH, guaB, IMP dehydrogenase [EC:1.1.1.205]"
+24,"K00099  dxr, 1-deoxy-D-xylulose-5-phosphate reductoisomerase [EC:1.1.1.267]"
+25,"K00116  mqo, malate dehydrogenase (quinone) [EC:1.1.5.4]"
+26,"K00126  fdsD, formate dehydrogenase subunit delta [EC:1.17.1.9]"
+27,"K00128  ALDH, aldehyde dehydrogenase (NAD+) [EC:1.2.1.3]"
+28,"K00128  ALDH, aldehyde dehydrogenase (NAD+) [EC:1.2.1.3]"
+29,"K00133  asd, aspartate-semialdehyde dehydrogenase [EC:1.2.1.11]"
+30,"K00134  GAPDH, gapA, glyceraldehyde 3-phosphate dehydrogenase (phosphorylating) [EC:1.2.1.12]"
+31,"K00140  mmsA, iolA, ALDH6A1, malonate-semialdehyde dehydrogenase (acetylating) / methylmalonate-semialdehyde dehydrogenase [EC:1.2.1.18 1.2.1.27]"
+32,"K00145  argC, N-acetyl-gamma-glutamyl-phosphate reductase [EC:1.2.1.38]"
+33,"K00147  proA, glutamate-5-semialdehyde dehydrogenase [EC:1.2.1.41]"
+34,"K00150  gap2, gapB, glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) [EC:1.2.1.59]"
+35,"K00151  hpaE, hpcC, 5-carboxymethyl-2-hydroxymuconic-semialdehyde dehydrogenase [EC:1.2.1.60]"
+36,"K00153  E1.1.1.306, S-(hydroxymethyl)mycothiol dehydrogenase [EC:1.1.1.306]"
+37,"K00156  poxB, pyruvate dehydrogenase (quinone) [EC:1.2.5.1]"
+38,"K00161  PDHA, pdhA, pyruvate dehydrogenase E1 component alpha subunit [EC:1.2.4.1]"
+39,"K00161  PDHA, pdhA, pyruvate dehydrogenase E1 component alpha subunit [EC:1.2.4.1]"
+40,"K00162  PDHB, pdhB, pyruvate dehydrogenase E1 component beta subunit [EC:1.2.4.1]"
+41,"K00162  PDHB, pdhB, pyruvate dehydrogenase E1 component beta subunit [EC:1.2.4.1]"
+42,"K00163  aceE, pyruvate dehydrogenase E1 component [EC:1.2.4.1]"
+43,"K00209  fabV, ter, enoyl-[acyl-carrier protein] reductase / trans-2-enoyl-CoA reductase (NAD+) [EC:1.3.1.9 1.3.1.44]"
+44,"K00209  fabV, ter, enoyl-[acyl-carrier protein] reductase / trans-2-enoyl-CoA reductase (NAD+) [EC:1.3.1.9 1.3.1.44]"
+45,"K00209  fabV, ter, enoyl-[acyl-carrier protein] reductase / trans-2-enoyl-CoA reductase (NAD+) [EC:1.3.1.9 1.3.1.44]"
+46,"K00215  dapB, 4-hydroxy-tetrahydrodipicolinate reductase [EC:1.17.1.8]"
+47,"K00219  fadH, 2,4-dienoyl-CoA reductase (NADPH2) [EC:1.3.1.34]"
+48,"K00226  pyrD, dihydroorotate dehydrogenase (fumarate) [EC:1.3.98.1]"
+49,"K00228  CPOX, hemF, coproporphyrinogen III oxidase [EC:1.3.3.3]"
+50,"K00230  hemG, menaquinone-dependent protoporphyrinogen oxidase [EC:1.3.5.3]"
+51,"K00239  sdhA, frdA, succinate dehydrogenase flavoprotein subunit [EC:1.3.5.1]"
+52,"K00240  sdhB, frdB, succinate dehydrogenase iron-sulfur subunit [EC:1.3.5.1]"
+53,"K00241  sdhC, frdC, succinate dehydrogenase cytochrome b subunit"
+54,"K00243  K00243, uncharacterized protein"
+55,"K00249  ACADM, acd, acyl-CoA dehydrogenase [EC:1.3.8.7]"
+56,"K00259  ald, alanine dehydrogenase [EC:1.4.1.1]"
+57,"K00261  GLUD1_2, gdhA, glutamate dehydrogenase (NAD(P)+) [EC:1.4.1.3]"
+58,"K00262  E1.4.1.4, gdhA, glutamate dehydrogenase (NADP+) [EC:1.4.1.4]"
+59,"K00265  gltB, glutamate synthase (NADPH) large chain [EC:1.4.1.13]"
+60,"K00265  gltB, glutamate synthase (NADPH) large chain [EC:1.4.1.13]"
+61,"K00266  gltD, glutamate synthase (NADPH) small chain [EC:1.4.1.13]"
+62,"K00281  GLDC, gcvP, glycine dehydrogenase [EC:1.4.4.2]"
+63,"K00285  dadA, D-amino-acid dehydrogenase [EC:1.4.5.1]"
+64,"K00286  proC, pyrroline-5-carboxylate reductase [EC:1.5.1.2]"
+65,"K00287  DHFR, folA, dihydrofolate reductase [EC:1.5.1.3]"
+66,"K00313  fixC, electron transfer flavoprotein-quinone oxidoreductase [EC:1.5.5.-]"
+67,"K00330  nuoA, NADH-quinone oxidoreductase subunit A [EC:7.1.1.2]"
+68,"K00330  nuoA, NADH-quinone oxidoreductase subunit A [EC:7.1.1.2]"
+69,"K00382  DLD, lpd, pdhD, dihydrolipoamide dehydrogenase [EC:1.8.1.4]"
+70,"K00384  trxB, TRR, thioredoxin reductase (NADPH) [EC:1.8.1.9]"
+71,"K00384  trxB, TRR, thioredoxin reductase (NADPH) [EC:1.8.1.9]"
+72,"K00389  yidH, putative membrane protein"
+73,"K00389  yidH, putative membrane protein"
+74,"K00389  yidH, putative membrane protein"
+75,"K00389  yidH, putative membrane protein"
+76,"K00389  yidH, putative membrane protein"
+77,"K00389  yidH, putative membrane protein"
+78,"K00389  yidH, putative membrane protein"
+79,"K00389  yidH, putative membrane protein"
+80,"K00389  yidH, putative membrane protein"
+81,"K00389  yidH, putative membrane protein"
+82,"K00389  yidH, putative membrane protein"
+83,"K00389  yidH, putative membrane protein"
+84,"K00389  yidH, putative membrane protein"
+85,"K00389  yidH, putative membrane protein"
+86,"K00389  yidH, putative membrane protein"
+87,"K00389  yidH, putative membrane protein"
+88,"K00389  yidH, putative membrane protein"
+89,"K00389  yidH, putative membrane protein"
+90,"K00389  yidH, putative membrane protein"
+91,"K00389  yidH, putative membrane protein"
+92,"K00389  yidH, putative membrane protein"
+93,"K00389  yidH, putative membrane protein"
+94,"K00389  yidH, putative membrane protein"
+95,"K00389  yidH, putative membrane protein"
+96,"K00389  yidH, putative membrane protein"
+97,"K00389  yidH, putative membrane protein"
+98,"K00389  yidH, putative membrane protein"
+99,"K00389  yidH, putative membrane protein"
+100,"K00389  yidH, putative membrane protein"
+101,"K00389  yidH, putative membrane protein"
+102,"K00389  yidH, putative membrane protein"
+103,"K00390  cysH, phosphoadenosine phosphosulfate reductase [EC:1.8.4.8 1.8.4.10]"
+104,"K00426  cydB, cytochrome bd ubiquinol oxidase subunit II [EC:7.1.1.7]"
+105,"K00426  cydB, cytochrome bd ubiquinol oxidase subunit II [EC:7.1.1.7]"
+106,"K00459  ncd2, npd, nitronate monooxygenase [EC:1.13.12.16]"
+107,"K00520  merA, mercuric reductase [EC:1.16.1.1]"
+108,"K00525  E1.17.4.1A, nrdA, nrdE, ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1]"
+109,"K00526  E1.17.4.1B, nrdB, nrdF, ribonucleoside-diphosphate reductase beta chain [EC:1.17.4.1]"
+110,"K00529  hcaD, 3-phenylpropionate/trans-cinnamate dioxygenase ferredoxin reductase component [EC:1.18.1.3]"
+111,"K00537  arsC, arsenate reductase (glutaredoxin) [EC:1.20.4.1]"
+112,"K00554  trmD, tRNA (guanine37-N1)-methyltransferase [EC:2.1.1.228]"
+113,"K00554  trmD, tRNA (guanine37-N1)-methyltransferase [EC:2.1.1.228]"
+114,"K00556  trmH, tRNA (guanosine-2'-O-)-methyltransferase [EC:2.1.1.34]"
+115,"K00558  DNMT1, dcm, DNA (cytosine-5)-methyltransferase 1 [EC:2.1.1.37]"
+116,"K00560  thyA, TYMS, thymidylate synthase [EC:2.1.1.45]"
+117,"K00564  rsmC, 16S rRNA (guanine1207-N2)-methyltransferase [EC:2.1.1.172]"
+118,"K00566  mnmA, trmU, tRNA-uridine 2-sulfurtransferase [EC:2.8.1.13]"
+119,"K00566  mnmA, trmU, tRNA-uridine 2-sulfurtransferase [EC:2.8.1.13]"
+120,"K00567  ogt, MGMT, methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63]"
+121,"K00598  tam, trans-aconitate 2-methyltransferase [EC:2.1.1.144]"
+122,"K00602  purH, phosphoribosylaminoimidazolecarboxamide formyltransferase / IMP cyclohydrolase [EC:2.1.2.3 3.5.4.10]"
+123,"K00603  fctD, glutamate formiminotransferase / 5-formyltetrahydrofolate cyclo-ligase [EC:2.1.2.5 6.3.3.2]"
+124,"K00603  fctD, glutamate formiminotransferase / 5-formyltetrahydrofolate cyclo-ligase [EC:2.1.2.5 6.3.3.2]"
+125,"K00603  fctD, glutamate formiminotransferase / 5-formyltetrahydrofolate cyclo-ligase [EC:2.1.2.5 6.3.3.2]"
+126,"K00604  MTFMT, fmt, methionyl-tRNA formyltransferase [EC:2.1.2.9]"
+127,"K00605  gcvT, AMT, aminomethyltransferase [EC:2.1.2.10]"
+128,"K00606  panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase [EC:2.1.2.11]"
+129,"K00609  pyrB, PYR2, aspartate carbamoyltransferase catalytic subunit [EC:2.1.3.2]"
+130,"K00611  OTC, argF, argI, ornithine carbamoyltransferase [EC:2.1.3.3]"
+131,"K00619  argA, amino-acid N-acetyltransferase [EC:2.3.1.1]"
+132,"K00620  argJ, glutamate N-acetyltransferase / amino-acid N-acetyltransferase [EC:2.3.1.35 2.3.1.1]"
+133,"K00626  ACAT, atoB, acetyl-CoA C-acetyltransferase [EC:2.3.1.9]"
+134,"K00627  DLAT, aceF, pdhC, pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [EC:2.3.1.12]"
+135,"K00627  DLAT, aceF, pdhC, pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [EC:2.3.1.12]"
+136,"K00632  fadA, fadI, acetyl-CoA acyltransferase [EC:2.3.1.16]"
+137,"K00632  fadA, fadI, acetyl-CoA acyltransferase [EC:2.3.1.16]"
+138,"K00640  cysE, serine O-acetyltransferase [EC:2.3.1.30]"
+139,"K00641  metX, homoserine O-acetyltransferase/O-succinyltransferase [EC:2.3.1.31 2.3.1.46]"
+140,"K00645  fabD, MCAT, MCT1, [acyl-carrier-protein] S-malonyltransferase [EC:2.3.1.39]"
+141,"K00647  fabB, 3-oxoacyl-[acyl-carrier-protein] synthase I [EC:2.3.1.41]"
+142,"K00648  fabH, 3-oxoacyl-[acyl-carrier-protein] synthase III [EC:2.3.1.180]"
+143,"K00655  plsC, 1-acyl-sn-glycerol-3-phosphate acyltransferase [EC:2.3.1.51]"
+144,"K00667  FAS2, fatty acid synthase subunit alpha, fungi type [EC:2.3.1.86]"
+145,"K00667  FAS2, fatty acid synthase subunit alpha, fungi type [EC:2.3.1.86]"
+146,"K00667  FAS2, fatty acid synthase subunit alpha, fungi type [EC:2.3.1.86]"
+147,"K00667  FAS2, fatty acid synthase subunit alpha, fungi type [EC:2.3.1.86]"
+148,"K00674  dapD, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase [EC:2.3.1.117]"
+149,"K00696  E2.4.1.14, sucrose-phosphate synthase [EC:2.4.1.14]"
+150,"K00697  otsA, trehalose 6-phosphate synthase [EC:2.4.1.15 2.4.1.347]"
+151,"K00700  GBE1, glgB, 1,4-alpha-glucan branching enzyme [EC:2.4.1.18]"
+152,"K00721  DPM1, dolichol-phosphate mannosyltransferase [EC:2.4.1.83]"
+153,"K00728  POMT, pmt, dolichyl-phosphate-mannose-protein mannosyltransferase [EC:2.4.1.109]"
+154,"K00728  POMT, pmt, dolichyl-phosphate-mannose-protein mannosyltransferase [EC:2.4.1.109]"
+155,"K00758  deoA, TYMP, thymidine phosphorylase [EC:2.4.2.4]"
+156,"K00760  hprT, hpt, HPRT1, hypoxanthine phosphoribosyltransferase [EC:2.4.2.8]"
+157,"K00761  upp, UPRT, uracil phosphoribosyltransferase [EC:2.4.2.9]"
+158,"K00762  pyrE, orotate phosphoribosyltransferase [EC:2.4.2.10]"
+159,"K00763  pncB, NAPRT1, nicotinate phosphoribosyltransferase [EC:6.3.4.21]"
+160,"K00764  purF, PPAT, amidophosphoribosyltransferase [EC:2.4.2.14]"
+161,"K00765  hisG, ATP phosphoribosyltransferase [EC:2.4.2.17]"
+162,"K00766  trpD, anthranilate phosphoribosyltransferase [EC:2.4.2.18]"
+163,"K00767  nadC, QPRT, nicotinate-nucleotide pyrophosphorylase (carboxylating) [EC:2.4.2.19]"
+164,"K00773  tgt, queuine tRNA-ribosyltransferase [EC:2.4.2.29]"
+165,"K00782  lldG, L-lactate dehydrogenase complex protein LldG"
+166,"K00782  lldG, L-lactate dehydrogenase complex protein LldG"
+167,"K00782  lldG, L-lactate dehydrogenase complex protein LldG"
+168,"K00783  rlmH, 23S rRNA (pseudouridine1915-N3)-methyltransferase [EC:2.1.1.177]"
+169,"K00788  thiE, thiamine-phosphate pyrophosphorylase [EC:2.5.1.3]"
+170,"K00789  metK, MAT, S-adenosylmethionine synthetase [EC:2.5.1.6]"
+171,"K00790  murA, UDP-N-acetylglucosamine 1-carboxyvinyltransferase [EC:2.5.1.7]"
+172,"K00791  miaA, TRIT1, tRNA dimethylallyltransferase [EC:2.5.1.75]"
+173,"K00794  ribH, RIB4, 6,7-dimethyl-8-ribityllumazine synthase [EC:2.5.1.78]"
+174,"K00796  folP, dihydropteroate synthase [EC:2.5.1.15]"
+175,"K00796  folP, dihydropteroate synthase [EC:2.5.1.15]"
+176,"K00800  aroA, 3-phosphoshikimate 1-carboxyvinyltransferase [EC:2.5.1.19]"
+177,"K00801  FDFT1, farnesyl-diphosphate farnesyltransferase [EC:2.5.1.21]"
+178,"K00801  FDFT1, farnesyl-diphosphate farnesyltransferase [EC:2.5.1.21]"
+179,"K00806  uppS, undecaprenyl diphosphate synthase [EC:2.5.1.31]"
+180,"K00806  uppS, undecaprenyl diphosphate synthase [EC:2.5.1.31]"
+181,"K00812  aspB, aspartate aminotransferase [EC:2.6.1.1]"
+182,"K00817  hisC, histidinol-phosphate aminotransferase [EC:2.6.1.9]"
+183,"K00820  glmS, GFPT, glutamine---fructose-6-phosphate transaminase (isomerizing) [EC:2.6.1.16]"
+184,"K00820  glmS, GFPT, glutamine---fructose-6-phosphate transaminase (isomerizing) [EC:2.6.1.16]"
+185,"K00821  argD, acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17]"
+186,"K00826  E2.6.1.42, ilvE, branched-chain amino acid aminotransferase [EC:2.6.1.42]"
+187,"K00831  serC, PSAT1, phosphoserine aminotransferase [EC:2.6.1.52]"
+188,"K00832  tyrB, aromatic-amino-acid transaminase [EC:2.6.1.57]"
+189,"K00847  E2.7.1.4, scrK, fructokinase [EC:2.7.1.4]"
+190,"K00857  tdk, TK, thymidine kinase [EC:2.7.1.21]"
+191,"K00858  ppnK, NADK, NAD+ kinase [EC:2.7.1.23]"
+192,"K00859  coaE, dephospho-CoA kinase [EC:2.7.1.24]"
+193,"K00859  coaE, dephospho-CoA kinase [EC:2.7.1.24]"
+194,"K00864  glpK, GK, glycerol kinase [EC:2.7.1.30]"
+195,"K00867  coaA, type I pantothenate kinase [EC:2.7.1.33]"
+196,"K00868  pdxK, pdxY, pyridoxine kinase [EC:2.7.1.35]"
+197,"K00872  thrB, homoserine kinase [EC:2.7.1.39]"
+198,"K00873  PK, pyk, pyruvate kinase [EC:2.7.1.40]"
+199,"K00876  udk, UCK, uridine kinase [EC:2.7.1.48]"
+200,"K00886  ppgK, polyphosphate glucokinase [EC:2.7.1.63]"
+201,"K00891  aroK, aroL, shikimate kinase [EC:2.7.1.71]"
+202,"K00919  ispE, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase [EC:2.7.1.148]"
+203,"K00927  PGK, pgk, phosphoglycerate kinase [EC:2.7.2.3]"
+204,"K00930  argB, acetylglutamate kinase [EC:2.7.2.8]"
+205,"K00931  proB, glutamate 5-kinase [EC:2.7.2.11]"
+206,"K00936  pdtaS, two-component system, sensor histidine kinase PdtaS [EC:2.7.13.3]"
+207,"K00937  ppk1, polyphosphate kinase [EC:2.7.4.1]"
+208,"K00939  adk, AK, adenylate kinase [EC:2.7.4.3]"
+209,"K00940  ndk, NME, nucleoside-diphosphate kinase [EC:2.7.4.6]"
+210,"K00941  thiD, hydroxymethylpyrimidine/phosphomethylpyrimidine kinase [EC:2.7.1.49 2.7.4.7]"
+211,"K00942  gmk, GUK1, guanylate kinase [EC:2.7.4.8]"
+212,"K00943  tmk, DTYMK, dTMP kinase [EC:2.7.4.9]"
+213,"K00946  thiL, thiamine-monophosphate kinase [EC:2.7.4.16]"
+214,"K00948  PRPS, prsA, ribose-phosphate pyrophosphokinase [EC:2.7.6.1]"
+215,"K00954  E2.7.7.3A, coaD, kdtB, pantetheine-phosphate adenylyltransferase [EC:2.7.7.3]"
+216,"K00955  cysNC, bifunctional enzyme CysN/CysC [EC:2.7.7.4 2.7.1.25]"
+217,"K00957  cysD, sulfate adenylyltransferase subunit 2 [EC:2.7.7.4]"
+218,"K00962  pnp, PNPT1, polyribonucleotide nucleotidyltransferase [EC:2.7.7.8]"
+219,"K00963  UGP2, galU, galF, UTP--glucose-1-phosphate uridylyltransferase [EC:2.7.7.9]"
+220,"K00966  GMPP, mannose-1-phosphate guanylyltransferase [EC:2.7.7.13]"
+221,"K00969  nadD, nicotinate-nucleotide adenylyltransferase [EC:2.7.7.18]"
+222,"K00973  rfbA, rmlA, rffH, glucose-1-phosphate thymidylyltransferase [EC:2.7.7.24]"
+223,"K00974  cca, tRNA nucleotidyltransferase (CCA-adding enzyme) [EC:2.7.7.72 3.1.3.- 3.1.4.-]"
+224,"K00975  glgC, glucose-1-phosphate adenylyltransferase [EC:2.7.7.27]"
+225,"K00981  E2.7.7.41, CDS1, CDS2, cdsA, phosphatidate cytidylyltransferase [EC:2.7.7.41]"
+226,"K00982  glnE, [glutamine synthetase] adenylyltransferase / [glutamine synthetase]-adenylyl-L-tyrosine phosphorylase [EC:2.7.7.42 2.7.7.89]"
+227,"K00989  rph, ribonuclease PH [EC:2.7.7.56]"
+228,"K00995  pgsA, PGS1, CDP-diacylglycerol---glycerol-3-phosphate 3-phosphatidyltransferase [EC:2.7.8.5]"
+229,"K00997  acpS, holo-[acyl-carrier protein] synthase [EC:2.7.8.7]"
+230,"K01005  tagT_U_V, polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase [EC:2.7.8.-]"
+231,"K01005  tagT_U_V, polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase [EC:2.7.8.-]"
+232,"K01005  tagT_U_V, polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase [EC:2.7.8.-]"
+233,"K01011  TST, MPST, sseA, thiosulfate/3-mercaptopyruvate sulfurtransferase [EC:2.8.1.1 2.8.1.2]"
+234,"K01028  scoA, 3-oxoacid CoA-transferase subunit A [EC:2.8.3.5]"
+235,"K01029  scoB, 3-oxoacid CoA-transferase subunit B [EC:2.8.3.5]"
+236,"K01056  PTH1, PTRH1, pth, spoVC, peptidyl-tRNA hydrolase, PTH1 family [EC:3.1.1.29]"
+237,"K01069  gloB, gloC, HAGH, hydroxyacylglutathione hydrolase [EC:3.1.2.6]"
+238,"K01069  gloB, gloC, HAGH, hydroxyacylglutathione hydrolase [EC:3.1.2.6]"
+239,"K01069  gloB, gloC, HAGH, hydroxyacylglutathione hydrolase [EC:3.1.2.6]"
+240,"K01079  serB, PSPH, phosphoserine phosphatase [EC:3.1.3.3]"
+241,"K01082  cysQ, MET22, BPNT1, 3'(2'), 5'-bisphosphate nucleotidase [EC:3.1.3.7]"
+242,"K01089  hisB, imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase [EC:4.2.1.19 3.1.3.15]"
+243,"K01091  gph, phosphoglycolate phosphatase [EC:3.1.3.18]"
+244,"K01092  E3.1.3.25, IMPA, suhB, myo-inositol-1(or 4)-monophosphatase [EC:3.1.3.25]"
+245,"K01104  E3.1.3.48, protein-tyrosine phosphatase [EC:3.1.3.48]"
+246,"K01129  dgt, dGTPase [EC:3.1.5.1]"
+247,"K01142  E3.1.11.2, xthA, exodeoxyribonuclease III [EC:3.1.11.2]"
+248,"K01159  ruvC, crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10]"
+249,"K01175  ybfF, esterase [EC:3.1.-.-]"
+250,"K01194  TREH, treA, treF, alpha,alpha-trehalase [EC:3.2.1.28]"
+251,"K01246  tag, DNA-3-methyladenine glycosylase I [EC:3.2.2.20]"
+252,"K01246  tag, DNA-3-methyladenine glycosylase I [EC:3.2.2.20]"
+253,"K01250  rihA, pyrimidine-specific ribonucleoside hydrolase [EC:3.2.2.-]"
+254,"K01251  AHCY, ahcY, adenosylhomocysteinase [EC:3.13.2.1]"
+255,"K01252  entB, dhbB, vibB, mxcF, bifunctional isochorismate lyase / aryl carrier protein [EC:3.3.2.1 6.3.2.14]"
+256,"K01255  CARP, pepA, leucyl aminopeptidase [EC:3.4.11.1]"
+257,"K01259  pip, proline iminopeptidase [EC:3.4.11.5]"
+258,"K01262  pepP, Xaa-Pro aminopeptidase [EC:3.4.11.9]"
+259,"K01284  dcp, peptidyl-dipeptidase Dcp [EC:3.4.15.5]"
+260,"K01304  pcp, pyroglutamyl-peptidase [EC:3.4.19.3]"
+261,"K01356  lexA, repressor LexA [EC:3.4.21.88]"
+262,"K01358  clpP, CLPP, ATP-dependent Clp protease, protease subunit [EC:3.4.21.92]"
+263,"K01358  clpP, CLPP, ATP-dependent Clp protease, protease subunit [EC:3.4.21.92]"
+264,"K01420  fnr, CRP/FNR family transcriptional regulator, anaerobic regulatory protein"
+265,"K01420  fnr, CRP/FNR family transcriptional regulator, anaerobic regulatory protein"
+266,"K01420  fnr, CRP/FNR family transcriptional regulator, anaerobic regulatory protein"
+267,"K01420  fnr, CRP/FNR family transcriptional regulator, anaerobic regulatory protein"
+268,"K01420  fnr, CRP/FNR family transcriptional regulator, anaerobic regulatory protein"
+269,"K01420  fnr, CRP/FNR family transcriptional regulator, anaerobic regulatory protein"
+270,"K01420  fnr, CRP/FNR family transcriptional regulator, anaerobic regulatory protein"
+271,"K01420  fnr, CRP/FNR family transcriptional regulator, anaerobic regulatory protein"
+272,"K01433  purU, formyltetrahydrofolate deformylase [EC:3.5.1.10]"
+273,"K01439  dapE, succinyl-diaminopimelate desuccinylase [EC:3.5.1.18]"
+274,"K01439  dapE, succinyl-diaminopimelate desuccinylase [EC:3.5.1.18]"
+275,"K01462  PDF, def, peptide deformylase [EC:3.5.1.88]"
+276,"K01462  PDF, def, peptide deformylase [EC:3.5.1.88]"
+277,"K01463  bshB1, N-acetylglucosamine malate deacetylase 1 [EC:3.5.1.-]"
+278,"K01488  add, ADA, adenosine deaminase [EC:3.5.4.4]"
+279,"K01489  cdd, CDA, cytidine deaminase [EC:3.5.4.5]"
+280,"K01491  folD, methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase [EC:1.5.1.5 3.5.4.9]"
+281,"K01494  dcd, dCTP deaminase [EC:3.5.4.13]"
+282,"K01495  GCH1, folE, GTP cyclohydrolase IA [EC:3.5.4.16]"
+283,"K01495  GCH1, folE, GTP cyclohydrolase IA [EC:3.5.4.16]"
+284,"K01496  hisI, phosphoribosyl-AMP cyclohydrolase [EC:3.5.4.19]"
+285,"K01500  fchA, methenyltetrahydrofolate cyclohydrolase [EC:3.5.4.9]"
+286,"K01507  ppa, inorganic pyrophosphatase [EC:3.6.1.1]"
+287,"K01515  nudF, ADP-ribose pyrophosphatase [EC:3.6.1.13 3.6.1.-]"
+288,"K01519  rdgB, ITPA, XTP/dITP diphosphohydrolase [EC:3.6.1.66]"
+289,"K01520  dut, DUT, dUTP pyrophosphatase [EC:3.6.1.23]"
+290,"K01523  hisE, phosphoribosyl-ATP pyrophosphohydrolase [EC:3.6.1.31]"
+291,"K01524  ppx-gppA, exopolyphosphatase / guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase [EC:3.6.1.11 3.6.1.40]"
+292,"K01533  copB, P-type Cu2+ transporter [EC:7.2.2.9]"
+293,"K01552  ecfA, energy-coupling factor transport system ATP-binding protein [EC:7.-.-.-]"
+294,"K01552  ecfA, energy-coupling factor transport system ATP-binding protein [EC:7.-.-.-]"
+295,"K01552  ecfA, energy-coupling factor transport system ATP-binding protein [EC:7.-.-.-]"
+296,"K01563  dhaA, haloalkane dehalogenase [EC:3.8.1.5]"
+297,"K01579  panD, aspartate 1-decarboxylase [EC:4.1.1.11]"
+298,"K01586  lysA, diaminopimelate decarboxylase [EC:4.1.1.20]"
+299,"K01589  purK, 5-(carboxyamino)imidazole ribonucleotide synthase [EC:6.3.4.18]"
+300,"K01591  pyrF, orotidine-5'-phosphate decarboxylase [EC:4.1.1.23]"
+301,"K01596  E4.1.1.32, pckA, PCK, phosphoenolpyruvate carboxykinase (GTP) [EC:4.1.1.32]"
+302,"K01599  hemE, UROD, uroporphyrinogen decarboxylase [EC:4.1.1.37]"
+303,"K01609  trpC, indole-3-glycerol phosphate synthase [EC:4.1.1.48]"
+304,"K01616  kgd, multifunctional 2-oxoglutarate metabolism enzyme [EC:2.2.1.5 4.1.1.71 1.2.4.2 2.3.1.61]"
+305,"K01619  deoC, DERA, deoxyribose-phosphate aldolase [EC:4.1.2.4]"
+306,"K01620  ltaE, threonine aldolase [EC:4.1.2.48]"
+307,"K01622  K01622, fructose 1,6-bisphosphate aldolase/phosphatase [EC:4.1.2.13 3.1.3.11]"
+308,"K01625  eda, 2-dehydro-3-deoxyphosphogluconate aldolase / (4S)-4-hydroxy-2-oxoglutarate aldolase [EC:4.1.2.14 4.1.3.42]"
+309,"K01633  folB, 7,8-dihydroneopterin aldolase/epimerase/oxygenase [EC:4.1.2.25 5.1.99.8 1.13.11.81]"
+310,"K01637  E4.1.3.1, aceA, isocitrate lyase [EC:4.1.3.1]"
+311,"K01638  aceB, glcB, malate synthase [EC:2.3.3.9]"
+312,"K01644  citE, citrate lyase subunit beta / citryl-CoA lyase [EC:4.1.3.34]"
+313,"K01647  CS, gltA, citrate synthase [EC:2.3.3.1]"
+314,"K01647  CS, gltA, citrate synthase [EC:2.3.3.1]"
+315,"K01649  leuA, IMS, 2-isopropylmalate synthase [EC:2.3.3.13]"
+316,"K01652  E2.2.1.6L, ilvB, ilvG, ilvI, acetolactate synthase I/II/III large subunit [EC:2.2.1.6]"
+317,"K01652  E2.2.1.6L, ilvB, ilvG, ilvI, acetolactate synthase I/II/III large subunit [EC:2.2.1.6]"
+318,"K01652  E2.2.1.6L, ilvB, ilvG, ilvI, acetolactate synthase I/II/III large subunit [EC:2.2.1.6]"
+319,"K01653  E2.2.1.6S, ilvH, ilvN, acetolactate synthase I/III small subunit [EC:2.2.1.6]"
+320,"K01657  trpE, anthranilate synthase component I [EC:4.1.3.27]"
+321,"K01658  trpG, anthranilate synthase component II [EC:4.1.3.27]"
+322,"K01662  dxs, 1-deoxy-D-xylulose-5-phosphate synthase [EC:2.2.1.7]"
+323,"K01673  cynT, can, carbonic anhydrase [EC:4.2.1.1]"
+324,"K01673  cynT, can, carbonic anhydrase [EC:4.2.1.1]"
+325,"K01679  E4.2.1.2B, fumC, FH, fumarate hydratase, class II [EC:4.2.1.2]"
+326,"K01681  ACO, acnA, aconitate hydratase [EC:4.2.1.3]"
+327,"K01687  ilvD, dihydroxy-acid dehydratase [EC:4.2.1.9]"
+328,"K01689  ENO, eno, enolase [EC:4.2.1.11]"
+329,"K01692  paaF, echA, enoyl-CoA hydratase [EC:4.2.1.17]"
+330,"K01695  trpA, tryptophan synthase alpha chain [EC:4.2.1.20]"
+331,"K01696  trpB, tryptophan synthase beta chain [EC:4.2.1.20]"
+332,"K01697  CBS, cystathionine beta-synthase [EC:4.2.1.22]"
+333,"K01698  hemB, ALAD, porphobilinogen synthase [EC:4.2.1.24]"
+334,"K01703  leuC, IPMI-L, 3-isopropylmalate/(R)-2-methylmalate dehydratase large subunit [EC:4.2.1.33 4.2.1.35]"
+335,"K01704  leuD, IPMI-S, 3-isopropylmalate/(R)-2-methylmalate dehydratase small subunit [EC:4.2.1.33 4.2.1.35]"
+336,"K01710  rfbB, rmlB, rffG, dTDP-glucose 4,6-dehydratase [EC:4.2.1.46]"
+337,"K01712  hutU, UROC1, urocanate hydratase [EC:4.2.1.49]"
+338,"K01714  dapA, 4-hydroxy-tetrahydrodipicolinate synthase [EC:4.3.3.7]"
+339,"K01715  crt, enoyl-CoA hydratase [EC:4.2.1.17]"
+340,"K01720  prpD, 2-methylcitrate dehydratase [EC:4.2.1.79]"
+341,"K01733  thrC, threonine synthase [EC:4.2.3.1]"
+342,"K01735  aroB, 3-dehydroquinate synthase [EC:4.2.3.4]"
+343,"K01736  aroC, chorismate synthase [EC:4.2.3.5]"
+344,"K01738  cysK, cysteine synthase [EC:2.5.1.47]"
+345,"K01739  metB, cystathionine gamma-synthase [EC:2.5.1.48]"
+346,"K01739  metB, cystathionine gamma-synthase [EC:2.5.1.48]"
+347,"K01740  metY, O-acetylhomoserine (thiol)-lyase [EC:2.5.1.49]"
+348,"K01744  aspA, aspartate ammonia-lyase [EC:4.3.1.1]"
+349,"K01745  hutH, HAL, histidine ammonia-lyase [EC:4.3.1.3]"
+350,"K01749  hemC, HMBS, hydroxymethylbilane synthase [EC:2.5.1.61]"
+351,"K01752  E4.3.1.17, sdaA, sdaB, tdcG, L-serine dehydratase [EC:4.3.1.17]"
+352,"K01755  argH, ASL, argininosuccinate lyase [EC:4.3.2.1]"
+353,"K01756  purB, ADSL, adenylosuccinate lyase [EC:4.3.2.2]"
+354,"K01768  E4.6.1.1, adenylate cyclase [EC:4.6.1.1]"
+355,"K01772  hemH, FECH, protoporphyrin/coproporphyrin ferrochelatase [EC:4.98.1.1 4.99.1.9]"
+356,"K01775  alr, alanine racemase [EC:5.1.1.1]"
+357,"K01776  murI, glutamate racemase [EC:5.1.1.3]"
+358,"K01778  dapF, diaminopimelate epimerase [EC:5.1.1.7]"
+359,"K01783  rpe, RPE, ribulose-phosphate 3-epimerase [EC:5.1.3.1]"
+360,"K01784  galE, GALE, UDP-glucose 4-epimerase [EC:5.1.3.2]"
+361,"K01791  wecB, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) [EC:5.1.3.14]"
+362,"K01803  TPI, tpiA, triosephosphate isomerase (TIM) [EC:5.3.1.1]"
+363,"K01809  manA, MPI, mannose-6-phosphate isomerase [EC:5.3.1.8]"
+364,"K01810  GPI, pgi, glucose-6-phosphate isomerase [EC:5.3.1.9]"
+365,"K01814  hisA, phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase [EC:5.3.1.16]"
+366,"K01823  idi, IDI, isopentenyl-diphosphate Delta-isomerase [EC:5.3.3.2]"
+367,"K01834  PGAM, gpmA, 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase [EC:5.4.2.11]"
+368,"K01835  pgm, phosphoglucomutase [EC:5.4.2.2]"
+369,"K01845  hemL, glutamate-1-semialdehyde 2,1-aminomutase [EC:5.4.3.8]"
+370,"K01858  INO1, ISYNA1, myo-inositol-1-phosphate synthase [EC:5.5.1.4]"
+371,"K01866  YARS, tyrS, tyrosyl-tRNA synthetase [EC:6.1.1.1]"
+372,"K01867  WARS, trpS, tryptophanyl-tRNA synthetase [EC:6.1.1.2]"
+373,"K01868  TARS, thrS, threonyl-tRNA synthetase [EC:6.1.1.3]"
+374,"K01869  LARS, leuS, leucyl-tRNA synthetase [EC:6.1.1.4]"
+375,"K01870  IARS, ileS, isoleucyl-tRNA synthetase [EC:6.1.1.5]"
+376,"K01872  AARS, alaS, alanyl-tRNA synthetase [EC:6.1.1.7]"
+377,"K01873  VARS, valS, valyl-tRNA synthetase [EC:6.1.1.9]"
+378,"K01874  MARS, metG, methionyl-tRNA synthetase [EC:6.1.1.10]"
+379,"K01875  SARS, serS, seryl-tRNA synthetase [EC:6.1.1.11]"
+380,"K01881  PARS, proS, prolyl-tRNA synthetase [EC:6.1.1.15]"
+381,"K01883  CARS, cysS, cysteinyl-tRNA synthetase [EC:6.1.1.16]"
+382,"K01887  RARS, argS, arginyl-tRNA synthetase [EC:6.1.1.19]"
+383,"K01889  FARSA, pheS, phenylalanyl-tRNA synthetase alpha chain [EC:6.1.1.20]"
+384,"K01890  FARSB, pheT, phenylalanyl-tRNA synthetase beta chain [EC:6.1.1.20]"
+385,"K01892  HARS, hisS, histidyl-tRNA synthetase [EC:6.1.1.21]"
+386,"K01894  gluQ, glutamyl-Q tRNA(Asp) synthetase [EC:6.1.1.-]"
+387,"K01895  ACSS1_2, acs, acetyl-CoA synthetase [EC:6.2.1.1]"
+388,"K01895  ACSS1_2, acs, acetyl-CoA synthetase [EC:6.2.1.1]"
+389,"K01895  ACSS1_2, acs, acetyl-CoA synthetase [EC:6.2.1.1]"
+390,"K01895  ACSS1_2, acs, acetyl-CoA synthetase [EC:6.2.1.1]"
+391,"K01903  sucC, succinyl-CoA synthetase beta subunit [EC:6.2.1.5]"
+392,"K01905  acdA, acetate---CoA ligase (ADP-forming) subunit alpha [EC:6.2.1.13]"
+393,"K01905  acdA, acetate---CoA ligase (ADP-forming) subunit alpha [EC:6.2.1.13]"
+394,"K01909  mbtM, long-chain-fatty-acid--[acyl-carrier-protein] ligase [EC:6.2.1.20]"
+395,"K01911  menE, o-succinylbenzoate---CoA ligase [EC:6.2.1.26]"
+396,"K01912  paaK, phenylacetate-CoA ligase [EC:6.2.1.30]"
+397,"K01915  glnA, GLUL, glutamine synthetase [EC:6.3.1.2]"
+398,"K01915  glnA, GLUL, glutamine synthetase [EC:6.3.1.2]"
+399,"K01918  panC, pantoate--beta-alanine ligase [EC:6.3.2.1]"
+400,"K01919  gshA, glutamate--cysteine ligase [EC:6.3.2.2]"
+401,"K01921  ddl, D-alanine-D-alanine ligase [EC:6.3.2.4]"
+402,"K01924  murC, UDP-N-acetylmuramate--alanine ligase [EC:6.3.2.8]"
+403,"K01925  murD, UDP-N-acetylmuramoylalanine--D-glutamate ligase [EC:6.3.2.9]"
+404,"K01928  murE, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase [EC:6.3.2.13]"
+405,"K01929  murF, UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase [EC:6.3.2.10]"
+406,"K01933  purM, phosphoribosylformylglycinamidine cyclo-ligase [EC:6.3.3.1]"
+407,"K01939  purA, ADSS, adenylosuccinate synthase [EC:6.3.4.4]"
+408,"K01940  argG, ASS1, argininosuccinate synthase [EC:6.3.4.5]"
+409,"K01945  purD, phosphoribosylamine---glycine ligase [EC:6.3.4.13]"
+410,"K01951  guaA, GMPS, GMP synthase (glutamine-hydrolysing) [EC:6.3.5.2]"
+411,"K01951  guaA, GMPS, GMP synthase (glutamine-hydrolysing) [EC:6.3.5.2]"
+412,"K01955  carB, CPA2, carbamoyl-phosphate synthase large subunit [EC:6.3.5.5]"
+413,"K01956  carA, CPA1, carbamoyl-phosphate synthase small subunit [EC:6.3.5.5]"
+414,"K01958  PC, pyc, pyruvate carboxylase [EC:6.4.1.1]"
+415,"K01961  accC, acetyl-CoA carboxylase, biotin carboxylase subunit [EC:6.4.1.2 6.3.4.14]"
+416,"K01961  accC, acetyl-CoA carboxylase, biotin carboxylase subunit [EC:6.4.1.2 6.3.4.14]"
+417,"K01989  K01989, putative tryptophan/tyrosine transport system substrate-binding protein"
+418,"K01989  K01989, putative tryptophan/tyrosine transport system substrate-binding protein"
+419,"K01992  ABC-2.P, ABC-2 type transport system permease protein"
+420,"K01992  ABC-2.P, ABC-2 type transport system permease protein"
+421,"K01992  ABC-2.P, ABC-2 type transport system permease protein"
+422,"K01992  ABC-2.P, ABC-2 type transport system permease protein"
+423,"K01997  livH, branched-chain amino acid transport system permease protein"
+424,"K02003  ABC.CD.A, putative ABC transport system ATP-binding protein"
+425,"K02003  ABC.CD.A, putative ABC transport system ATP-binding protein"
+426,"K02003  ABC.CD.A, putative ABC transport system ATP-binding protein"
+427,"K02003  ABC.CD.A, putative ABC transport system ATP-binding protein"
+428,"K02003  ABC.CD.A, putative ABC transport system ATP-binding protein"
+429,"K02003  ABC.CD.A, putative ABC transport system ATP-binding protein"
+430,"K02004  ABC.CD.P, putative ABC transport system permease protein"
+431,"K02028  ABC.PA.A, polar amino acid transport system ATP-binding protein [EC:7.4.2.1]"
+432,"K02036  pstB, phosphate transport system ATP-binding protein [EC:7.3.2.1]"
+433,"K02037  pstC, phosphate transport system permease protein"
+434,"K02039  phoU, phosphate transport system protein"
+435,"K02040  pstS, phosphate transport system substrate-binding protein"
+436,"K02064  thiB, tbpA, thiamine transport system substrate-binding protein"
+437,"K02074  ABC.ZM.A, zinc/manganese transport system ATP-binding protein"
+438,"K02076  zurR, zur, Fur family transcriptional regulator, zinc uptake regulator"
+439,"K02078  acpP, acyl carrier protein"
+440,"K02111  ATPF1A, atpA, F-type H+/Na+-transporting ATPase subunit alpha [EC:7.1.2.2 7.2.2.1]"
+441,"K02112  ATPF1B, atpD, F-type H+/Na+-transporting ATPase subunit beta [EC:7.1.2.2 7.2.2.1]"
+442,"K02115  ATPF1G, atpG, F-type H+-transporting ATPase subunit gamma"
+443,"K02168  betT, betS, choline/glycine/proline betaine transport protein"
+444,"K02199  ccmG, dsbE, cytochrome c biogenesis protein CcmG, thiol:disulfide interchange protein DsbE"
+445,"K02199  ccmG, dsbE, cytochrome c biogenesis protein CcmG, thiol:disulfide interchange protein DsbE"
+446,"K02257  COX10, ctaB, cyoE, heme o synthase [EC:2.5.1.141]"
+447,"K02259  COX15, ctaA, heme a synthase [EC:1.17.99.9]"
+448,"K02274  coxA, ctaD, cytochrome c oxidase subunit I [EC:7.1.1.9]"
+449,"K02275  coxB, ctaC, cytochrome c oxidase subunit II [EC:7.1.1.9]"
+450,"K02276  coxC, ctaE, cytochrome c oxidase subunit III [EC:7.1.1.9]"
+451,"K02277  coxD, ctaF, cytochrome c oxidase subunit IV [EC:7.1.1.9]"
+452,"K02291  crtB, 15-cis-phytoene synthase [EC:2.5.1.32]"
+453,"K02302  cysG, uroporphyrin-III C-methyltransferase / precorrin-2 dehydrogenase / sirohydrochlorin ferrochelatase [EC:2.1.1.107 1.3.1.76 4.99.1.4]"
+454,"K02313  dnaA, chromosomal replication initiator protein"
+455,"K02314  dnaB, replicative DNA helicase [EC:5.6.2.3]"
+456,"K02316  dnaG, DNA primase [EC:2.7.7.101]"
+457,"K02334  dpo, DNA polymerase bacteriophage-type [EC:2.7.7.7]"
+458,"K02335  polA, DNA polymerase I [EC:2.7.7.7]"
+459,"K02337  dnaE, DNA polymerase III subunit alpha [EC:2.7.7.7]"
+460,"K02338  dnaN, DNA polymerase III subunit beta [EC:2.7.7.7]"
+461,"K02340  holA, DNA polymerase III subunit delta [EC:2.7.7.7]"
+462,"K02346  dinB, DNA polymerase IV [EC:2.7.7.7]"
+463,"K02355  fusA, GFM, EFG, elongation factor G"
+464,"K02356  efp, elongation factor P"
+465,"K02357  tsf, TSFM, elongation factor Ts"
+466,"K02358  tuf, TUFM, elongation factor Tu"
+467,"K02372  fabZ, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase [EC:4.2.1.59]"
+468,"K02433  gatA, QRSL1, aspartyl-tRNA(Asn)/glutamyl-tRNA(Gln) amidotransferase subunit A [EC:6.3.5.6 6.3.5.7]"
+469,"K02433  gatA, QRSL1, aspartyl-tRNA(Asn)/glutamyl-tRNA(Gln) amidotransferase subunit A [EC:6.3.5.6 6.3.5.7]"
+470,"K02434  gatB, PET112, aspartyl-tRNA(Asn)/glutamyl-tRNA(Gln) amidotransferase subunit B [EC:6.3.5.6 6.3.5.7]"
+471,"K02435  gatC, GATC, aspartyl-tRNA(Asn)/glutamyl-tRNA(Gln) amidotransferase subunit C [EC:6.3.5.6 6.3.5.7]"
+472,"K02437  gcvH, GCSH, glycine cleavage system H protein"
+473,"K02438  glgX, glycogen debranching enzyme [EC:3.2.1.196]"
+474,"K02439  glpE, thiosulfate sulfurtransferase [EC:2.8.1.1]"
+475,"K02446  glpX, fructose-1,6-bisphosphatase II [EC:3.1.3.11]"
+476,"K02469  gyrA, DNA gyrase subunit A [EC:5.6.2.2]"
+477,"K02469  gyrA, DNA gyrase subunit A [EC:5.6.2.2]"
+478,"K02469  gyrA, DNA gyrase subunit A [EC:5.6.2.2]"
+479,"K02469  gyrA, DNA gyrase subunit A [EC:5.6.2.2]"
+480,"K02471  bacA, bclA, vitamin B12/bleomycin/antimicrobial peptide transport system ATP-binding/permease protein"
+481,"K02471  bacA, bclA, vitamin B12/bleomycin/antimicrobial peptide transport system ATP-binding/permease protein"
+482,"K02471  bacA, bclA, vitamin B12/bleomycin/antimicrobial peptide transport system ATP-binding/permease protein"
+483,"K02472  wecC, UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase [EC:1.1.1.336]"
+484,"K02492  hemA, glutamyl-tRNA reductase [EC:1.2.1.70]"
+485,"K02493  hemK, prmC, HEMK, release factor glutamine methyltransferase [EC:2.1.1.297]"
+486,"K02493  hemK, prmC, HEMK, release factor glutamine methyltransferase [EC:2.1.1.297]"
+487,"K02500  hisF, imidazole glycerol-phosphate synthase subunit HisF [EC:4.3.2.10]"
+488,"K02501  hisH, imidazole glycerol-phosphate synthase subunit HisH [EC:4.3.2.10]"
+489,"K02509  hpaH, 2-oxo-hept-3-ene-1,7-dioate hydratase [EC:4.2.1.-]"
+490,"K02518  infA, translation initiation factor IF-1"
+491,"K02519  infB, MTIF2, translation initiation factor IF-2"
+492,"K02520  infC, MTIF3, translation initiation factor IF-3"
+493,"K02525  kdgR, LacI family transcriptional regulator, kdg operon repressor"
+494,"K02528  ksgA, 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase [EC:2.1.1.182]"
+495,"K02548  menA, 1,4-dihydroxy-2-naphthoate polyprenyltransferase [EC:2.5.1.74]"
+496,"K02549  menC, o-succinylbenzoate synthase [EC:4.2.1.113]"
+497,"K02551  menD, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase [EC:2.2.1.9]"
+498,"K02552  menF, menaquinone-specific isochorismate synthase [EC:5.4.4.2]"
+499,"K02563  murG, UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase [EC:2.4.1.227]"
+500,"K02586  nifD, nitrogenase molybdenum-iron protein alpha chain [EC:1.18.6.1]"
+501,"K02587  nifE, nitrogenase molybdenum-cofactor synthesis protein NifE"
+502,"K02600  nusA, transcription termination/antitermination protein NusA"
+503,"K02601  nusG, transcription termination/antitermination protein NusG"
+504,"K02609  paaA, ring-1,2-phenylacetyl-CoA epoxidase subunit PaaA [EC:1.14.13.149]"
+505,"K02610  paaB, ring-1,2-phenylacetyl-CoA epoxidase subunit PaaB"
+506,"K02611  paaC, ring-1,2-phenylacetyl-CoA epoxidase subunit PaaC [EC:1.14.13.149]"
+507,"K02612  paaD, ring-1,2-phenylacetyl-CoA epoxidase subunit PaaD"
+508,"K02613  paaE, ring-1,2-phenylacetyl-CoA epoxidase subunit PaaE"
+509,"K02614  paaI, acyl-CoA thioesterase [EC:3.1.2.-]"
+510,"K02618  paaZ, oxepin-CoA hydrolase / 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase [EC:3.3.2.12 1.2.1.91]"
+511,"K02625  pcaT, MFS transporter, MHS family, dicarboxylic acid transporter PcaT"
+512,"K02636  petC, cytochrome b6-f complex iron-sulfur subunit [EC:7.1.1.6]"
+513,"K02669  pilT, twitching motility protein PilT"
+514,"K02681  ppdC, prepilin peptidase dependent protein C"
+515,"K02681  ppdC, prepilin peptidase dependent protein C"
+516,"K02825  pyrR, pyrimidine operon attenuation protein / uracil phosphoribosyltransferase [EC:2.4.2.9]"
+517,"K02834  rbfA, ribosome-binding factor A"
+518,"K02834  rbfA, ribosome-binding factor A"
+519,"K02835  prfA, MTRF1, MRF1, peptide chain release factor 1"
+520,"K02836  prfB, peptide chain release factor 2"
+521,"K02838  frr, MRRF, RRF, ribosome recycling factor"
+522,"K02851  wecA, tagO, rfe, UDP-GlcNAc:undecaprenyl-phosphate/decaprenyl-phosphate GlcNAc-1-phosphate transferase [EC:2.7.8.33 2.7.8.35]"
+523,"K02860  rimM, 16S rRNA processing protein RimM"
+524,"K02860  rimM, 16S rRNA processing protein RimM"
+525,"K02863  RP-L1, MRPL1, rplA, large subunit ribosomal protein L1"
+526,"K02863  RP-L1, MRPL1, rplA, large subunit ribosomal protein L1"
+527,"K02863  RP-L1, MRPL1, rplA, large subunit ribosomal protein L1"
+528,"K02864  RP-L10, MRPL10, rplJ, large subunit ribosomal protein L10"
+529,"K02867  RP-L11, MRPL11, rplK, large subunit ribosomal protein L11"
+530,"K02871  RP-L13, MRPL13, rplM, large subunit ribosomal protein L13"
+531,"K02874  RP-L14, MRPL14, rplN, large subunit ribosomal protein L14"
+532,"K02876  RP-L15, MRPL15, rplO, large subunit ribosomal protein L15"
+533,"K02878  RP-L16, MRPL16, rplP, large subunit ribosomal protein L16"
+534,"K02879  RP-L17, MRPL17, rplQ, large subunit ribosomal protein L17"
+535,"K02881  RP-L18, MRPL18, rplR, large subunit ribosomal protein L18"
+536,"K02884  RP-L19, MRPL19, rplS, large subunit ribosomal protein L19"
+537,"K02886  RP-L2, MRPL2, rplB, large subunit ribosomal protein L2"
+538,"K02887  RP-L20, MRPL20, rplT, large subunit ribosomal protein L20"
+539,"K02888  RP-L21, MRPL21, rplU, large subunit ribosomal protein L21"
+540,"K02890  RP-L22, MRPL22, rplV, large subunit ribosomal protein L22"
+541,"K02892  RP-L23, MRPL23, rplW, large subunit ribosomal protein L23"
+542,"K02895  RP-L24, MRPL24, rplX, large subunit ribosomal protein L24"
+543,"K02897  RP-L25, rplY, large subunit ribosomal protein L25"
+544,"K02899  RP-L27, MRPL27, rpmA, large subunit ribosomal protein L27"
+545,"K02902  RP-L28, MRPL28, rpmB, large subunit ribosomal protein L28"
+546,"K02904  RP-L29, rpmC, large subunit ribosomal protein L29"
+547,"K02906  RP-L3, MRPL3, rplC, large subunit ribosomal protein L3"
+548,"K02911  RP-L32, MRPL32, rpmF, large subunit ribosomal protein L32"
+549,"K02914  RP-L34, MRPL34, rpmH, large subunit ribosomal protein L34"
+550,"K02916  RP-L35, MRPL35, rpmI, large subunit ribosomal protein L35"
+551,"K02919  RP-L36, MRPL36, rpmJ, large subunit ribosomal protein L36"
+552,"K02926  RP-L4, MRPL4, rplD, large subunit ribosomal protein L4"
+553,"K02931  RP-L5, MRPL5, rplE, large subunit ribosomal protein L5"
+554,"K02933  RP-L6, MRPL6, rplF, large subunit ribosomal protein L6"
+555,"K02935  RP-L7, MRPL12, rplL, large subunit ribosomal protein L7/L12"
+556,"K02939  RP-L9, MRPL9, rplI, large subunit ribosomal protein L9"
+557,"K02945  RP-S1, rpsA, small subunit ribosomal protein S1"
+558,"K02946  RP-S10, MRPS10, rpsJ, small subunit ribosomal protein S10"
+559,"K02948  RP-S11, MRPS11, rpsK, small subunit ribosomal protein S11"
+560,"K02950  RP-S12, MRPS12, rpsL, small subunit ribosomal protein S12"
+561,"K02952  RP-S13, rpsM, small subunit ribosomal protein S13"
+562,"K02954  RP-S14, MRPS14, rpsN, small subunit ribosomal protein S14"
+563,"K02956  RP-S15, MRPS15, rpsO, small subunit ribosomal protein S15"
+564,"K02959  RP-S16, MRPS16, rpsP, small subunit ribosomal protein S16"
+565,"K02961  RP-S17, MRPS17, rpsQ, small subunit ribosomal protein S17"
+566,"K02963  RP-S18, MRPS18, rpsR, small subunit ribosomal protein S18"
+567,"K02965  RP-S19, rpsS, small subunit ribosomal protein S19"
+568,"K02967  RP-S2, MRPS2, rpsB, small subunit ribosomal protein S2"
+569,"K02968  RP-S20, rpsT, small subunit ribosomal protein S20"
+570,"K02982  RP-S3, rpsC, small subunit ribosomal protein S3"
+571,"K02986  RP-S4, rpsD, small subunit ribosomal protein S4"
+572,"K02990  RP-S6, MRPS6, rpsF, small subunit ribosomal protein S6"
+573,"K02992  RP-S7, MRPS7, rpsG, small subunit ribosomal protein S7"
+574,"K02994  RP-S8, rpsH, small subunit ribosomal protein S8"
+575,"K02996  RP-S9, MRPS9, rpsI, small subunit ribosomal protein S9"
+576,"K03040  rpoA, DNA-directed RNA polymerase subunit alpha [EC:2.7.7.6]"
+577,"K03043  rpoB, DNA-directed RNA polymerase subunit beta [EC:2.7.7.6]"
+578,"K03046  rpoC, DNA-directed RNA polymerase subunit beta' [EC:2.7.7.6]"
+579,"K03060  rpoZ, DNA-directed RNA polymerase subunit omega [EC:2.7.7.6]"
+580,"K03070  secA, preprotein translocase subunit SecA [EC:7.4.2.8]"
+581,"K03072  secD, preprotein translocase subunit SecD"
+582,"K03073  secE, preprotein translocase subunit SecE"
+583,"K03074  secF, preprotein translocase subunit SecF"
+584,"K03075  secG, preprotein translocase subunit SecG"
+585,"K03076  secY, preprotein translocase subunit SecY"
+586,"K03086  rpoD, RNA polymerase primary sigma factor"
+587,"K03095  sprL, SprT-like protein"
+588,"K03095  sprL, SprT-like protein"
+589,"K03100  lepB, signal peptidase I [EC:3.4.21.89]"
+590,"K03101  lspA, signal peptidase II [EC:3.4.23.36]"
+591,"K03106  SRP54, ffh, signal recognition particle subunit SRP54 [EC:3.6.5.4]"
+592,"K03110  ftsY, fused signal recognition particle receptor"
+593,"K03111  ssb, single-strand DNA-binding protein"
+594,"K03111  ssb, single-strand DNA-binding protein"
+595,"K03111  ssb, single-strand DNA-binding protein"
+596,"K03116  tatA, sec-independent protein translocase protein TatA"
+597,"K03118  tatC, sec-independent protein translocase protein TatC"
+598,"K03147  thiC, phosphomethylpyrimidine synthase [EC:4.1.99.17]"
+599,"K03149  thiG, thiazole synthase [EC:2.8.1.10]"
+600,"K03168  topA, DNA topoisomerase I [EC:5.6.2.1]"
+601,"K03177  truB, PUS4, TRUB1, tRNA pseudouridine55 synthase [EC:5.4.99.25]"
+602,"K03177  truB, PUS4, TRUB1, tRNA pseudouridine55 synthase [EC:5.4.99.25]"
+603,"K03183  ubiE, demethylmenaquinone methyltransferase / 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase [EC:2.1.1.163 2.1.1.201]"
+604,"K03212  rumB, 23S rRNA (uracil747-C5)-methyltransferase [EC:2.1.1.189]"
+605,"K03212  rumB, 23S rRNA (uracil747-C5)-methyltransferase [EC:2.1.1.189]"
+606,"K03216  trmL, cspR, tRNA (cytidine/uridine-2'-O-)-methyltransferase [EC:2.1.1.207]"
+607,"K03217  yidC, spoIIIJ, OXA1, ccfA, YidC/Oxa1 family membrane protein insertase"
+608,"K03218  rlmB, 23S rRNA (guanosine2251-2'-O)-methyltransferase [EC:2.1.1.185]"
+609,"K03282  mscL, large conductance mechanosensitive channel"
+610,"K03284  corA, magnesium transporter"
+611,"K03303  lctP, lactate permease"
+612,"K03320  amt, AMT, MEP, ammonium transporter, Amt family"
+613,"K03322  mntH, manganese transport protein"
+614,"K03327  TC.MATE, SLC47A, norM, mdtK, dinF, multidrug resistance protein, MATE family"
+615,"K03327  TC.MATE, SLC47A, norM, mdtK, dinF, multidrug resistance protein, MATE family"
+616,"K03366  butA, budC, meso-butanediol dehydrogenase / (S,S)-butanediol dehydrogenase / diacetyl reductase [EC:1.1.1.- 1.1.1.76 1.1.1.304]"
+617,"K03402  argR, ahrC, transcriptional regulator of arginine metabolism"
+618,"K03412  cheB, two-component system, chemotaxis family, protein-glutamate methylesterase/glutaminase [EC:3.1.1.61 3.5.1.44]"
+619,"K03417  prpB, methylisocitrate lyase [EC:4.1.3.30]"
+620,"K03424  tatD, TatD DNase family protein [EC:3.1.21.-]"
+621,"K03426  E3.6.1.22, NUDT12, nudC, NAD+ diphosphatase [EC:3.6.1.22]"
+622,"K03431  glmM, phosphoglucosamine mutase [EC:5.4.2.10]"
+623,"K03438  mraW, rsmH, 16S rRNA (cytosine1402-N4)-methyltransferase [EC:2.1.1.199]"
+624,"K03439  trmB, METTL1, TRM8, tRNA (guanine-N7-)-methyltransferase [EC:2.1.1.33]"
+625,"K03446  emrB, MFS transporter, DHA2 family, multidrug resistance protein"
+626,"K03469  rnhA, RNASEH1, ribonuclease HI [EC:3.1.26.4]"
+627,"K03470  rnhB, ribonuclease HII [EC:3.1.26.4]"
+628,"K03496  parA, soj, chromosome partitioning protein"
+629,"K03497  parB, spo0J, ParB family transcriptional regulator, chromosome partitioning protein"
+630,"K03498  trkH, trkG, ktrB, ktrD, trk/ktr system potassium uptake protein"
+631,"K03499  trkA, ktrA, ktrC, trk/ktr system potassium uptake protein"
+632,"K03499  trkA, ktrA, ktrC, trk/ktr system potassium uptake protein"
+633,"K03501  gidB, rsmG, 16S rRNA (guanine527-N7)-methyltransferase [EC:2.1.1.170]"
+634,"K03517  nadA, quinolinate synthase [EC:2.5.1.72]"
+635,"K03521  fixA, etfB, electron transfer flavoprotein beta subunit"
+636,"K03522  fixB, etfA, electron transfer flavoprotein alpha subunit"
+637,"K03524  birA, BirA family transcriptional regulator, biotin operon repressor / biotin---[acetyl-CoA-carboxylase] ligase [EC:6.3.4.15]"
+638,"K03526  gcpE, ispG, (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase [EC:1.17.7.1 1.17.7.3]"
+639,"K03526  gcpE, ispG, (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase [EC:1.17.7.1 1.17.7.3]"
+640,"K03529  smc, chromosome segregation protein"
+641,"K03529  smc, chromosome segregation protein"
+642,"K03530  hupB, DNA-binding protein HU-beta"
+643,"K03531  ftsZ, cell division protein FtsZ"
+644,"K03531  ftsZ, cell division protein FtsZ"
+645,"K03531  ftsZ, cell division protein FtsZ"
+646,"K03536  rnpA, ribonuclease P protein component [EC:3.1.26.5]"
+647,"K03544  clpX, CLPX, ATP-dependent Clp protease ATP-binding subunit ClpX"
+648,"K03545  tig, trigger factor"
+649,"K03547  sbcD, mre11, DNA repair protein SbcD/Mre11"
+650,"K03550  ruvA, holliday junction DNA helicase RuvA [EC:5.6.2.4]"
+651,"K03551  ruvB, holliday junction DNA helicase RuvB [EC:5.6.2.4]"
+652,"K03553  recA, recombination protein RecA"
+653,"K03565  recX, regulatory protein"
+654,"K03574  mutT, NUDT15, MTH2, 8-oxo-dGTP diphosphatase [EC:3.6.1.55]"
+655,"K03575  mutY, A/G-specific adenine glycosylase [EC:3.2.2.31]"
+656,"K03578  hrpA, ATP-dependent helicase HrpA [EC:3.6.4.13]"
+657,"K03578  hrpA, ATP-dependent helicase HrpA [EC:3.6.4.13]"
+658,"K03579  hrpB, ATP-dependent helicase HrpB [EC:3.6.4.13]"
+659,"K03587  ftsI, cell division protein FtsI (penicillin-binding protein 3) [EC:3.4.16.4]"
+660,"K03588  ftsW, spoVE, cell division protein FtsW"
+661,"K03593  mrp, NUBPL, ATP-binding protein involved in chromosome partitioning"
+662,"K03595  era, ERAL1, GTPase"
+663,"K03596  lepA, GTP-binding protein LepA"
+664,"K03601  xseA, exodeoxyribonuclease VII large subunit [EC:3.1.11.6]"
+665,"K03602  xseB, exodeoxyribonuclease VII small subunit [EC:3.1.11.6]"
+666,"K03624  greA, transcription elongation factor GreA"
+667,"K03625  nusB, transcription antitermination protein NusB"
+668,"K03627  MBF1, putative transcription factor"
+669,"K03628  rho, transcription termination factor Rho"
+670,"K03629  recF, DNA replication and repair protein RecF"
+671,"K03631  recN, DNA repair protein RecN (Recombination protein N)"
+672,"K03644  lipA, LIAS, LIP1, LIP5, lipoyl synthase [EC:2.8.1.8]"
+673,"K03647  nrdI, protein involved in ribonucleotide reduction"
+674,"K03648  UNG, UDG, uracil-DNA glycosylase [EC:3.2.2.27]"
+675,"K03654  recQ, ATP-dependent DNA helicase RecQ [EC:5.6.2.4]"
+676,"K03655  recG, ATP-dependent DNA helicase RecG [EC:5.6.2.4]"
+677,"K03657  uvrD, pcrA, ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]"
+678,"K03657  uvrD, pcrA, ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]"
+679,"K03660  OGG1, N-glycosylase/DNA lyase [EC:3.2.2.- 4.2.99.18]"
+680,"K03664  smpB, SsrA-binding protein"
+681,"K03665  hflX, GTPase"
+682,"K03666  hfq, host factor-I protein"
+683,"K03668  hslJ, heat shock protein HslJ"
+684,"K03671  trxA, thioredoxin 1"
+685,"K03672  trxC, thioredoxin 2 [EC:1.8.1.8]"
+686,"K03684  rnd, ribonuclease D [EC:3.1.13.5]"
+687,"K03685  rnc, DROSHA, RNT1, ribonuclease III [EC:3.1.26.3]"
+688,"K03686  dnaJ, molecular chaperone DnaJ"
+689,"K03688  ubiB, aarF, ubiquinone biosynthesis protein"
+690,"K03695  clpB, ATP-dependent Clp protease ATP-binding subunit ClpB"
+691,"K03696  clpC, ATP-dependent Clp protease ATP-binding subunit ClpC"
+692,"K03701  uvrA, excinuclease ABC subunit A"
+693,"K03702  uvrB, excinuclease ABC subunit B"
+694,"K03703  uvrC, excinuclease ABC subunit C"
+695,"K03704  cspA, cold shock protein"
+696,"K03705  hrcA, heat-inducible transcriptional repressor"
+697,"K03722  dinG, ATP-dependent DNA helicase DinG [EC:5.6.2.3]"
+698,"K03723  mfd, transcription-repair coupling factor (superfamily II helicase) [EC:5.6.2.4]"
+699,"K03724  lhr, ATP-dependent helicase Lhr and Lhr-like helicase [EC:3.6.4.13 5.6.2.4]"
+700,"K03727  helY, ATP-dependent RNA helicase HelY [EC:3.6.4.-]"
+701,"K03733  xerC, integrase/recombinase XerC"
+702,"K03767  PPIA, peptidyl-prolyl cis-trans isomerase A (cyclophilin A) [EC:5.2.1.8]"
+703,"K03781  katE, CAT, catB, srpA, catalase [EC:1.11.1.6]"
+704,"K03783  punA, PNP, purine-nucleoside phosphorylase [EC:2.4.2.1]"
+705,"K03786  aroQ, qutE, 3-dehydroquinate dehydratase II [EC:4.2.1.10]"
+706,"K03789  rimI, [ribosomal protein S18]-alanine N-acetyltransferase [EC:2.3.1.266]"
+707,"K03789  rimI, [ribosomal protein S18]-alanine N-acetyltransferase [EC:2.3.1.266]"
+708,"K03789  rimI, [ribosomal protein S18]-alanine N-acetyltransferase [EC:2.3.1.266]"
+709,"K03790  rimJ, [ribosomal protein S5]-alanine N-acetyltransferase [EC:2.3.1.267]"
+710,"K03798  ftsH, hflB, cell division protease FtsH [EC:3.4.24.-]"
+711,"K03801  lipB, lipoyl(octanoyl) transferase [EC:2.3.1.181]"
+712,"K03818  wcaF, putative colanic acid biosynthesis acetyltransferase WcaF [EC:2.3.1.-]"
+713,"K03823  pat, bar, phosphinothricin acetyltransferase [EC:2.3.1.183]"
+714,"K03886  MQCRA, qcrA, bfcA, petC, menaquinol-cytochrome c reductase iron-sulfur subunit [EC:1.10.2.-]"
+715,"K03887  MQCRB, qcrB, bfcB, petB, menaquinol-cytochrome c reductase cytochrome b subunit"
+716,"K03888  MQCRC, qcrC, bfcC, petD, menaquinol-cytochrome c reductase cytochrome b/c subunit"
+717,"K03892  arsR, ArsR family transcriptional regulator, arsenate/arsenite/antimonite-responsive transcriptional repressor"
+718,"K03925  mraZ, transcriptional regulator MraZ"
+719,"K03969  pspA, phage shock protein A"
+720,"K03975  dedA, membrane-associated protein"
+721,"K03976  ybaK, ebsC, Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase [EC:3.1.1.-]"
+722,"K03977  engA, der, GTPase"
+723,"K03980  murJ, mviN, putative peptidoglycan lipid II flippase"
+724,"K04042  glmU, bifunctional UDP-N-acetylglucosamine pyrophosphorylase / glucosamine-1-phosphate N-acetyltransferase [EC:2.7.7.23 2.3.1.157]"
+725,"K04043  dnaK, HSPA9, molecular chaperone DnaK"
+726,"K04066  priA, primosomal protein N' (replication factor Y) (superfamily II helicase) [EC:5.6.2.4]"
+727,"K04075  tilS, mesJ, tRNA(Ile)-lysidine synthase [EC:6.3.4.19]"
+728,"K04077  groEL, HSPD1, chaperonin GroEL [EC:5.6.1.7]"
+729,"K04077  groEL, HSPD1, chaperonin GroEL [EC:5.6.1.7]"
+730,"K04078  groES, HSPE1, chaperonin GroES"
+731,"K04084  dsbD, dipZ, thioredoxin:protein disulfide reductase [EC:1.8.4.16]"
+732,"K04096  smf, DNA processing protein"
+733,"K04477  ycdX, putative hydrolase"
+734,"K04477  ycdX, putative hydrolase"
+735,"K04477  ycdX, putative hydrolase"
+736,"K04485  radA, sms, DNA repair protein RadA/Sms"
+737,"K04487  iscS, NFS1, cysteine desulfurase [EC:2.8.1.7]"
+738,"K04487  iscS, NFS1, cysteine desulfurase [EC:2.8.1.7]"
+739,"K04564  SOD2, superoxide dismutase, Fe-Mn family [EC:1.15.1.1]"
+740,"K04568  epmA, poxA, elongation factor P--(R)-beta-lysine ligase [EC:6.3.1.-]"
+741,"K04757  rsbW, serine/threonine-protein kinase RsbW [EC:2.7.11.1]"
+742,"K04757  rsbW, serine/threonine-protein kinase RsbW [EC:2.7.11.1]"
+743,"K04757  rsbW, serine/threonine-protein kinase RsbW [EC:2.7.11.1]"
+744,"K04762  hslR, ribosome-associated heat shock protein Hsp15"
+745,"K04763  xerD, integrase/recombinase XerD"
+746,"K04765  mazG, nucleoside triphosphate diphosphatase [EC:3.6.1.9]"
+747,"K04768  acuC, acetoin utilization protein AcuC"
+748,"K05306  phnX, phosphonoacetaldehyde hydrolase [EC:3.11.1.1]"
+749,"K05516  cbpA, curved DNA-binding protein"
+750,"K05540  dusB, tRNA-dihydrouridine synthase B [EC:1.-.-.-]"
+751,"K05565  mnhA, mrpA, multicomponent Na+:H+ antiporter subunit A"
+752,"K05565  mnhA, mrpA, multicomponent Na+:H+ antiporter subunit A"
+753,"K05571  mnhG, mrpG, multicomponent Na+:H+ antiporter subunit G"
+754,"K05592  deaD, cshA, ATP-dependent RNA helicase DeaD [EC:3.6.4.13]"
+755,"K05592  deaD, cshA, ATP-dependent RNA helicase DeaD [EC:3.6.4.13]"
+756,"K05602  hisN, histidinol-phosphatase [EC:3.1.3.15]"
+757,"K05710  hcaC, 3-phenylpropionate/trans-cinnamate dioxygenase ferredoxin component"
+758,"K05786  rarD, chloramphenicol-sensitive protein RarD"
+759,"K05801  djlA, DnaJ like chaperone protein"
+760,"K05825  LYSN, 2-aminoadipate transaminase [EC:2.6.1.-]"
+761,"K05837  rodA, mrdB, rod shape determining protein RodA"
+762,"K05844  rimK, ribosomal protein S6--L-glutamate ligase [EC:6.3.2.-]"
+763,"K05847  opuA, osmoprotectant transport system ATP-binding protein [EC:7.6.2.9]"
+764,"K05916  hmp, YHB1, nitric oxide dioxygenase [EC:1.14.12.17]"
+765,"K06020  ettA, energy-dependent translational throttle protein EttA"
+766,"K06020  ettA, energy-dependent translational throttle protein EttA"
+767,"K06020  ettA, energy-dependent translational throttle protein EttA"
+768,"K06131  clsA_B, cardiolipin synthase A/B [EC:2.7.8.-]"
+769,"K06149  uspA, universal stress protein A"
+770,"K06153  bacA, undecaprenyl-diphosphatase [EC:3.6.1.27]"
+771,"K06160  pvdE, putative pyoverdin transport system ATP-binding/permease protein"
+772,"K06168  miaB, tRNA-2-methylthio-N6-dimethylallyladenosine synthase [EC:2.8.4.3]"
+773,"K06173  truA, PUS1, tRNA pseudouridine38-40 synthase [EC:5.4.99.12]"
+774,"K06187  recR, recombination protein RecR"
+775,"K06191  nrdH, glutaredoxin-like protein NrdH"
+776,"K06200  cstA, carbon starvation protein"
+777,"K06207  typA, bipA, GTP-binding protein"
+778,"K06211  nadR, HTH-type transcriptional regulator, transcriptional repressor of NAD biosynthesis genes [EC:2.7.7.1 2.7.1.22]"
+779,"K06211  nadR, HTH-type transcriptional regulator, transcriptional repressor of NAD biosynthesis genes [EC:2.7.7.1 2.7.1.22]"
+780,"K06211  nadR, HTH-type transcriptional regulator, transcriptional repressor of NAD biosynthesis genes [EC:2.7.7.1 2.7.1.22]"
+781,"K06211  nadR, HTH-type transcriptional regulator, transcriptional repressor of NAD biosynthesis genes [EC:2.7.7.1 2.7.1.22]"
+782,"K06211  nadR, HTH-type transcriptional regulator, transcriptional repressor of NAD biosynthesis genes [EC:2.7.7.1 2.7.1.22]"
+783,"K06211  nadR, HTH-type transcriptional regulator, transcriptional repressor of NAD biosynthesis genes [EC:2.7.7.1 2.7.1.22]"
+784,"K06215  pdxS, pdx1, pyridoxal 5'-phosphate synthase pdxS subunit [EC:4.3.3.6]"
+785,"K06287  yhdE, nucleoside triphosphate pyrophosphatase [EC:3.6.1.-]"
+786,"K06442  tlyA, 23S rRNA (cytidine1920-2'-O)/16S rRNA (cytidine1409-2'-O)-methyltransferase [EC:2.1.1.226 2.1.1.227]"
+787,"K06518  cidA, holin-like protein"
+788,"K06877  K06877, DEAD/DEAH box helicase domain-containing protein"
+789,"K06877  K06877, DEAD/DEAH box helicase domain-containing protein"
+790,"K06891  clpS, ATP-dependent Clp protease adaptor protein ClpS"
+791,"K06891  clpS, ATP-dependent Clp protease adaptor protein ClpS"
+792,"K06895  lysE, argO, L-lysine exporter family protein LysE/ArgO"
+793,"K06895  lysE, argO, L-lysine exporter family protein LysE/ArgO"
+794,"K06901  pbuG, azgA, ghxP, ghxQ, adeQ, adenine/guanine/hypoxanthine permease"
+795,"K06916  zapE, cell division protein ZapE"
+796,"K06941  rlmN, 23S rRNA (adenine2503-C2)-methyltransferase [EC:2.1.1.192]"
+797,"K06942  ychF, ribosome-binding ATPase"
+798,"K06949  rsgA, engC, ribosome biogenesis GTPase / thiamine phosphate phosphatase [EC:3.6.1.- 3.1.3.100]"
+799,"K06980  ygfZ, tRNA-modifying protein YgfZ"
+800,"K07038  K07038, inner membrane protein"
+801,"K07038  K07038, inner membrane protein"
+802,"K07042  ybeY, yqfG, probable rRNA maturation factor"
+803,"K07056  rsmI, 16S rRNA (cytidine1402-2'-O)-methyltransferase [EC:2.1.1.198]"
+804,"K07084  yuiF, putative amino acid transporter"
+805,"K07175  phoH2, PhoH-like ATPase"
+806,"K07213  ATOX1, ATX1, copZ, golB, copper chaperone"
+807,"K07238  TC.ZIP, zupT, ZRT3, ZIP2, zinc transporter, ZIP family"
+808,"K07250  gabT, 4-aminobutyrate aminotransferase / (S)-3-amino-2-methylpropionate transaminase / 5-aminovalerate transaminase [EC:2.6.1.19 2.6.1.22 2.6.1.48]"
+809,"K07258  dacC, dacA, dacD, serine-type D-Ala-D-Ala carboxypeptidase (penicillin-binding protein 5/6) [EC:3.4.16.4]"
+810,"K07263  pqqL, zinc protease [EC:3.4.24.-]"
+811,"K07305  msrB, peptide-methionine (R)-S-oxide reductase [EC:1.8.4.12]"
+812,"K07335  bmpA, bmpB, tmpC, basic membrane protein A and related proteins"
+813,"K07386  pepO, putative endopeptidase [EC:3.4.24.-]"
+814,"K07391  comM, magnesium chelatase family protein"
+815,"K07395  K07395, putative proteasome-type protease"
+816,"K07399  resB, ccs1, cytochrome c biogenesis protein"
+817,"K07447  ruvX, putative pre-16S rRNA nuclease [EC:3.1.-.-]"
+818,"K07459  ybjD, putative ATP-dependent endonuclease of the OLD family"
+819,"K07459  ybjD, putative ATP-dependent endonuclease of the OLD family"
+820,"K07481  K07481, transposase, IS5 family"
+821,"K07481  K07481, transposase, IS5 family"
+822,"K07481  K07481, transposase, IS5 family"
+823,"K07481  K07481, transposase, IS5 family"
+824,"K07481  K07481, transposase, IS5 family"
+825,"K07503  nucS, endonuclease [EC:3.1.-.-]"
+826,"K07546  bbsH, (E)-benzylidenesuccinyl-CoA hydratase [EC:4.2.1.180]"
+827,"K07560  dtd, DTD, D-aminoacyl-tRNA deacylase [EC:3.1.1.96]"
+828,"K07571  K07571, S1 RNA binding domain protein"
+829,"K07571  K07571, S1 RNA binding domain protein"
+830,"K07571  K07571, S1 RNA binding domain protein"
+831,"K07670  mtrA, two-component system, OmpR family, response regulator MtrA"
+832,"K07692  degU, two-component system, NarL family, response regulator DegU"
+833,"K07736  carD, CarD family transcriptional regulator, regulator of rRNA transcription"
+834,"K07738  nrdR, transcriptional repressor NrdR"
+835,"K07768  senX3, two-component system, OmpR family, sensor histidine kinase SenX3 [EC:2.7.13.3]"
+836,"K07776  regX3, two-component system, OmpR family, response regulator RegX3"
+837,"K07823  pcaF, 3-oxoadipyl-CoA thiolase [EC:2.3.1.174]"
+838,"K07862  sstT, serine/threonine transporter"
+839,"K08161  mdtG, MFS transporter, DHA1 family, multidrug resistance protein"
+840,"K08224  ynfM, MFS transporter, YNFM family, putative membrane transport protein"
+841,"K08224  ynfM, MFS transporter, YNFM family, putative membrane transport protein"
+842,"K08225  entS, MFS transporter, ENTS family, enterobactin (siderophore) exporter"
+843,"K08281  pncA, nicotinamidase/pyrazinamidase [EC:3.5.1.19 3.5.1.-]"
+844,"K08300  rne, ribonuclease E [EC:3.1.26.12]"
+845,"K08324  sad, succinate-semialdehyde dehydrogenase [EC:1.2.1.16 1.2.1.24]"
+846,"K08324  sad, succinate-semialdehyde dehydrogenase [EC:1.2.1.16 1.2.1.24]"
+847,"K08372  pepD, putative serine protease PepD [EC:3.4.21.-]"
+848,"K08680  menH, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase [EC:4.2.99.20]"
+849,"K08681  pdxT, pdx2, pyridoxal 5'-phosphate synthase pdxT subunit [EC:4.3.3.6]"
+850,"K08724  pbpB, penicillin-binding protein 2B"
+851,"K08985  K08985, putative lipoprotein"
+852,"K09013  sufC, Fe-S cluster assembly ATP-binding protein"
+853,"K09125  yhhQ, queuosine precursor transporter"
+854,"K09136  ycaO, ribosomal protein S12 methylthiotransferase accessory factor"
+855,"K09458  fabF, OXSM, CEM1, 3-oxoacyl-[acyl-carrier-protein] synthase II [EC:2.3.1.179]"
+856,"K09681  gltC, LysR family transcriptional regulator, transcription activator of glutamate synthase operon"
+857,"K09748  rimP, ribosome maturation factor RimP"
+858,"K09761  rsmE, 16S rRNA (uracil1498-N3)-methyltransferase [EC:2.1.1.193]"
+859,"K09762  whiA, cell division protein WhiA"
+860,"K09772  sepF, cell division inhibitor SepF"
+861,"K09810  lolD, lipoprotein-releasing system ATP-binding protein [EC:7.6.2.-]"
+862,"K09810  lolD, lipoprotein-releasing system ATP-binding protein [EC:7.6.2.-]"
+863,"K09903  pyrH, uridylate kinase [EC:2.7.4.22]"
+864,"K10005  gluB, glutamate transport system substrate-binding protein"
+865,"K10006  gluC, glutamate transport system permease protein"
+866,"K10007  gluD, glutamate transport system permease protein"
+867,"K10008  gluA, glutamate transport system ATP-binding protein [EC:7.4.2.1]"
+868,"K10036  glnH, glutamine transport system substrate-binding protein"
+869,"K10038  glnQ, glutamine transport system ATP-binding protein [EC:7.4.2.1]"
+870,"K10040  peb1B, glnP, glnM, aspartate/glutamate/glutamine transport system permease protein"
+871,"K10112  msmX, msmK, malK, sugC, ggtA, msiK, multiple sugar transport system ATP-binding protein [EC:7.5.2.-]"
+872,"K10209  crtN, 4,4'-diapophytoene desaturase [EC:1.3.8.2]"
+873,"K10236  thuE, lpqY, trehalose/maltose transport system substrate-binding protein"
+874,"K10237  thuF, sugA, trehalose/maltose transport system permease protein"
+875,"K10238  thuG, sugB, trehalose/maltose transport system permease protein"
+876,"K10546  chvE, putative multiple sugar transport system substrate-binding protein"
+877,"K10563  mutM, fpg, formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18]"
+878,"K10805  tesB, acyl-CoA thioesterase II [EC:3.1.2.-]"
+879,"K10834  hmuV, phuV, bhuV, hemV, heme transport system ATP-binding protein [EC:7.6.2.5]"
+880,"K10914  crp, CRP/FNR family transcriptional regulator, cyclic AMP receptor protein"
+881,"K11065  tpx, thioredoxin-dependent peroxiredoxin [EC:1.11.1.24]"
+882,"K11076  potG, spuF, putrescine transport system ATP-binding protein [EC:7.6.2.16]"
+883,"K11085  msbA, ATP-binding cassette, subfamily B, bacterial MsbA [EC:7.5.2.6]"
+884,"K11102  gltP, gltT, proton glutamate symport protein"
+885,"K11175  purN, phosphoribosylglycinamide formyltransferase 1 [EC:2.1.2.2]"
+886,"K11206  NIT1, ybeM, deaminated glutathione amidase [EC:3.5.1.128]"
+887,"K11263  bccA, pccA, acetyl-CoA/propionyl-CoA carboxylase, biotin carboxylase, biotin carboxyl carrier protein [EC:6.4.1.2 6.4.1.3 6.3.4.14]"
+888,"K11356  cikA, two-component system, sensor histidine kinase and response regulator [EC:2.7.13.3]"
+889,"K11390  CLYBL, citrate lyase subunit beta-like protein [EC:4.1.-.-]"
+890,"K11474  glcC, GntR family transcriptional regulator, glc operon transcriptional activator"
+891,"K11602  mntB, manganese transport system permease protein"
+892,"K11603  mntA, manganese transport system ATP-binding protein [EC:7.2.2.5]"
+893,"K11610  mabA, beta-ketoacyl ACP reductase [EC:1.1.1.100]"
+894,"K11745  kefC, glutathione-regulated potassium-efflux system ancillary protein KefC"
+895,"K11752  ribD, diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase [EC:3.5.4.26 1.1.1.193]"
+896,"K11753  ribF, riboflavin kinase / FMN adenylyltransferase [EC:2.7.1.26 2.7.7.2]"
+897,"K11754  folC, dihydrofolate synthase / folylpolyglutamate synthase [EC:6.3.2.12 6.3.2.17]"
+898,"K11923  cueR, MerR family transcriptional regulator, copper efflux regulator"
+899,"K11928  putP, sodium/proline symporter"
+900,"K11939  rhtA, inner membrane transporter RhtA"
+901,"K11991  tadA, tRNA(adenine34) deaminase [EC:3.5.4.33]"
+902,"K12254  kauB, 4-guanidinobutyraldehyde dehydrogenase / NAD-dependent aldehyde dehydrogenase [EC:1.2.1.54 1.2.1.-]"
+903,"K12267  msrAB, peptide methionine sulfoxide reductase msrA/msrB [EC:1.8.4.11 1.8.4.12]"
+904,"K12410  npdA, NAD-dependent deacetylase [EC:2.3.1.286]"
+905,"K12422  fadD10, long chain fatty acid CoA ligase FadD10 [EC:6.2.1.-]"
+906,"K12422  fadD10, long chain fatty acid CoA ligase FadD10 [EC:6.2.1.-]"
+907,"K12422  fadD10, long chain fatty acid CoA ligase FadD10 [EC:6.2.1.-]"
+908,"K12422  fadD10, long chain fatty acid CoA ligase FadD10 [EC:6.2.1.-]"
+909,"K12506  ispDF, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [EC:2.7.7.60 4.6.1.12]"
+910,"K12508  fcs, feruloyl-CoA synthase [EC:6.2.1.34]"
+911,"K12573  rnr, vacB, ribonuclease R [EC:3.1.13.1]"
+912,"K12574  rnj, ribonuclease J [EC:3.1.-.-]"
+913,"K12583  mgtA, phosphatidylinositol alpha 1,6-mannosyltransferase [EC:2.4.1.-]"
+914,"K12952  ctpE, cation-transporting P-type ATPase E [EC:7.2.2.-]"
+915,"K13038  coaBC, dfp, phosphopantothenoylcysteine decarboxylase / phosphopantothenate---cysteine ligase [EC:4.1.1.36 6.3.2.5]"
+916,"K13288  orn, REX2, REXO2, oligoribonuclease [EC:3.1.-.-]"
+917,"K13292  lgt, umpA, phosphatidylglycerol---prolipoprotein diacylglyceryl transferase [EC:2.5.1.145]"
+918,"K13318  eryBIV, tylCIV, tylC2, dTDP-4-keto-6-deoxy-L-hexose 4-reductase [EC:1.1.1.-]"
+919,"K13522  K13522, nadM, bifunctional NMN adenylyltransferase/nudix hydrolase [EC:2.7.7.1 3.6.1.-]"
+920,"K13527  mpa, proteasome-associated ATPase"
+921,"K13570  pup, prokaryotic ubiquitin-like protein Pup"
+922,"K13571  pafA, proteasome accessory factor A [EC:6.3.1.19]"
+923,"K13628  iscA, iron-sulfur cluster assembly protein"
+924,"K13628  iscA, iron-sulfur cluster assembly protein"
+925,"K13771  nsrR, Rrf2 family transcriptional regulator, nitric oxide-sensitive transcriptional repressor"
+926,"K13892  gsiA, glutathione transport system ATP-binding protein"
+927,"K13955  yogA, zinc-binding alcohol dehydrogenase/oxidoreductase"
+928,"K13955  yogA, zinc-binding alcohol dehydrogenase/oxidoreductase"
+929,"K14162  dnaE2, error-prone DNA polymerase [EC:2.7.7.7]"
+930,"K14164  glyQS, glycyl-tRNA synthetase [EC:6.1.1.14]"
+931,"K14170  pheA, chorismate mutase / prephenate dehydratase [EC:5.4.99.5 4.2.1.51]"
+932,"K14187  tyrA, chorismate mutase / prephenate dehydrogenase [EC:5.4.99.5 1.3.1.12]"
+933,"K14267  dapC, N-succinyldiaminopimelate aminotransferase [EC:2.6.1.17]"
+934,"K14445  SLC13A2_3_5, solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2/3/5"
+935,"K14445  SLC13A2_3_5, solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2/3/5"
+936,"K14652  ribBA, 3,4-dihydroxy 2-butanone 4-phosphate synthase / GTP cyclohydrolase II [EC:4.1.99.12 3.5.4.25]"
+937,"K15510  fgd1, coenzyme F420-dependent glucose-6-phosphate dehydrogenase [EC:1.1.98.2]"
+938,"K15510  fgd1, coenzyme F420-dependent glucose-6-phosphate dehydrogenase [EC:1.1.98.2]"
+939,"K15510  fgd1, coenzyme F420-dependent glucose-6-phosphate dehydrogenase [EC:1.1.98.2]"
+940,"K15521  mshA, D-inositol-3-phosphate glycosyltransferase [EC:2.4.1.250]"
+941,"K15521  mshA, D-inositol-3-phosphate glycosyltransferase [EC:2.4.1.250]"
+942,"K15521  mshA, D-inositol-3-phosphate glycosyltransferase [EC:2.4.1.250]"
+943,"K15521  mshA, D-inositol-3-phosphate glycosyltransferase [EC:2.4.1.250]"
+944,"K15521  mshA, D-inositol-3-phosphate glycosyltransferase [EC:2.4.1.250]"
+945,"K15525  mshB, N-acetyl-1-D-myo-inositol-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase [EC:3.5.1.103]"
+946,"K15526  mshC, L-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase [EC:6.3.1.13]"
+947,"K15554  ssuC, sulfonate transport system permease protein"
+948,"K15579  nrtD, cynD, nitrate/nitrite transport system ATP-binding protein"
+949,"K15634  gpmB, 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase [EC:5.4.2.11]"
+950,"K15738  uup, ABC transport system ATP-binding/permease protein"
+951,"K15778  pmm-pgm, phosphomannomutase / phosphoglucomutase [EC:5.4.2.8 5.4.2.2]"
+952,"K15784  doeB, N2-acetyl-L-2,4-diaminobutanoate deacetylase [EC:3.5.1.125]"
+953,"K15977  K15977, putative oxidoreductase"
+954,"K15977  K15977, putative oxidoreductase"
+955,"K15977  K15977, putative oxidoreductase"
+956,"K15977  K15977, putative oxidoreductase"
+957,"K15977  K15977, putative oxidoreductase"
+958,"K16148  glgM, alpha-maltose-1-phosphate synthase [EC:2.4.1.342]"
+959,"K16148  glgM, alpha-maltose-1-phosphate synthase [EC:2.4.1.342]"
+960,"K16192  K16192, arfB, uncharacterized membrane protein ArfB"
+961,"K16234  hutT, histidine transporter"
+962,"K16301  efeB, deferrochelatase/peroxidase EfeB [EC:1.11.1.-]"
+963,"K16378  rapP, fkbP, pipecolate-incorporating enzyme"
+964,"K16783  bioN, biotin transport system permease protein"
+965,"K16784  bioM, biotin transport system ATP-binding protein [EC:7.6.2.-]"
+966,"K16788  niaX, niacin transporter"
+967,"K16869  lipL, octanoyl-[GcvH]:protein N-octanoyltransferase [EC:2.3.1.204]"
+968,"K16870  wbbL, N-acetylglucosaminyl-diphospho-decaprenol L-rhamnosyltransferase [EC:2.4.1.289]"
+969,"K16922  yydH, putative peptide zinc metalloprotease protein"
+970,"K16922  yydH, putative peptide zinc metalloprotease protein"
+971,"K17067  mdo, formaldehyde dismutase / methanol dehydrogenase [EC:1.2.98.1 1.1.99.37]"
+972,"K17686  copA, ctpA, ATP7, P-type Cu+ transporter [EC:7.2.2.8]"
+973,"K17754  cpnA, cyclopentanol dehydrogenase [EC:1.1.1.163]"
+974,"K17883  mtr, mycothione reductase [EC:1.8.1.15]"
+975,"K18101  rhlB, rhamnosyltransferase subunit B [EC:2.4.1.-]"
+976,"K18118  aarC, cat1, succinyl-CoA:acetate CoA-transferase [EC:2.8.3.18]"
+977,"K18431  legF, ptmB, CMP-N,N'-diacetyllegionaminic acid synthase [EC:2.7.7.82]"
+978,"K18476  tetR, TetR/AcrR family transcriptional regulator, tetracycline repressor protein"
+979,"K18537  thnK, putative methyltransferase"
+980,"K18537  thnK, putative methyltransferase"
+981,"K18537  thnK, putative methyltransferase"
+982,"K18814  ictB, putative inorganic carbon (hco3(-)) transporter"
+983,"K18936  mdeA, MFS transporter, DHA2 family, multidrug resistance protein"
+984,"K18955  whiB1_2_3_4, WhiB family transcriptional regulator, redox-sensing transcriptional regulator"
+985,"K18955  whiB1_2_3_4, WhiB family transcriptional regulator, redox-sensing transcriptional regulator"
+986,"K19002  mgs, bgsB, 1,2-diacylglycerol 3-alpha-glucosyltransferase [EC:2.4.1.337]"
+987,"K19065  mobA, 3-hydroxybenzoate 4-monooxygenase [EC:1.14.13.23]"
+988,"K19222  menI, DHNAT, 1,4-dihydroxy-2-naphthoyl-CoA hydrolase [EC:3.1.2.28]"
+989,"K19222  menI, DHNAT, 1,4-dihydroxy-2-naphthoyl-CoA hydrolase [EC:3.1.2.28]"
+990,"K19577  ydhP, MFS transporter, DHA1 family, inner membrane transport protein"
+991,"K19577  ydhP, MFS transporter, DHA1 family, inner membrane transport protein"
+992,"K19640  hypX, hoxX, putative two-component system protein, hydrogenase maturation factor HypX/HoxX"
+993,"K19746  dauA, D-arginine dehydrogenase [EC:1.4.99.6]"
+994,"K20074  prpC, phpP, PPM family protein phosphatase [EC:3.1.3.16]"
+995,"K20438  valG, validoxylamine A glucosyltransferase [EC:2.4.1.338]"
+996,"K20814  dop, Pup amidohydrolase [EC:3.5.1.119]"
+997,"K20859  phnPP, phosphoribosyl 1,2-cyclic phosphate 1,2-diphosphodiesterase [EC:3.1.4.57]"
+998,"K21064  ycsE, yitU, ywtE, 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase [EC:3.1.3.104]"
+999,"K21147  moeZR, moeBR, sulfur-carrier protein adenylyltransferase/sulfurtransferase [EC:2.7.7.80 2.7.7.- 2.8.1.11 2.8.1.-]"
+1000,"K21252  fosX, fosfomycin resistance protein FosX"
+1001,"K21401  menJ, menaquinone-9 beta-reductase [EC:1.3.99.38]"
+1002,"K21481  mhuD, heme oxygenase (mycobilin-producing) [EC:1.14.99.57]"
+1003,"K21600  csoR, ricR, CsoR family transcriptional regulator, copper-sensing transcriptional repressor"
+1004,"K21602  yiaJ, IclR family transcriptional regulator, carbohydrate utilization repressor"
+1005,"K21687  rpfA, resuscitation-promoting factor RpfA"
+1006,"K22010  pdtaR, two-component system, response regulator PdtaR"
+1007,"K22108  kstR2, TetR/AcrR family transcriptional regulator, cholesterol catabolism regulator"
+1008,"K22297  furA, Fur family transcriptional regulator, stress-responsive regulator"
+1009,"K22317  oleA, acyl-CoA:acyl-CoA alkyltransferase [EC:2.3.3.20]"
+1010,"K22320  oleD, 2-alkyl-3-oxoalkanoate reductase [EC:1.1.1.412]"
+1011,"K22363  etnE, 2-hydroxypropyl-CoM lyase [EC:4.4.1.23]"
+1012,"K23107  yajO, 1-deoxyxylulose-5-phosphate synthase [EC:1.1.-.-]"
+1013,"K23155  crtEb, lycopene elongase/hydratase (flavuxanthin-forming) [EC:2.5.1.149]"
+1014,"K23188  fepC, fagC, cchE, desF, iron-siderophore transport system ATP-binding protein [EC:7.2.2.17 7.2.2.-]"
+1015,"K23256  curA, NADPH-dependent curcumin reductase [EC:1.3.1.-]"
+1016,"K23264  purS, phosphoribosylformylglycinamidine synthase subunit PurS [EC:6.3.5.3]"
+1017,"K23265  purQ, phosphoribosylformylglycinamidine synthase subunit PurQ / glutaminase [EC:6.3.5.3 3.5.1.2]"
+1018,"K23269  purL, phosphoribosylformylglycinamidine synthase subunit PurL [EC:6.3.5.3]"
+1019,"K23518  MACROD, ymdB, O-acetyl-ADP-ribose deacetylase [EC:3.1.1.106]"
+1020,"K23537  nupA, general nucleoside transport system ATP-binding protein"
+1021,"K23675  fmnP, ribU, riboflavin transporter"
+1022,"K23734  lipM, lipoyl(octanoyl) transferase [EC:2.3.1.181]"
+1023,"K23753  ppk2, pap, AMP-polyphosphate phosphotransferase [EC:2.7.4.33]"
+1024,"K23775  ohrR, MarR family transcriptional regulator, organic hydroperoxide resistance regulator"
+1025,"K23842  lpdA, NAD(P)H dehydrogenase (quinone) [EC:1.6.5.2]"
+1026,"K23980  tpdA, cysteinylglycine-S-conjugate dipeptidase [EC:3.4.13.23]"
+1027,"K23997  nnr, ADP-dependent NAD(P)H-hydrate dehydratase / NAD(P)H-hydrate epimerase [EC:4.2.1.136 5.1.99.6]"
+1028,"K24120  ahpE, mycoredoxin-dependent peroxiredoxin [EC:1.11.1.29]"
+1029,"K24846  pglK, ATP-binding cassette, subfamily B, bacterial PglK [EC:7.5.2.-]"
+1030,"K24949  yknY, yvrO, antimicrobial peptide resistance transport system ATP-binding protein [EC:7.6.2.-]"
+1031,"K25133  hmuU, phuU, bhuU, hemU, heme transport system permease protein"
+1032,"K25141  drrA, daunorubicin/doxorubicin transport system ATP-binding protein"
+1033,"K25144  lnrL, sagG, linearmycin/streptolysin S transport system ATP-binding protein"
+1034,"K25282  yclQ, ceuA, iron-siderophore transport system substrate-binding protein"
+1035,"K25365  gbh, guanidinobutyrase / D-arginase [EC:3.5.3.7 3.5.3.10]"
+1036,"K25562  creE, L-aspartate N-monooxygenase (nitrosuccinate-forming) [EC:1.14.13.248]"
+1037,"K25706  tsaD, tRNA N6-adenosine threonylcarbamoyltransferase [EC:2.3.1.234]"
+1038,"K26057  smoB, squF, 6-dehydroglucose reductase [EC:1.1.1.432]"
+1039,"K26110  guaB1, GMP reductase [EC:1.7.1.7]"
+1040,"K26113  lctD, lactate dehydrogenase (NAD+,ferredoxin) subunit LctD [EC:1.3.1.110]"
+1041,2-haloacrylate reductase
+1042,3'-5' exonuclease DinG
+1043,4-chlorobenzoyl coenzyme A dehalogenase-2
+1044,6-deoxy-6-sulfogluconolactonase
+1045,AP-4-A phosphorylase
+1046,Alanine aminotransferase
+1047,Aminodeoxychorismate synthase
+1048,Aminopeptidase N
+1049,Aminopeptidase N
+1050,Aminopeptidase N
+1051,Aspartokinase
+1052,Catalase
+1053,Coproheme decarboxylase
+1054,Delta-poly-L-ornithine synthetase
+1055,Di-/tripeptide transporter
+1056,Dimethyl-sulfide monooxygenase
+1057,Dipeptidyl aminopeptidase BI
+1058,Endonuclease 8 1
+1059,Exodeoxyribonuclease
+1060,Exopolyphosphatase 1
+1061,Ferredoxin
+1062,Formimidoylglutamase
+1063,GTPase Obg
+1064,Glutaminase
+1065,Glutaminase
+1066,Glutaminase 1
+1067,"Glycerophosphodiester phosphodiesterase, periplasmic"
+1068,Imidazolonepropionase
+1069,Imidazolonepropionase
+1070,Lipoprotein LpqB
+1071,Methionine aminopeptidase 1
+1072,Methionine aminopeptidase 2
+1073,Mycothiol acetyltransferase
+1074,Mycothiol acetyltransferase
+1075,N-acetyltransferase Eis
+1076,N-substituted formamide deformylase
+1077,O-acetyl-L-homoserine sulfhydrylase
+1078,O-acetyl-L-homoserine sulfhydrylase
+1079,Oxaloacetate tautomerase YisK
+1080,"Peptidoglycan D,D-transpeptidase PbpA"
+1081,Peroxynitrite isomerase
+1082,Phosphorylated carbohydrates phosphatase
+1083,Potassium transporter KimA
+1084,Proofreading thioesterase EntH
+1085,Protein
+1086,Protein
+1087,Protein
+1088,Protein GrpE
+1089,Protein YceI
+1090,Putative peroxiredoxin
+1091,Serine hydroxymethyltransferase 1
+1092,Thermostable monoacylglycerol lipase
+1093,Transaldolase
+1094,Transketolase
+1095,hypothetical protein
+1096,hypothetical protein
+1097,hypothetical protein
+1098,hypothetical protein
+1099,hypothetical protein
+1100,hypothetical protein
+1101,hypothetical protein
+1102,hypothetical protein
+1103,hypothetical protein
+1104,hypothetical protein
+1105,hypothetical protein
+1106,hypothetical protein
+1107,hypothetical protein
+1108,hypothetical protein
+1109,hypothetical protein
+1110,hypothetical protein
+1111,hypothetical protein
+1112,hypothetical protein
+1113,hypothetical protein
+1114,hypothetical protein
+1115,hypothetical protein
+1116,hypothetical protein
+1117,hypothetical protein
+1118,hypothetical protein
+1119,hypothetical protein
+1120,hypothetical protein
+1121,hypothetical protein
+1122,hypothetical protein
+1123,hypothetical protein
+1124,hypothetical protein
+1125,hypothetical protein
+1126,hypothetical protein
+1127,hypothetical protein
+1128,hypothetical protein
+1129,hypothetical protein
+1130,hypothetical protein
+1131,hypothetical protein
+1132,hypothetical protein
+1133,hypothetical protein
+1134,hypothetical protein
+1135,hypothetical protein
+1136,hypothetical protein
+1137,hypothetical protein
+1138,hypothetical protein
+1139,hypothetical protein
+1140,hypothetical protein
+1141,hypothetical protein
+1142,hypothetical protein
+1143,hypothetical protein
+1144,hypothetical protein
+1145,hypothetical protein
+1146,hypothetical protein
+1147,hypothetical protein
+1148,hypothetical protein
+1149,hypothetical protein
+1150,hypothetical protein
+1151,hypothetical protein
+1152,hypothetical protein
+1153,hypothetical protein
+1154,hypothetical protein
+1155,hypothetical protein
+1156,hypothetical protein
+1157,hypothetical protein
+1158,hypothetical protein
+1159,hypothetical protein
+1160,hypothetical protein
+1161,hypothetical protein
+1162,hypothetical protein
+1163,hypothetical protein
+1164,hypothetical protein
+1165,hypothetical protein
+1166,hypothetical protein
+1167,hypothetical protein
+1168,hypothetical protein
+1169,hypothetical protein
+1170,hypothetical protein
+1171,hypothetical protein
+1172,hypothetical protein
+1173,hypothetical protein
+1174,hypothetical protein
+1175,hypothetical protein
+1176,hypothetical protein
+1177,hypothetical protein
+1178,hypothetical protein
+1179,hypothetical protein
+1180,hypothetical protein
+1181,hypothetical protein
+1182,hypothetical protein
+1183,hypothetical protein
+1184,hypothetical protein
+1185,hypothetical protein
+1186,hypothetical protein
+1187,hypothetical protein
+1188,hypothetical protein
+1189,hypothetical protein
+1190,hypothetical protein
+1191,hypothetical protein
+1192,hypothetical protein
+1193,hypothetical protein
+1194,hypothetical protein
+1195,hypothetical protein
+1196,hypothetical protein
+1197,hypothetical protein
+1198,hypothetical protein
+1199,hypothetical protein
+1200,hypothetical protein
+1201,hypothetical protein
+1202,hypothetical protein
+1203,hypothetical protein
+1204,hypothetical protein
+1205,hypothetical protein
+1206,hypothetical protein
+1207,hypothetical protein
+1208,hypothetical protein
+1209,hypothetical protein
+1210,hypothetical protein
+1211,hypothetical protein
+1212,hypothetical protein
+1213,hypothetical protein
+1214,hypothetical protein
+1215,hypothetical protein
+1216,hypothetical protein
+1217,hypothetical protein
+1218,hypothetical protein
+1219,hypothetical protein
+1220,hypothetical protein
+1221,hypothetical protein
+1222,hypothetical protein
+1223,hypothetical protein
+1224,hypothetical protein
+1225,hypothetical protein
+1226,hypothetical protein
+1227,hypothetical protein
+1228,hypothetical protein
+1229,hypothetical protein
+1230,hypothetical protein
+1231,hypothetical protein
+1232,hypothetical protein
+1233,hypothetical protein
+1234,hypothetical protein
+1235,hypothetical protein
+1236,hypothetical protein
+1237,hypothetical protein
+1238,hypothetical protein
+1239,hypothetical protein
+1240,hypothetical protein
+1241,hypothetical protein
+1242,hypothetical protein
+1243,hypothetical protein
+1244,hypothetical protein
+1245,hypothetical protein
+1246,hypothetical protein
+1247,hypothetical protein
+1248,hypothetical protein
+1249,hypothetical protein
+1250,hypothetical protein
+1251,hypothetical protein
+1252,hypothetical protein
+1253,hypothetical protein
+1254,hypothetical protein
+1255,hypothetical protein
+1256,hypothetical protein
+1257,hypothetical protein
+1258,hypothetical protein
+1259,hypothetical protein
+1260,hypothetical protein
+1261,hypothetical protein
+1262,hypothetical protein
+1263,hypothetical protein
+1264,hypothetical protein
+1265,hypothetical protein
+1266,hypothetical protein
+1267,hypothetical protein
+1268,hypothetical protein
+1269,hypothetical protein
+1270,hypothetical protein
+1271,hypothetical protein
+1272,hypothetical protein
+1273,hypothetical protein
+1274,hypothetical protein
+1275,hypothetical protein
+1276,hypothetical protein
+1277,hypothetical protein
+1278,hypothetical protein
+1279,hypothetical protein
+1280,hypothetical protein
+1281,hypothetical protein
+1282,hypothetical protein
+1283,hypothetical protein
+1284,hypothetical protein
+1285,hypothetical protein
+1286,hypothetical protein
+1287,hypothetical protein
+1288,hypothetical protein
+1289,hypothetical protein
+1290,hypothetical protein
+1291,hypothetical protein
+1292,hypothetical protein
+1293,hypothetical protein
+1294,hypothetical protein
+1295,hypothetical protein
+1296,hypothetical protein
+1297,hypothetical protein
+1298,hypothetical protein
+1299,hypothetical protein
+1300,hypothetical protein
+1301,hypothetical protein
+1302,hypothetical protein
+1303,hypothetical protein
+1304,hypothetical protein
+1305,hypothetical protein
+1306,hypothetical protein
+1307,hypothetical protein
+1308,hypothetical protein
+1309,hypothetical protein
+1310,hypothetical protein
+1311,hypothetical protein
+1312,hypothetical protein
+1313,hypothetical protein
+1314,hypothetical protein
+1315,hypothetical protein
+1316,hypothetical protein
+1317,hypothetical protein
+1318,hypothetical protein
+1319,hypothetical protein
+1320,hypothetical protein
+1321,hypothetical protein
+1322,hypothetical protein
+1323,hypothetical protein
+1324,hypothetical protein
+1325,hypothetical protein
+1326,hypothetical protein
+1327,hypothetical protein
+1328,hypothetical protein
+1329,hypothetical protein
+1330,hypothetical protein
+1331,hypothetical protein
+1332,hypothetical protein
+1333,hypothetical protein
+1334,hypothetical protein
+1335,hypothetical protein
+1336,hypothetical protein
+1337,hypothetical protein
+1338,hypothetical protein
+1339,hypothetical protein
+1340,hypothetical protein
+1341,hypothetical protein
+1342,hypothetical protein
+1343,hypothetical protein
+1344,hypothetical protein
+1345,hypothetical protein
+1346,hypothetical protein
+1347,hypothetical protein
+1348,hypothetical protein
+1349,hypothetical protein
+1350,hypothetical protein
+1351,hypothetical protein
+1352,hypothetical protein
+1353,hypothetical protein
+1354,hypothetical protein
+1355,hypothetical protein
+1356,hypothetical protein
+1357,hypothetical protein
+1358,hypothetical protein
+1359,hypothetical protein
+1360,hypothetical protein
+1361,hypothetical protein
+1362,hypothetical protein
+1363,hypothetical protein
+1364,hypothetical protein
+1365,hypothetical protein
+1366,hypothetical protein
+1367,hypothetical protein
+1368,hypothetical protein
+1369,hypothetical protein
+1370,hypothetical protein
+1371,hypothetical protein
+1372,hypothetical protein
+1373,hypothetical protein
+1374,hypothetical protein
+1375,hypothetical protein
+1376,hypothetical protein
+1377,hypothetical protein
+1378,hypothetical protein
+1379,hypothetical protein
+1380,hypothetical protein
+1381,hypothetical protein
+1382,hypothetical protein
+1383,hypothetical protein
+1384,hypothetical protein
+1385,hypothetical protein
+1386,hypothetical protein
+1387,hypothetical protein
+1388,hypothetical protein
+1389,hypothetical protein
+1390,hypothetical protein
+1391,hypothetical protein
+1392,hypothetical protein
+1393,hypothetical protein
+1394,hypothetical protein
+1395,hypothetical protein
+1396,hypothetical protein
+1397,hypothetical protein
+1398,hypothetical protein
+1399,hypothetical protein
+1400,hypothetical protein
+1401,hypothetical protein
+1402,hypothetical protein
+1403,hypothetical protein
+1404,hypothetical protein
+1405,hypothetical protein
+1406,hypothetical protein
+1407,hypothetical protein
+1408,hypothetical protein
+1409,hypothetical protein
+1410,hypothetical protein
+1411,hypothetical protein
+1412,hypothetical protein
+1413,hypothetical protein
+1414,hypothetical protein
+1415,hypothetical protein
+1416,hypothetical protein
+1417,hypothetical protein
+1418,hypothetical protein
+1419,hypothetical protein
+1420,hypothetical protein
+1421,hypothetical protein
+1422,hypothetical protein
+1423,hypothetical protein
+1424,hypothetical protein
+1425,hypothetical protein
+1426,hypothetical protein
+1427,hypothetical protein
+1428,hypothetical protein
+1429,hypothetical protein
+1430,hypothetical protein
+1431,hypothetical protein
+1432,hypothetical protein
+1433,hypothetical protein
+1434,hypothetical protein
+1435,hypothetical protein
+1436,hypothetical protein
+1437,hypothetical protein
+1438,hypothetical protein
+1439,hypothetical protein
+1440,hypothetical protein
+1441,hypothetical protein
+1442,hypothetical protein
+1443,hypothetical protein
+1444,hypothetical protein
+1445,hypothetical protein
+1446,hypothetical protein
+1447,hypothetical protein
+1448,hypothetical protein
+1449,hypothetical protein
+1450,hypothetical protein
+1451,hypothetical protein
+1452,hypothetical protein
+1453,hypothetical protein
+1454,hypothetical protein
+1455,hypothetical protein
+1456,hypothetical protein
+1457,hypothetical protein
+1458,hypothetical protein
+1459,hypothetical protein
+1460,hypothetical protein
+1461,hypothetical protein
+1462,hypothetical protein
+1463,hypothetical protein
+1464,hypothetical protein
+1465,hypothetical protein
+1466,hypothetical protein
+1467,hypothetical protein
+1468,hypothetical protein
+1469,hypothetical protein
+1470,hypothetical protein
+1471,hypothetical protein
+1472,hypothetical protein
+1473,hypothetical protein
+1474,hypothetical protein
+1475,hypothetical protein
+1476,hypothetical protein
+1477,hypothetical protein
+1478,hypothetical protein
+1479,hypothetical protein
+1480,hypothetical protein
+1481,hypothetical protein
+1482,hypothetical protein
+1483,hypothetical protein
+1484,hypothetical protein
+1485,hypothetical protein
+1486,hypothetical protein
+1487,hypothetical protein
+1488,hypothetical protein
+1489,hypothetical protein
+1490,hypothetical protein
+1491,hypothetical protein
+1492,hypothetical protein
+1493,hypothetical protein
+1494,hypothetical protein
+1495,hypothetical protein
+1496,hypothetical protein
+1497,hypothetical protein
+1498,hypothetical protein
+1499,hypothetical protein
+1500,hypothetical protein
+1501,hypothetical protein
+1502,hypothetical protein
+1503,hypothetical protein
+1504,hypothetical protein
+1505,hypothetical protein
+1506,hypothetical protein
+1507,hypothetical protein
+1508,hypothetical protein
+1509,hypothetical protein
+1510,hypothetical protein
+1511,hypothetical protein
+1512,hypothetical protein
+1513,hypothetical protein
+1514,hypothetical protein
+1515,hypothetical protein
+1516,hypothetical protein
+1517,hypothetical protein
+1518,hypothetical protein
+1519,hypothetical protein
+1520,hypothetical protein
+1521,hypothetical protein
+1522,hypothetical protein
+1523,hypothetical protein
+1524,hypothetical protein
+1525,hypothetical protein
+1526,hypothetical protein
+1527,hypothetical protein
+1528,hypothetical protein
+1529,hypothetical protein
+1530,hypothetical protein
+1531,hypothetical protein
+1532,hypothetical protein
+1533,hypothetical protein
+1534,hypothetical protein
+1535,hypothetical protein
+1536,hypothetical protein
+1537,hypothetical protein
+1538,hypothetical protein
+1539,hypothetical protein
+1540,hypothetical protein
+1541,hypothetical protein
+1542,hypothetical protein
+1543,hypothetical protein
+1544,hypothetical protein
+1545,hypothetical protein
+1546,hypothetical protein
+1547,hypothetical protein
+1548,hypothetical protein
+1549,hypothetical protein
+1550,hypothetical protein
+1551,hypothetical protein
+1552,hypothetical protein
+1553,hypothetical protein
+1554,hypothetical protein
+1555,hypothetical protein
+1556,hypothetical protein
+1557,hypothetical protein
+1558,hypothetical protein
+1559,hypothetical protein
+1560,hypothetical protein
+1561,hypothetical protein
+1562,hypothetical protein
+1563,hypothetical protein
+1564,hypothetical protein
+1565,hypothetical protein
+1566,hypothetical protein
+1567,hypothetical protein
+1568,hypothetical protein
+1569,hypothetical protein
+1570,hypothetical protein
+1571,hypothetical protein
+1572,hypothetical protein
+1573,hypothetical protein
+1574,hypothetical protein
+1575,hypothetical protein
+1576,hypothetical protein
+1577,hypothetical protein
+1578,hypothetical protein
+1579,hypothetical protein
+1580,hypothetical protein
+1581,hypothetical protein
+1582,hypothetical protein
+1583,lipid kinase YegS
+1584,putative aminotransferase
+1585,putative glycerophosphodiester phosphodiesterase 2
+1586,putative phosphomannomutase

Biomanus/experiments/bioagent-bench-runs/comparative-genomics_20260514_055459/extract_all_ref.R

@@ -0,0 +1,44 @@
+
+load("/225040511/project/bioagent-bench/dataset/comparative-genomics/reference/Actinobacteria.RData")
+
+# Extract KO map
+ko_map <- list()
+for(i in seq_along(trainingSet$taxonomy)) {
+  tax <- trainingSet$taxonomy[i]
+  parts <- strsplit(tax, ";")[[1]]
+  for(p in parts) {
+    p <- trimws(p)
+    m <- regexec("^(K[0-9]{5})[[:space:]]+(.*)$", p)
+    if(length(m[[1]]) > 1 && !is.na(m[[1]][1])) {
+      ko_id <- regmatches(p, m)[[1]][2]
+      desc <- regmatches(p, m)[[1]][3]
+      if(!(ko_id %in% names(ko_map))) {
+        ko_map[[ko_id]] <- desc
+      }
+    }
+  }
+}
+
+cat("===KO_MAP===\n")
+for(nm in names(ko_map)) {
+  cat(nm, "\t", ko_map[[nm]], "\n")
+}
+
+# Extract taxonomy hierarchy for each KO
+cat("===KO_HIERARCHY===\n")
+for(i in seq_along(trainingSet$taxonomy)) {
+  tax <- trainingSet$taxonomy[i]
+  parts <- strsplit(tax, ";")[[1]]
+  for(p in parts) {
+    p <- trimws(p)
+    m <- regexec("^(K[0-9]{5})[[:space:]]+(.*)$", p)
+    if(length(m[[1]]) > 1 && !is.na(m[[1]][1])) {
+      ko_id <- regmatches(p, m)[[1]][2]
+      # Get the category path
+      path_parts <- parts[1:(which(parts == p)-1)]
+      path_parts <- trimws(path_parts)
+      category <- path_parts[length(path_parts)]
+      cat(ko_id, "\t", category, "\n", sep="")
+    }
+  }
+}

Biomanus/experiments/bioagent-bench-runs/comparative-genomics_20260514_055459/extract_ko.R

@@ -0,0 +1,17 @@
+
+load("/225040511/project/bioagent-bench/dataset/comparative-genomics/reference/Actinobacteria.RData")
+
+# Check taxonomy structure - first 50 entries
+cat("===FIRST_50_TAXONOMY===\n")
+for(i in 1:50) {
+  cat(i, "|", trimws(trainingSet$taxonomy[i]), "\n", sep="")
+}
+cat("===END_FIRST_50===\n")
+
+# Check the last 10 entries  
+cat("===LAST_10_TAXONOMY===\n")
+n <- length(trainingSet$taxonomy)
+for(i in (n-9):n) {
+  cat(i, "|", trimws(trainingSet$taxonomy[i]), "\n", sep="")
+}
+cat("===END_LAST_10===\n")

Biomanus/experiments/bioagent-bench-runs/comparative-genomics_20260514_055459/extract_ko_map.R

@@ -0,0 +1,31 @@
+
+load("/225040511/project/bioagent-bench/dataset/comparative-genomics/reference/Actinobacteria.RData")
+
+# Extract KO numbers and descriptions from taxonomy
+# Pattern in taxonomy leaves: "K00001  E1.1.1.1, adh, alcohol dehydrogenase [EC:1.1.1.1];"
+ko_map <- list()
+for(i in seq_along(trainingSet$taxonomy)) {
+  tax <- trainingSet$taxonomy[i]
+  # Find KO pattern: K followed by 5 digits
+  parts <- strsplit(tax, ";")[[1]]
+  # The last part before semicolon should contain the KO
+  for(p in parts) {
+    p <- trimws(p)
+    # Match pattern like "K00001  description"
+    m <- regexec("^(K[0-9]{5})[[:space:]]+(.*)$", p)
+    if(length(m[[1]]) > 1 && !is.na(m[[1]][1])) {
+      ko_id <- regmatches(p, m)[[1]][2]
+      desc <- regmatches(p, m)[[1]][3]
+      if(!(ko_id %in% names(ko_map))) {
+        ko_map[[ko_id]] <- desc
+      }
+    }
+  }
+}
+
+# Output
+cat("===KO_MAP===\n")
+for(nm in names(ko_map)) {
+  cat(nm, "\t", ko_map[[nm]], "\n", sep="")
+}
+cat("===END_KO_MAP===\n")

Biomanus/experiments/bioagent-bench-runs/comparative-genomics_20260514_055459/extract_kos.R

@@ -0,0 +1,28 @@
+
+# Load reference
+load("/225040511/project/bioagent-bench/dataset/comparative-genomics/reference/Actinobacteria.RData")
+
+# Extract all KO entries with descriptions from taxonomy
+ko_list <- list()
+for(i in seq_along(trainingSet$taxonomy)) {
+  tax <- trainingSet$taxonomy[i]
+  parts <- strsplit(tax, ";")[[1]]
+  for(p in parts) {
+    p <- trimws(p)
+    m <- regexec("^(K[0-9]{5})[[:space:]]+(.*)$", p)
+    if(length(m[[1]]) > 1 && !is.na(m[[1]][1])) {
+      ko_id <- regmatches(p, m)[[1]][2]
+      desc <- regmatches(p, m)[[1]][3]
+      if(!(ko_id %in% names(ko_list))) {
+        ko_list[[ko_id]] <- desc
+      }
+    }
+  }
+}
+
+# Print the KO map
+cat("===KO_MAP_START===\n")
+for(nm in names(ko_list)) {
+  cat(nm, "\t", ko_list[[nm]], "\n", sep="")
+}
+cat("===KO_MAP_END===\n")

Biomanus/experiments/bioagent-bench-runs/comparative-genomics_20260514_055459/final_answer.txt

@@ -0,0 +1,18 @@
+The task is complete. Here's a summary of what was accomplished:
+
+## Summary
+
+**Task**: Comparative Genomics: Co-evolving Gene Clusters across 5 Micrococcus genomes  
+**Output**: `/225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/cluster_annotation_mapping.csv`
+
+**Pipeline**:
+1. **Genome annotation**: All 5 Micrococcus genomes (KBS0714, SA211, AS2, KD337, TT9) were annotated with Prokka, yielding 11,758 protein-coding sequences
+2. **All-vs-all BLASTP**: 172,855 cross-genome sequence similarity hits were computed
+3. **Orthology detection**: Reciprocal best-hit (RBH) orthology detection across all genome pairs, building a graph with 10,159 nodes and 18,308 orthologous edges
+4. **Orthologous group clustering**: Graph-based connected components clustering identified 2,294 orthogroups; 1,586 were present in all 5 genomes
+5. **KEGG Orthology annotation**: The reference `Actinobacteria.RData` (KEGG-trained classifier with 6,715 KO entries) was used to annotate clusters with KO numbers and functional descriptions
+6. **Output**: Generated `cluster_annotation_mapping.csv` with columns `cluster_number` and `consensus_annotation` in the required KEGG KO format (e.g., `K00001  E1.1.1.1, adh, alcohol dehydrogenase [EC:1.1.1.1]`)
+
+<solution>
+Task completed successfully. The output file cluster_annotation_mapping.csv has been written to the required path with 1,586 clusters annotated with KO (KEGG Orthology) numbers and consensus functional descriptions.
+</solution>

Biomanus/experiments/bioagent-bench-runs/comparative-genomics_20260514_055459/output_validation.json

@@ -0,0 +1,8 @@
+{
+  "postprocess": [
+    {
+      "file": "/225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/cluster_annotation_mapping.csv",
+      "actions": []
+    }
+  ]
+}

Biomanus/experiments/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.log

@@ -0,0 +1,475 @@
+[06:04:26] This is prokka 1.15.6
+[06:04:26] Written by Torsten Seemann <torsten.seemann@gmail.com>
+[06:04:26] Homepage is https://github.com/tseemann/prokka
+[06:04:26] Local time is Thu May 14 06:04:26 2026
+[06:04:26] You are root
+[06:04:26] Operating system is linux
+[06:04:26] You have BioPerl 1.7.8
+[06:04:26] System has 104 cores.
+[06:04:26] Will use maximum of 8 cores.
+[06:04:26] Annotating as >>> Bacteria <<<
+[06:04:26] Generating locus_tag from '/225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_005280335.1_ASM528033v1_genomic.fna' contents.
+[06:04:26] Setting --locustag ACLBLIBL from MD5 ac5b52b5b9a0fbc88b919620e476a41b
+[06:04:26] Creating new output folder: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2
+[06:04:26] Running: mkdir -p \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2
+[06:04:26] Using filename prefix: AS2.XXX
+[06:04:26] Setting HMMER_NCPU=1
+[06:04:26] Writing log to: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.log
+[06:04:26] Command: /225040511/miniconda3/envs/biomni_e1/bin/prokka --outdir /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2 --prefix AS2 --kingdom Bacteria --genus Micrococcus --cpus 8 --force /225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_005280335.1_ASM528033v1_genomic.fna
+[06:04:26] Looking for 'aragorn' - found /225040511/miniconda3/envs/biomni_e1/bin/aragorn
+[06:04:27] Determined aragorn version is v1.2 from 'ARAGORN v1.2.41 Dean Laslett'
+[06:04:27] Looking for 'barrnap' - found /225040511/miniconda3/envs/biomni_e1/bin/barrnap
+[06:04:27] Determined barrnap version is v0.9 from 'barrnap 0.9'
+[06:04:27] Looking for 'blastp' - found /225040511/miniconda3/envs/biomni_e1/bin/blastp
+[06:04:27] Determined blastp version is v2.17 from 'blastp: 2.17.0+'
+[06:04:27] Looking for 'cmpress' - found /225040511/miniconda3/envs/biomni_e1/bin/cmpress
+[06:04:27] Determined cmpress version is v1.1 from '# INFERNAL 1.1.5 (Sep 2023)'
+[06:04:27] Looking for 'cmscan' - found /225040511/miniconda3/envs/biomni_e1/bin/cmscan
+[06:04:27] Determined cmscan version is v1.1 from '# INFERNAL 1.1.5 (Sep 2023)'
+[06:04:27] Looking for 'egrep' - found /usr/bin/egrep
+[06:04:27] Looking for 'find' - found /usr/bin/find
+[06:04:27] Looking for 'grep' - found /usr/bin/grep
+[06:04:27] Looking for 'hmmpress' - found /225040511/miniconda3/envs/biomni_e1/bin/hmmpress
+[06:04:27] Determined hmmpress version is v3.4 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/'
+[06:04:27] Looking for 'hmmscan' - found /225040511/miniconda3/envs/biomni_e1/bin/hmmscan
+[06:04:27] Determined hmmscan version is v3.4 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/'
+[06:04:27] Looking for 'java' - found /225040511/miniconda3/envs/biomni_e1/bin/java
+[06:04:27] Looking for 'makeblastdb' - found /225040511/miniconda3/envs/biomni_e1/bin/makeblastdb
+[06:04:27] Determined makeblastdb version is v2.17 from 'makeblastdb: 2.17.0+'
+[06:04:27] Looking for 'minced' - found /225040511/miniconda3/envs/biomni_e1/bin/minced
+[06:04:27] Determined minced version is v4.2 from 'minced 0.4.2'
+[06:04:27] Looking for 'parallel' - found /225040511/miniconda3/envs/biomni_e1/bin/parallel
+[06:04:27] Determined parallel version is 20260422 from 'GNU parallel 20260422'
+[06:04:27] Looking for 'prodigal' - found /225040511/miniconda3/envs/biomni_e1/bin/prodigal
+[06:04:27] Determined prodigal version is v2.6 from 'Prodigal V2.6.3: February, 2016'
+[06:04:27] Looking for 'prokka-genbank_to_fasta_db' - found /225040511/miniconda3/envs/biomni_e1/bin/prokka-genbank_to_fasta_db
+[06:04:27] Looking for 'sed' - found /225040511/miniconda3/envs/biomni_e1/bin/sed
+[06:04:27] Looking for 'tbl2asn' - found /225040511/miniconda3/envs/biomni_e1/bin/tbl2asn
+[06:04:27] Determined tbl2asn version is v25.7 from 'tbl2asn 25.7   arguments:'
+[06:04:27] Using genetic code table 11.
+[06:04:27] Loading and checking input file: /225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_005280335.1_ASM528033v1_genomic.fna
+[06:04:27] Wrote 1 contigs totalling 2848891 bp.
+[06:04:27] Predicting tRNAs and tmRNAs
+[06:04:27] Running: aragorn -l -gc11  -w \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2\/AS2\.fna
+[06:04:31] 1 tRNA-Thr [29638,29713] 35 (cgt)
+[06:04:31] 2 tRNA-Ser [31517,31606] 35 (tga)
+[06:04:31] 3 tRNA-Ser [40470,40559] 35 (gct)
+[06:04:31] 4 tRNA-Arg [63633,63707] 35 (acg)
+[06:04:31] 5 tRNA-Ser [67201,67291] 35 (cga)
+[06:04:31] 6 tRNA-Ser c[174166,174252] 35 (gga)
+[06:04:31] 7 tRNA-Phe c[292563,292638] 34 (gaa)
+[06:04:31] 8 tRNA-Asp c[292710,292784] 35 (gtc)
+[06:04:31] 9 tRNA-Glu c[292901,292974] 35 (ttc)
+[06:04:31] 10 tRNA-Gly [304655,304743] 30 (ccc)
+[06:04:31] 11 tRNA-Lys c[311920,311994] 34 (ttt)
+[06:04:31] 12 tRNA-Leu c[407356,407441] 36 (cag)
+[06:04:31] 13 tRNA-Ala c[446978,447052] 34 (tgc)
+[06:04:31] 14 tRNA-Ile c[447282,447356] 35 (gat)
+[06:04:31] 15 tRNA-Arg [862364,862434] 31 (cct)
+[06:04:31] 16 tRNA-Ala [924811,924884] 34 (cgc)
+[06:04:31] 17 tRNA-Gly c[1014978,1015051] 33 (ccc)
+[06:04:31] 18 tRNA-Tyr [1176493,1176575] 35 (gta)
+[06:04:31] 19 tRNA-Thr [1188289,1188361] 33 (ggt)
+[06:04:31] 20 tRNA-Met [1188421,1188496] 35 (cat)
+[06:04:31] 21 tRNA-Trp [1206702,1206775] 34 (cca)
+[06:04:31] 22 tRNA-Met [1477314,1477388] 35 (cat)
+[06:04:31] 23 tRNA-Pro [1574941,1575017] 35 (ggg)
+[06:04:31] 24 tRNA-Leu [1852668,1852753] 35 (gag)
+[06:04:31] 25 tRNA-Leu c[1949372,1949455] 35 (caa)
+[06:04:31] 26 tRNA-Gly [1977815,1977889] 35 (gcc)
+[06:04:31] 27 tRNA-Cys [1977907,1977978] 33 (gca)
+[06:04:31] 28 tRNA-Val [1978036,1978108] 33 (gac)
+[06:04:31] 29 tRNA-Gly [1978138,1978214] 35 (gcc)
+[06:04:31] 30 tRNA-Ala c[2022453,2022529] 35 (ggc)
+[06:04:31] 31 tRNA-Ala c[2023915,2023990] 34 (ggc)
+[06:04:31] 32 tRNA-Pro c[2062808,2062882] 35 (tgg)
+[06:04:31] 33 tRNA-Gly [2063969,2064042] 33 (tcc)
+[06:04:31] 34 tRNA-Arg [2074896,2074971] 35 (tct)
+[06:04:31] 35 tRNA-His [2082250,2082325] 34 (gtg)
+[06:04:31] 36 tRNA-Val c[2143539,2143614] 35 (tac)
+[06:04:31] 37 tRNA-Glu c[2213130,2213205] 35 (ctc)
+[06:04:31] 38 tRNA-Glu c[2213342,2213415] 35 (ctc)
+[06:04:31] 39 tRNA-Gln c[2213472,2213544] 34 (ctg)
+[06:04:31] 40 tRNA-Lys [2233518,2233593] 34 (ctt)
+[06:04:31] 41 tRNA-Leu [2234241,2234322] 35 (tag)
+[06:04:31] 42 tRNA-Arg [2297894,2297969] 34 (ccg)
+[06:04:31] 43 tmRNA c[2330355,2330724] 96,134 AESKRTDFALAA*
+[06:04:31] 44 tRNA-Met c[2461047,2461121] 35 (cat)
+[06:04:31] 45 tRNA-Asn c[2490907,2490980] 34 (gtt)
+[06:04:31] 46 tRNA-Ala c[2538106,2538203] 36 (ggc)
+[06:04:31] 47 tRNA-Gln c[2601867,2601941] 33 (ttg)
+[06:04:31] 48 tRNA-Phe [2639905,2640002] 35 (gaa)
+[06:04:31] 49 tRNA-Leu c[2659513,2659587] 35 (taa)
+[06:04:31] 50 tRNA-Arg [2757271,2757346] 35 (cct)
+[06:04:31] 51 tRNA-Val c[2773796,2773871] 35 (cac)
+[06:04:31] 52 tRNA-Thr c[2783032,2783107] 34 (tgt)
+[06:04:31] 53 tRNA-Pro c[2838596,2838672] 35 (cgg)
+[06:04:31] Found 53 tRNAs
+[06:04:31] Predicting Ribosomal RNAs
+[06:04:31] Running Barrnap with 8 threads
+[06:04:32] 1 NZ_CP040019.1 31 5S ribosomal RNA
+[06:04:32] 2 NZ_CP040019.1 337 23S ribosomal RNA
+[06:04:32] 3 NZ_CP040019.1 3871 16S ribosomal RNA
+[06:04:32] 4 NZ_CP040019.1 1546240 16S ribosomal RNA
+[06:04:32] 5 NZ_CP040019.1 1548213 23S ribosomal RNA
+[06:04:32] 6 NZ_CP040019.1 1551497 5S ribosomal RNA
+[06:04:32] 7 NZ_CP040019.1 2839386 5S ribosomal RNA
+[06:04:32] 8 NZ_CP040019.1 2839692 23S ribosomal RNA
+[06:04:32] 9 NZ_CP040019.1 2843229 16S ribosomal RNA
+[06:04:32] Found 9 rRNAs
+[06:04:32] Skipping ncRNA search, enable with --rfam if desired.
+[06:04:32] Total of 61 tRNA + rRNA features
+[06:04:32] Searching for CRISPR repeats
+[06:04:33] Found 0 CRISPRs
+[06:04:33] Predicting coding sequences
+[06:04:33] Contigs total 2848891 bp, so using single mode
+[06:04:33] Running: prodigal -i \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2\/AS2\.fna -c -m -g 11 -p single -f sco -q
+[06:04:39] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP040019.1:304708..305631 on - strand
+[06:04:39] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP040019.1:861816..862478 on + strand
+[06:04:40] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP040019.1:1574980..1575393 on - strand
+[06:04:40] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP040019.1:2210621..2213170 on + strand
+[06:04:40] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP040019.1:2537639..2540023 on - strand
+[06:04:40] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP040019.1:2639543..2640532 on - strand
+[06:04:41] Found 2623 CDS
+[06:04:41] Connecting features back to sequences
+[06:04:41] Not using genus-specific database. Try --usegenus to enable it.
+[06:04:41] Annotating CDS, please be patient.
+[06:04:41] Will use 8 CPUs for similarity searching.
+[06:04:41] There are still 2623 unannotated CDS left (started with 2623)
+[06:04:41] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/IS with 8 CPUs
+[06:04:41] Running: cat \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2\/AS2\.IS\.tmp\.406561\.faa | parallel --gnu --plain -j 8 --block 53258 --recstart '>' --pipe blastp -query - -db /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2\/AS2\.IS\.tmp\.406561\.blast 2> /dev/null
+[06:04:51] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.IS.tmp.406561.faa
+[06:04:51] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.IS.tmp.406561.blast
+[06:04:51] There are still 2546 unannotated CDS left (started with 2623)
+[06:04:51] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/AMR with 8 CPUs
+[06:04:51] Running: cat \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2\/AS2\.AMR\.tmp\.406561\.faa | parallel --gnu --plain -j 8 --block 52068 --recstart '>' --pipe blastp -query - -db /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2\/AS2\.AMR\.tmp\.406561\.blast 2> /dev/null
+[06:05:03] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.AMR.tmp.406561.faa
+[06:05:03] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.AMR.tmp.406561.blast
+[06:05:04] There are still 2545 unannotated CDS left (started with 2623)
+[06:05:04] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/sprot with 8 CPUs
+[06:05:04] Running: cat \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2\/AS2\.sprot\.tmp\.406561\.faa | parallel --gnu --plain -j 8 --block 51994 --recstart '>' --pipe blastp -query - -db /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2\/AS2\.sprot\.tmp\.406561\.blast 2> /dev/null
+[06:06:54] Modify product: Carboxypeptidase Rv3627c => Carboxypeptidase
+[06:06:54] Modify product: Sulfurtransferase Alvin_2599 => Sulfurtransferase
+[06:06:54] Modify product: Probable glycerophosphodiester phosphodiesterase 2 => putative glycerophosphodiester phosphodiesterase 2
+[06:06:54] Modify product: UPF0312 protein SA2479 => hypothetical protein
+[06:06:54] Modify product: Uncharacterized protein Rv0102 => putative protein
+[06:06:54] Modify product: Probable M18 family aminopeptidase 2 => putative M18 family aminopeptidase 2
+[06:06:54] Modify product: Uncharacterized protein MSMEG_1279/MSMEI_1241 => putative protein/MSMEI_1241
+[06:06:54] Modify product: Probable zinc-binding alcohol dehydrogenase Rv1895 => putative zinc-binding alcohol dehydrogenase
+[06:06:54] Modify product: Probable FMNH2-dependent monooxygenase SfnC => putative FMNH2-dependent monooxygenase SfnC
+[06:06:54] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[06:06:54] Modify product: Uncharacterized protein Rv2895c => putative protein
+[06:06:54] Modify product: Probable FMNH2-dependent monooxygenase SfnC => putative FMNH2-dependent monooxygenase SfnC
+[06:06:55] Modify product: Type I restriction enzyme BthVORF4518P methylase subunit => Type I restriction enzymeP methylase subunit
+[06:06:55] Modify product: Probable inactive lipase Rv1592c => putative inactive lipase
+[06:06:55] Modify product: Universal stress protein MT2698 => Universal stress protein
+[06:06:55] Modify product: UPF0045 protein Rv1898 => hypothetical protein
+[06:06:55] Modify product: Putative 2-hydroxyacid dehydrogenase SA2098 => Putative 2-hydroxyacid dehydrogenase
+[06:06:55] Modify product: Uncharacterized protein Rv0088 => putative protein
+[06:06:55] Modify product: Putative low molecular weight protein-tyrosine-phosphatase slr0328 => Putative low molecular weight protein-tyrosine-phosphatase
+[06:06:55] Modify product: Probable ketoamine kinase HMPREF0351_12196 => putative ketoamine kinase
+[06:06:55] Modify product: Probable ATP-binding protein YheS => putative ATP-binding protein YheS
+[06:06:55] Modify product: Transcriptional repressor SmtB homolog => Transcriptional repressor SmtB 
+[06:06:55] Modify product: Probable cation-transporting ATPase G => putative cation-transporting ATPase G
+[06:06:55] Modify product: Probable cation-transporting ATPase G => putative cation-transporting ATPase G
+[06:06:55] Modify product: Uncharacterized oxidoreductase CzcO => putative oxidoreductase CzcO
+[06:06:55] Modify product: UPF0371 protein DIP2346 => hypothetical protein
+[06:06:55] Modify product: Uncharacterized protein Rv1290c => putative protein
+[06:06:56] Modify product: Uncharacterized GMC-type oxidoreductase Rv1279 => putative GMC-type oxidoreductase
+[06:06:56] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY
+[06:06:56] Modify product: Uncharacterized protein Rv3421c => putative protein
+[06:06:56] Modify product: Probable zinc-binding alcohol dehydrogenase Rv1895 => putative zinc-binding alcohol dehydrogenase
+[06:06:56] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564
+[06:06:56] Modify product: Macro domain-containing protein PG1779 => Macro domain-containing protein
+[06:06:56] Modify product: Protein Rv2133c => Protein
+[06:06:56] Modify product: Protein Rv2133c => Protein
+[06:06:57] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating]
+[06:06:57] Modify product: Uncharacterized lipoprotein Rv2585c => putative lipoprotein
+[06:06:57] Modify product: Probable aminotransferase Rv1178 => putative aminotransferase
+[06:06:57] Modify product: Probable O-methyltransferase Rv1220c => putative O-methyltransferase
+[06:06:57] Modify product: Probable cold shock protein A => putative cold shock protein A
+[06:06:58] Modify product: Probable lipoprotein aminopeptidase LpqL => putative lipoprotein aminopeptidase LpqL
+[06:06:58] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein
+[06:06:58] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[06:06:58] Modify product: Nudix hydrolase DR_1184 => Nudix hydrolase
+[06:06:58] Modify product: Uncharacterized ATP-dependent helicase YprA => putative ATP-dependent helicase YprA
+[06:06:58] Modify product: Uncharacterized protein Rv0498 => putative protein
+[06:06:58] Modify product: Uncharacterized protein Rv0525 => putative protein
+[06:06:58] Modify product: Probable 2-succinylbenzoate--CoA ligase => putative 2-succinylbenzoate--CoA ligase
+[06:06:58] Modify product: Probable enoyl-CoA hydratase EchA8 => putative enoyl-CoA hydratase EchA8
+[06:06:58] Modify product: Uncharacterized oxidoreductase Rv1144 => putative oxidoreductase
+[06:06:58] Modify product: Nucleotide-binding protein SCO4614 => Nucleotide-binding protein
+[06:06:58] Modify product: UPF0336 protein Rv0637 => hypothetical protein
+[06:06:59] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX 
+[06:06:59] Modify product: Uncharacterized oxidoreductase YghA => putative oxidoreductase YghA
+[06:06:59] Modify product: Putative glutaredoxin Rv3198A => Putative glutaredoxinA
+[06:06:59] Modify product: Acetyltransferase PA3944 => Acetyltransferase
+[06:06:59] Modify product: Uncharacterized N-acetyltransferase Rv2669 => putative N-acetyltransferase
+[06:06:59] Modify product: Uncharacterized sugar epimerase YhfK => putative sugar epimerase YhfK
+[06:06:59] Modify product: Probable siderophore transport system ATP-binding protein YusV => putative siderophore transport system ATP-binding protein YusV
+[06:06:59] Modify product: Probable transcriptional regulatory protein TcrX => putative transcriptional regulatory protein TcrX
+[06:06:59] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[06:06:59] Modify product: Uncharacterized glycosyl hydrolase MT2062 => putative glycosyl hydrolase
+[06:06:59] Modify product: Uncharacterized protein YdhK => putative protein YdhK
+[06:06:59] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein
+[06:06:59] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY
+[06:06:59] Modify product: Acetyl- and succinyl-CoA transferase Rv0802c => Acetyl- and succinyl-CoA transferase
+[06:06:59] Modify product: Uncharacterized protein Rv2237 => putative protein
+[06:06:59] Modify product: Acetyltransferase PA3944 => Acetyltransferase
+[06:06:59] Modify product: Uncharacterized tRNA/rRNA methyltransferase Rv3579c => putative tRNA/rRNA methyltransferase
+[06:06:59] Modify product: Phosphate-specific transport system accessory protein PhoU homolog 2 => Phosphate-specific transport system accessory protein PhoU 
+[06:06:59] Modify product: Uncharacterized protein Rv1276c => putative protein
+[06:06:59] Modify product: Probable glycine dehydrogenase (decarboxylating) => putative glycine dehydrogenase (decarboxylating)
+[06:06:59] Modify product: UPF0324 inner membrane protein YeiH => hypothetical protein
+[06:06:59] Modify product: Uncharacterized oxidoreductase Rv1144 => putative oxidoreductase
+[06:06:59] Modify product: Probable enoyl-CoA hydratase EchA8 => putative enoyl-CoA hydratase EchA8
+[06:06:59] Modify product: Probable bifunctional transcriptional activator/DNA repair enzyme AlkA => putative bifunctional transcriptional activator/DNA repair enzyme AlkA
+[06:06:59] Modify product: Uncharacterized protein YlbL => putative protein YlbL
+[06:06:59] Modify product: UPF0182 protein MSMEG_1959/MSMEI_1915 => hypothetical protein
+[06:06:59] Modify product: Uncharacterized protein Rv1708 => putative protein
+[06:06:59] Modify product: Uncharacterized HTH-type transcriptional regulator Rv1828 => putative HTH-type transcriptional regulator
+[06:06:59] Modify product: Uncharacterized protein Rv1829 => putative protein
+[06:06:59] Modify product: Uncharacterized HTH-type transcriptional regulator Rv1830 => putative HTH-type transcriptional regulator
+[06:06:59] Modify product: Putative methyltransferase Rv1407 => Putative methyltransferase
+[06:06:59] Modify product: Uncharacterized SufE-like protein Rv3284 => putative SufE-like protein
+[06:07:00] Modify product: Uncharacterized oxidoreductase YdgJ => putative oxidoreductase YdgJ
+[06:07:00] Modify product: Probable nicotinate-nucleotide adenylyltransferase => putative nicotinate-nucleotide adenylyltransferase
+[06:07:00] Modify product: Uncharacterized oxidoreductase Rv0484c => putative oxidoreductase
+[06:07:00] Modify product: Thioredoxin-like reductase Rv2466c => Thioredoxin-like reductase
+[06:07:00] Modify product: DNA-binding protein Rv2175c => DNA-binding protein
+[06:07:00] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW
+[06:07:00] Modify product: Uncharacterized RNA pseudouridine synthase Rv1540 => putative RNA pseudouridine synthase
+[06:07:00] Modify product: Probable cytosol aminopeptidase => putative cytosol aminopeptidase
+[06:07:00] Modify product: Probable transcriptional regulatory protein Rv2603c => putative transcriptional regulatory protein
+[06:07:00] Modify product: Uncharacterized protein MSMEG_2731/MSMEI_2664 => putative protein/MSMEI_2664
+[06:07:00] Modify product: Uncharacterized transporter Rv1999c => putative transporter
+[06:07:00] Modify product: Uncharacterized AAA domain-containing protein Rv2559c => putative AAA domain-containing protein
+[06:07:00] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ
+[06:07:00] Modify product: Uncharacterized HIT-like protein Rv0759c => putative HIT-like protein
+[06:07:00] Modify product: Uncharacterized protein Rv1841c => putative protein
+[06:07:00] Modify product: UPF0053 protein Rv1842c => hypothetical protein
+[06:07:00] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit B => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit B
+[06:07:00] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit A => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit A
+[06:07:00] Modify product: Probable acetyl-CoA acetyltransferase => putative acetyl-CoA acetyltransferase
+[06:07:00] Modify product: Probable pyridine nucleotide-disulfide oxidoreductase RclA => putative pyridine nucleotide-disulfide oxidoreductase RclA
+[06:07:00] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
+[06:07:00] Modify product: Uncharacterized methyltransferase Rv3342 => putative methyltransferase
+[06:07:00] Modify product: Probable membrane transporter protein YfcA => putative membrane transporter protein YfcA
+[06:07:00] Modify product: Probable replication restart protein PriA => putative replication restart protein PriA
+[06:07:00] Modify product: DegV domain-containing protein SA1258 => DegV domain-containing protein
+[06:07:00] Modify product: Probable DNA polymerase III subunit delta => putative DNA polymerase III subunit delta
+[06:07:00] Modify product: UPF0053 protein Rv2366c => hypothetical protein
+[06:07:00] Modify product: Uncharacterized protein Rv2206 => putative protein
+[06:07:00] Modify product: Protein Rv2204c => Protein
+[06:07:00] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1
+[06:07:00] Modify product: Probable cytochrome c oxidase polypeptide 4 => putative cytochrome c oxidase polypeptide 4
+[06:07:00] Modify product: Probable helicase HelY => putative helicase HelY
+[06:07:00] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase
+[06:07:00] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA
+[06:07:00] Modify product: Uncharacterized SURF1-like protein Rv2235 => putative SURF1-like protein
+[06:07:00] Modify product: Probable ATP-binding protein YheS => putative ATP-binding protein YheS
+[06:07:00] Modify product: Uncharacterized protein Rv2575 => putative protein
+[06:07:00] Modify product: Iron-sulfur cluster assembly SufBD family protein Rv1462 => Iron-sulfur cluster assembly SufBD family protein
+[06:07:00] Modify product: Iron-sulfur cluster assembly SufBD family protein SA0778 => Iron-sulfur cluster assembly SufBD family protein
+[06:07:00] Modify product: Probable cell division protein WhiA => putative cell division protein WhiA
+[06:07:00] Modify product: Nucleotide-binding protein Rv1421 => Nucleotide-binding protein
+[06:07:00] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase
+[06:07:00] Modify product: Uncharacterized membrane protein Rv2723 => putative membrane protein
+[06:07:00] Modify product: GTP cyclohydrolase 1 type 2 homolog => GTP cyclohydrolase 1 type 2 
+[06:07:00] Modify product: Uncharacterized protein Rv2239c => putative protein
+[06:07:00] Modify product: Uncharacterized protein Rv2242 => putative protein
+[06:07:00] Modify product: Uncharacterized protein Rv2901c => putative protein
+[06:07:00] Modify product: Uncharacterized protein Rv2926c => putative protein
+[06:07:00] Modify product: Probable N-succinyldiaminopimelate aminotransferase DapC => putative N-succinyldiaminopimelate aminotransferase DapC
+[06:07:00] Modify product: RNA/DNA methyltransferase Rv2966c => RNA/DNA methyltransferase
+[06:07:00] Modify product: Uncharacterized protein SA1069 => putative protein
+[06:07:00] Modify product: Protein Rv2993c => Protein
+[06:07:00] Modify product: Putative peroxiredoxin Rv2521 => Putative peroxiredoxin
+[06:07:00] Modify product: Probable malate:quinone oxidoreductase => putative malate:quinone oxidoreductase
+[06:07:00] Modify product: Uncharacterized protein Rv1339 => putative protein
+[06:07:00] Modify product: Uncharacterized protein Rv1324 => putative protein
+[06:07:00] Modify product: Uncharacterized protein Rv1322 => putative protein
+[06:07:00] Modify product: Aldo-keto reductase MSMEG_2408/MSMEI_2347 => Aldo-keto reductase/MSMEI_2347
+[06:07:00] Modify product: Uncharacterized oxidoreductase YghA => putative oxidoreductase YghA
+[06:07:00] Modify product: Uncharacterized protein Rv1841c => putative protein
+[06:07:00] Modify product: UPF0053 protein Rv1842c => hypothetical protein
+[06:07:00] Modify product: Uncharacterized oxidoreductase CzcO => putative oxidoreductase CzcO
+[06:07:00] Modify product: Probable cation-transporting ATPase G => putative cation-transporting ATPase G
+[06:07:00] Modify product: Probable phosphomannomutase => putative phosphomannomutase
+[06:07:00] Modify product: Uncharacterized metal-dependent hydrolase TatD => putative metal-dependent hydrolase TatD
+[06:07:00] Modify product: Putative transport protein Rv0205 => Putative transport protein
+[06:07:00] Modify product: Uncharacterized protein YihR => putative protein YihR
+[06:07:00] Modify product: Uncharacterized HTH-type transcriptional regulator YybR => putative HTH-type transcriptional regulator YybR
+[06:07:00] Modify product: Probable hydrolase sll0100 => putative hydrolase
+[06:07:00] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
+[06:07:00] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[06:07:00] Modify product: Probable transcriptional regulatory protein TcrX => putative transcriptional regulatory protein TcrX
+[06:07:00] Modify product: Probable threonine/serine exporter => putative threonine/serine exporter
+[06:07:00] Modify product: Uncharacterized protein Rv0525 => putative protein
+[06:07:00] Modify product: cAMP/cGMP dual specificity phosphodiesterase Rv0805 => cAMP/cGMP dual specificity phosphodiesterase
+[06:07:00] Cleaned 159 /product names
+[06:07:00] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.sprot.tmp.406561.faa
+[06:07:00] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.sprot.tmp.406561.blast
+[06:07:00] There are still 1391 unannotated CDS left (started with 2623)
+[06:07:00] Will use hmmer3 to search against /225040511/miniconda3/envs/biomni_e1/db/hmm/HAMAP.hmm with 8 CPUs
+[06:07:00] Running: cat \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2\/AS2\.HAMAP\.hmm\.tmp\.406561\.faa | parallel --gnu --plain -j 8 --block 24877 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /225040511/miniconda3/envs/biomni_e1/db/hmm/HAMAP.hmm /dev/stdin > \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2\/AS2\.HAMAP\.hmm\.tmp\.406561\.hmmer3 2> /dev/null
+[06:08:04] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.HAMAP.hmm.tmp.406561.faa
+[06:08:04] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.HAMAP.hmm.tmp.406561.hmmer3
+[06:08:04] Labelling remaining 1182 proteins as 'hypothetical protein'
+[06:08:04] Possible /pseudo 'Long-chain alkane monooxygenase' at NZ_CP040019.1 position 106330
+[06:08:04] Possible /pseudo 'IS481 family transposase ISKrh2' at NZ_CP040019.1 position 167070
+[06:08:04] Possible /pseudo 'IS256 family transposase ISMlu11' at NZ_CP040019.1 position 265295
+[06:08:04] Possible /pseudo 'Serine/threonine-protein kinase PknD' at NZ_CP040019.1 position 415784
+[06:08:04] Possible /pseudo 'Arsenate reductase' at NZ_CP040019.1 position 590977
+[06:08:04] Possible /pseudo 'putative cation-transporting ATPase G' at NZ_CP040019.1 position 761785
+[06:08:04] Possible /pseudo 'Arsenate-mycothiol transferase ArsC1' at NZ_CP040019.1 position 770468
+[06:08:04] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP040019.1 position 781800
+[06:08:04] Possible /pseudo 'Chaperone protein DnaJ' at NZ_CP040019.1 position 1039183
+[06:08:04] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP040019.1 position 1340350
+[06:08:04] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP040019.1 position 1360511
+[06:08:04] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP040019.1 position 1368352
+[06:08:04] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP040019.1 position 1371169
+[06:08:04] Possible /pseudo 'FK506-binding protein' at NZ_CP040019.1 position 1836839
+[06:08:04] Possible /pseudo 'Iron-sulfur cluster assembly SufBD family protein' at NZ_CP040019.1 position 1886567
+[06:08:04] Possible /pseudo 'N-acetyltransferase Eis' at NZ_CP040019.1 position 1938273
+[06:08:04] Possible /pseudo 'D-inositol-3-phosphate glycosyltransferase' at NZ_CP040019.1 position 2180445
+[06:08:04] Possible /pseudo 'Fluoride-specific ion channel FluC' at NZ_CP040019.1 position 2329853
+[06:08:04] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP040019.1 position 2474605
+[06:08:04] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP040019.1 position 2490265
+[06:08:04] Possible /pseudo 'IS3 family transposase ISBli17' at NZ_CP040019.1 position 2778878
+[06:08:04] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP040019.1 position 2794140
+[06:08:04] Found 1054 unique /gene codes.
+[06:08:04] Fixed 2 duplicate /gene - acdA_1 acdA_2
+[06:08:04] Fixed 2 duplicate /gene - bkdB_1 bkdB_2
+[06:08:04] Fixed 2 duplicate /gene - dmoA_1 dmoA_2
+[06:08:04] Fixed 3 duplicate /gene - pknD_1 pknD_2 pknD_3
+[06:08:04] Fixed 2 duplicate /gene - ladA_1 ladA_2
+[06:08:04] Fixed 5 duplicate /gene - acsA_1 acsA_2 acsA_3 acsA_4 acsA_5
+[06:08:04] Fixed 2 duplicate /gene - lspA_1 lspA_2
+[06:08:04] Fixed 3 duplicate /gene - tagU_1 tagU_2 tagU_3
+[06:08:04] Fixed 2 duplicate /gene - metB_1 metB_2
+[06:08:04] Fixed 2 duplicate /gene - whiB_1 whiB_2
+[06:08:04] Fixed 2 duplicate /gene - glsA_1 glsA_2
+[06:08:04] Fixed 2 duplicate /gene - dapE_1 dapE_2
+[06:08:04] Fixed 4 duplicate /gene - arsC_1 arsC_2 arsC_3 arsC_4
+[06:08:04] Fixed 3 duplicate /gene - ydhP_1 ydhP_2 ydhP_3
+[06:08:04] Fixed 2 duplicate /gene - aldR_1 aldR_2
+[06:08:04] Fixed 2 duplicate /gene - echA8_1 echA8_2
+[06:08:04] Fixed 2 duplicate /gene - tcrX_1 tcrX_2
+[06:08:04] Fixed 2 duplicate /gene - mrpD_1 mrpD_2
+[06:08:04] Fixed 2 duplicate /gene - ilvG_1 ilvG_2
+[06:08:04] Fixed 2 duplicate /gene - czcO_1 czcO_2
+[06:08:04] Fixed 2 duplicate /gene - gsiD_1 gsiD_2
+[06:08:04] Fixed 2 duplicate /gene - arsC1_1 arsC1_2
+[06:08:04] Fixed 3 duplicate /gene - gsiA_1 gsiA_2 gsiA_3
+[06:08:04] Fixed 6 duplicate /gene - btuD_1 btuD_2 btuD_3 btuD_4 btuD_5 btuD_6
+[06:08:04] Fixed 2 duplicate /gene - menE_1 menE_2
+[06:08:04] Fixed 4 duplicate /gene - gloB_1 gloB_2 gloB_3 gloB_4
+[06:08:04] Fixed 2 duplicate /gene - sucD_1 sucD_2
+[06:08:04] Fixed 4 duplicate /gene - hin_1 hin_2 hin_3 hin_4
+[06:08:04] Fixed 2 duplicate /gene - pgsA2_1 pgsA2_2
+[06:08:04] Fixed 2 duplicate /gene - glgC_1 glgC_2
+[06:08:04] Fixed 2 duplicate /gene - arnC_1 arnC_2
+[06:08:04] Fixed 2 duplicate /gene - atpH_1 atpH_2
+[06:08:04] Fixed 2 duplicate /gene - gyrA_1 gyrA_2
+[06:08:04] Fixed 2 duplicate /gene - hdfR_1 hdfR_2
+[06:08:04] Fixed 2 duplicate /gene - iscS_1 iscS_2
+[06:08:04] Fixed 2 duplicate /gene - sfnC_1 sfnC_2
+[06:08:04] Fixed 4 duplicate /gene - ywjA_1 ywjA_2 ywjA_3 ywjA_4
+[06:08:04] Fixed 3 duplicate /gene - ctpG_1 ctpG_2 ctpG_3
+[06:08:04] Fixed 2 duplicate /gene - rspR_1 rspR_2
+[06:08:04] Fixed 2 duplicate /gene - hbpA_1 hbpA_2
+[06:08:04] Fixed 2 duplicate /gene - sad_1 sad_2
+[06:08:04] Fixed 2 duplicate /gene - fluC_1 fluC_2
+[06:08:04] Fixed 2 duplicate /gene - trxB_1 trxB_2
+[06:08:04] Fixed 5 duplicate /gene - mmgC_1 mmgC_2 mmgC_3 mmgC_4 mmgC_5
+[06:08:04] Fixed 2 duplicate /gene - ccs1_1 ccs1_2
+[06:08:04] Fixed 2 duplicate /gene - map_1 map_2
+[06:08:04] Fixed 2 duplicate /gene - metQ_1 metQ_2
+[06:08:04] Fixed 2 duplicate /gene - prmC_1 prmC_2
+[06:08:04] Fixed 2 duplicate /gene - lepB_1 lepB_2
+[06:08:04] Fixed 2 duplicate /gene - murE_1 murE_2
+[06:08:04] Fixed 2 duplicate /gene - cobB_1 cobB_2
+[06:08:04] Fixed 2 duplicate /gene - citE_1 citE_2
+[06:08:04] Fixed 2 duplicate /gene - caiT_1 caiT_2
+[06:08:04] Fixed 2 duplicate /gene - menB_1 menB_2
+[06:08:04] Fixed 7 duplicate /gene - mshA_1 mshA_2 mshA_3 mshA_4 mshA_5 mshA_6 mshA_7
+[06:08:04] Fixed 2 duplicate /gene - eis_1 eis_2
+[06:08:04] Fixed 2 duplicate /gene - liaR_1 liaR_2
+[06:08:04] Fixed 2 duplicate /gene - mshD_1 mshD_2
+[06:08:04] Fixed 2 duplicate /gene - fcs_1 fcs_2
+[06:08:04] Fixed 2 duplicate /gene - metI_1 metI_2
+[06:08:04] Fixed 2 duplicate /gene - fadA6_1 fadA6_2
+[06:08:04] Fixed 2 duplicate /gene - fprA_1 fprA_2
+[06:08:04] Fixed 2 duplicate /gene - coaE_1 coaE_2
+[06:08:04] Fixed 2 duplicate /gene - dinG_1 dinG_2
+[06:08:04] Fixed 2 duplicate /gene - ltaE_1 ltaE_2
+[06:08:04] Fixed 2 duplicate /gene - ubiE_1 ubiE_2
+[06:08:04] Fixed 2 duplicate /gene - adh_1 adh_2
+[06:08:04] Fixed 4 duplicate /gene - resA_1 resA_2 resA_3 resA_4
+[06:08:04] Fixed 2 duplicate /gene - metN_1 metN_2
+[06:08:04] Fixed 2 duplicate /gene - hutI_1 hutI_2
+[06:08:04] Fixed 2 duplicate /gene - ettA_1 ettA_2
+[06:08:04] Fixed 2 duplicate /gene - dabB_1 dabB_2
+[06:08:04] Fixed 4 duplicate /gene - sasA_1 sasA_2 sasA_3 sasA_4
+[06:08:04] Fixed 2 duplicate /gene - xerC_1 xerC_2
+[06:08:04] Fixed 2 duplicate /gene - bkdA_1 bkdA_2
+[06:08:04] Fixed 2 duplicate /gene - stp_1 stp_2
+[06:08:04] Fixed 2 duplicate /gene - cadA_1 cadA_2
+[06:08:04] Fixed 3 duplicate /gene - tam_1 tam_2 tam_3
+[06:08:04] Fixed 2 duplicate /gene - noc_1 noc_2
+[06:08:04] Fixed 2 duplicate /gene - purD_1 purD_2
+[06:08:04] Fixed 2 duplicate /gene - yghA_1 yghA_2
+[06:08:04] Fixed 2 duplicate /gene - pcaR_1 pcaR_2
+[06:08:04] Fixed 2 duplicate /gene - desR_1 desR_2
+[06:08:04] Fixed 2 duplicate /gene - rimJ_1 rimJ_2
+[06:08:04] Fixed 3 duplicate /gene - dnaJ_1 dnaJ_2 dnaJ_3
+[06:08:04] Fixed 2 duplicate /gene - guaA_1 guaA_2
+[06:08:04] Fixed 2 duplicate /gene - acp_1 acp_2
+[06:08:04] Fixed 2 duplicate /gene - paaJ_1 paaJ_2
+[06:08:04] Fixed 7 duplicate /gene - uup_1 uup_2 uup_3 uup_4 uup_5 uup_6 uup_7
+[06:08:04] Fixed 2 duplicate /gene - yheS_1 yheS_2
+[06:08:04] Fixed 2 duplicate /gene - pdhC_1 pdhC_2
+[06:08:04] Fixed 2 duplicate /gene - yknY_1 yknY_2
+[06:08:04] Fixed 3 duplicate /gene - galE_1 galE_2 galE_3
+[06:08:04] Fixed 2 duplicate /gene - lcfB_1 lcfB_2
+[06:08:04] Fixed 3 duplicate /gene - cmtR_1 cmtR_2 cmtR_3
+[06:08:04] Fixed 2 duplicate /gene - gyrB_1 gyrB_2
+[06:08:04] Fixed 2 duplicate /gene - def_1 def_2
+[06:08:04] Fixed 2 duplicate /gene - copZ_1 copZ_2
+[06:08:04] Fixed 2 duplicate /gene - fkbP_1 fkbP_2
+[06:08:04] Fixed 3 duplicate /gene - pepN_1 pepN_2 pepN_3
+[06:08:04] Fixed 100 colliding /gene names.
+[06:08:04] Adding /locus_tag identifiers
+[06:08:04] Assigned 2685 locus_tags to CDS and RNA features.
+[06:08:04] Writing outputs to /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/
+[06:08:25] Generating annotation statistics file
+[06:08:25] Generating Genbank and Sequin files
+[06:08:25] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.15.6 from https://github.com/tseemann/prokka' -Z \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2\/AS2\.err -i \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2\/AS2\.fsa 2> /dev/null
+[06:08:39] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/errorsummary.val
+[06:08:39] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.dr
+[06:08:39] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.fixedproducts
+[06:08:39] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.ecn
+[06:08:39] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.val
+[06:08:39] Repairing broken .GBK output that tbl2asn produces...
+[06:08:39] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2\/AS2\.gbf > \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/AS2\/AS2\.gbk
+[06:08:39] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.gbf
+[06:08:39] Output files:
+[06:08:39] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.faa
+[06:08:39] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.err
+[06:08:39] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.ffn
+[06:08:39] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.sqn
+[06:08:39] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.txt
+[06:08:39] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.tbl
+[06:08:39] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.gbk
+[06:08:39] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.tsv
+[06:08:39] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.log
+[06:08:39] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.gff
+[06:08:39] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.fna
+[06:08:39] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.fsa
+[06:08:39] Annotation finished successfully.
+[06:08:39] Walltime used: 4.22 minutes
+[06:08:39] If you use this result please cite the Prokka paper:
+[06:08:39] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
+[06:08:39] Type 'prokka --citation' for more details.
+[06:08:39] Share and enjoy!

Biomanus/experiments/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/AS2/AS2.txt

@@ -0,0 +1,7 @@
+organism: Micrococcus species strain 
+contigs: 1
+bases: 2848891
+CDS: 2623
+rRNA: 9
+tRNA: 52
+tmRNA: 1

Biomanus/experiments/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.log

@@ -0,0 +1,443 @@
+[06:01:20] This is prokka 1.15.6
+[06:01:20] Written by Torsten Seemann <torsten.seemann@gmail.com>
+[06:01:20] Homepage is https://github.com/tseemann/prokka
+[06:01:20] Local time is Thu May 14 06:01:19 2026
+[06:01:20] You are root
+[06:01:20] Operating system is linux
+[06:01:20] You have BioPerl 1.7.8
+[06:01:20] System has 104 cores.
+[06:01:20] Will use maximum of 8 cores.
+[06:01:20] Annotating as >>> Bacteria <<<
+[06:01:20] Generating locus_tag from '/225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_002008305.4_ASM200830v4_genomic.fna' contents.
+[06:01:20] Setting --locustag MOLHKGIG from MD5 6851402062f9a6db2d633ff9bc46b2f3
+[06:01:20] Creating new output folder: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714
+[06:01:20] Running: mkdir -p \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714
+[06:01:20] Using filename prefix: KBS0714.XXX
+[06:01:20] Setting HMMER_NCPU=1
+[06:01:20] Writing log to: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.log
+[06:01:20] Command: /225040511/miniconda3/envs/biomni_e1/bin/prokka --outdir /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714 --prefix KBS0714 --kingdom Bacteria --genus Micrococcus --cpus 8 --force /225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_002008305.4_ASM200830v4_genomic.fna
+[06:01:20] Looking for 'aragorn' - found /225040511/miniconda3/envs/biomni_e1/bin/aragorn
+[06:01:20] Determined aragorn version is v1.2 from 'ARAGORN v1.2.41 Dean Laslett'
+[06:01:20] Looking for 'barrnap' - found /225040511/miniconda3/envs/biomni_e1/bin/barrnap
+[06:01:20] Determined barrnap version is v0.9 from 'barrnap 0.9'
+[06:01:20] Looking for 'blastp' - found /225040511/miniconda3/envs/biomni_e1/bin/blastp
+[06:01:22] Determined blastp version is v2.17 from 'blastp: 2.17.0+'
+[06:01:22] Looking for 'cmpress' - found /225040511/miniconda3/envs/biomni_e1/bin/cmpress
+[06:01:22] Determined cmpress version is v1.1 from '# INFERNAL 1.1.5 (Sep 2023)'
+[06:01:22] Looking for 'cmscan' - found /225040511/miniconda3/envs/biomni_e1/bin/cmscan
+[06:01:22] Determined cmscan version is v1.1 from '# INFERNAL 1.1.5 (Sep 2023)'
+[06:01:22] Looking for 'egrep' - found /usr/bin/egrep
+[06:01:22] Looking for 'find' - found /usr/bin/find
+[06:01:22] Looking for 'grep' - found /usr/bin/grep
+[06:01:22] Looking for 'hmmpress' - found /225040511/miniconda3/envs/biomni_e1/bin/hmmpress
+[06:01:22] Determined hmmpress version is v3.4 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/'
+[06:01:22] Looking for 'hmmscan' - found /225040511/miniconda3/envs/biomni_e1/bin/hmmscan
+[06:01:22] Determined hmmscan version is v3.4 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/'
+[06:01:22] Looking for 'java' - found /225040511/miniconda3/envs/biomni_e1/bin/java
+[06:01:22] Looking for 'makeblastdb' - found /225040511/miniconda3/envs/biomni_e1/bin/makeblastdb
+[06:01:23] Determined makeblastdb version is v2.17 from 'makeblastdb: 2.17.0+'
+[06:01:23] Looking for 'minced' - found /225040511/miniconda3/envs/biomni_e1/bin/minced
+[06:01:23] Determined minced version is v4.2 from 'minced 0.4.2'
+[06:01:23] Looking for 'parallel' - found /225040511/miniconda3/envs/biomni_e1/bin/parallel
+[06:01:23] Determined parallel version is 20260422 from 'GNU parallel 20260422'
+[06:01:23] Looking for 'prodigal' - found /225040511/miniconda3/envs/biomni_e1/bin/prodigal
+[06:01:23] Determined prodigal version is v2.6 from 'Prodigal V2.6.3: February, 2016'
+[06:01:23] Looking for 'prokka-genbank_to_fasta_db' - found /225040511/miniconda3/envs/biomni_e1/bin/prokka-genbank_to_fasta_db
+[06:01:23] Looking for 'sed' - found /225040511/miniconda3/envs/biomni_e1/bin/sed
+[06:01:23] Looking for 'tbl2asn' - found /225040511/miniconda3/envs/biomni_e1/bin/tbl2asn
+[06:01:23] Determined tbl2asn version is v25.7 from 'tbl2asn 25.7   arguments:'
+[06:01:23] Using genetic code table 11.
+[06:01:23] Loading and checking input file: /225040511/project/bioagent-bench/dataset/comparative-genomics/data/GCF_002008305.4_ASM200830v4_genomic.fna
+[06:01:23] Wrote 1 contigs totalling 2522703 bp.
+[06:01:23] Predicting tRNAs and tmRNAs
+[06:01:23] Running: aragorn -l -gc11  -w \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714\/KBS0714\.fna
+[06:01:26] 1 tRNA-Ile [11095,11169] 35 (gat)
+[06:01:26] 2 tRNA-Ala [11400,11474] 34 (tgc)
+[06:01:26] 3 tRNA-Leu [28649,28734] 35 (cag)
+[06:01:26] 4 tRNA-Lys [124259,124332] 34 (ttt)
+[06:01:26] 5 tRNA-Glu [137770,137843] 35 (ttc)
+[06:01:26] 6 tRNA-Asp [137959,138033] 35 (gtc)
+[06:01:26] 7 tRNA-Phe [138105,138180] 34 (gaa)
+[06:01:26] 8 tRNA-Ser [245784,245870] 35 (gga)
+[06:01:26] 9 tRNA-Ser c[315614,315704] 35 (cga)
+[06:01:26] 10 tRNA-Arg c[318941,319015] 35 (acg)
+[06:01:26] 11 tRNA-Ser c[330464,330553] 35 (gct)
+[06:01:26] 12 tRNA-Ser c[339160,339248] 35 (tga)
+[06:01:26] 13 tRNA-Thr c[340979,341054] 35 (cgt)
+[06:01:26] 14 tRNA-Pro [368575,368651] 35 (cgg)
+[06:01:26] 15 tRNA-Thr [381544,381620] 35 (tgt)
+[06:01:26] 16 tRNA-Val [383938,384013] 35 (cac)
+[06:01:26] 17 tRNA-Arg c[400154,400229] 35 (cct)
+[06:01:26] 18 tRNA-Leu [499685,499760] 35 (taa)
+[06:01:26] 19 tRNA-Gln [546090,546163] 33 (ttg)
+[06:01:26] 20 tRNA-Ala [608522,608619] 36 (ggc)
+[06:01:26] 21 tRNA-Asn [643583,643655] 33 (gtt)
+[06:01:26] 22 tRNA-Met [705763,705837] 35 (cat)
+[06:01:26] 23 tmRNA [812896,813265] 96,134 AESKRTDFALAA*
+[06:01:26] 24 tRNA-Arg c[846154,846227] 34 (ccg)
+[06:01:26] 25 tRNA-Leu c[900527,900608] 35 (tag)
+[06:01:26] 26 tRNA-Lys c[901247,901324] 35 (ctt)
+[06:01:26] 27 tRNA-Gln [931597,931669] 34 (ctg)
+[06:01:26] 28 tRNA-Glu [931724,931797] 35 (ctc)
+[06:01:26] 29 tRNA-Glu [931926,932000] 35 (ctc)
+[06:01:26] 30 tRNA-Val [1010731,1010806] 35 (tac)
+[06:01:26] 31 tRNA-His c[1034437,1034512] 34 (gtg)
+[06:01:26] 32 tRNA-Arg c[1041690,1041765] 35 (tct)
+[06:01:26] 33 tRNA-Ala c[1053998,1054087] 31 (cgc)
+[06:01:26] 34 tRNA-Gly c[1055246,1055318] 33 (tcc)
+[06:01:26] 35 tRNA-Pro [1056384,1056458] 35 (tgg)
+[06:01:26] 36 tRNA-Ala [1094883,1094958] 34 (ggc)
+[06:01:26] 37 tRNA-Ala [1096345,1096421] 35 (ggc)
+[06:01:26] 38 tRNA-Gly c[1138144,1138219] 35 (gcc)
+[06:01:26] 39 tRNA-Val c[1138247,1138319] 33 (gac)
+[06:01:26] 40 tRNA-Cys c[1138377,1138448] 33 (gca)
+[06:01:26] 41 tRNA-Gly c[1138466,1138540] 35 (gcc)
+[06:01:26] 42 tRNA-Leu [1177274,1177357] 35 (caa)
+[06:01:26] 43 tRNA-Leu c[1264464,1264549] 35 (gag)
+[06:01:26] 44 tRNA-Ile [1353125,1353219] 35 (gat)
+[06:01:26] 45 tRNA-Pro c[1535472,1535548] 35 (ggg)
+[06:01:26] 46 tmRNA* [1638170,1638576] 272,316 ASAARTCRPPAWWA*
+[06:01:26] 47 tRNA-Met c[1658678,1658752] 35 (cat)
+[06:01:26] 48 tRNA-Trp c[1893471,1893544] 34 (cca)
+[06:01:26] 49 tRNA-Met c[1911202,1911276] 35 (cat)
+[06:01:26] 50 tRNA-Thr c[1911336,1911408] 33 (ggt)
+[06:01:26] 51 tRNA-Tyr c[1922631,1922714] 35 (gta)
+[06:01:26] 52 tRNA-Arg c[1944250,1944342] 37 (cct)
+[06:01:26] 53 tRNA-Gly [2062710,2062783] 33 (ccc)
+[06:01:26] 54 tRNA-Ala c[2158546,2158619] 34 (cgc)
+[06:01:26] Found 54 tRNAs
+[06:01:26] Predicting Ribosomal RNAs
+[06:01:26] Running Barrnap with 8 threads
+[06:01:27] 1 NZ_CP042169.1 362528 16S ribosomal RNA
+[06:01:27] 2 NZ_CP042169.1 364492 23S ribosomal RNA
+[06:01:27] 3 NZ_CP042169.1 367774 5S ribosomal RNA
+[06:01:27] 4 NZ_CP042169.1 1562474 5S ribosomal RNA
+[06:01:27] 5 NZ_CP042169.1 1562781 23S ribosomal RNA
+[06:01:27] 6 NZ_CP042169.1 1566309 16S ribosomal RNA
+[06:01:27] Found 6 rRNAs
+[06:01:27] Skipping ncRNA search, enable with --rfam if desired.
+[06:01:27] Total of 58 tRNA + rRNA features
+[06:01:27] Searching for CRISPR repeats
+[06:01:27] CRISPR1 NZ_CP042169.1 2422827 with 8 spacers
+[06:01:27] CRISPR2 NZ_CP042169.1 2427487 with 11 spacers
+[06:01:27] Found 2 CRISPRs
+[06:01:27] Predicting coding sequences
+[06:01:27] Contigs total 2522703 bp, so using single mode
+[06:01:27] Running: prodigal -i \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714\/KBS0714\.fna -c -m -g 11 -p single -f sco -q
+[06:01:33] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:606702..609095 on + strand
+[06:01:33] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:643616..643948 on - strand
+[06:01:33] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:1053740..1054213 on + strand
+[06:01:34] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:1352703..1354082 on - strand
+[06:01:34] Excluding CDS which overlaps existing RNA (tRNA) at NZ_CP042169.1:1943376..1944674 on - strand
+[06:01:34] Found 2252 CDS
+[06:01:34] Connecting features back to sequences
+[06:01:34] Not using genus-specific database. Try --usegenus to enable it.
+[06:01:34] Annotating CDS, please be patient.
+[06:01:34] Will use 8 CPUs for similarity searching.
+[06:01:35] There are still 2252 unannotated CDS left (started with 2252)
+[06:01:35] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/IS with 8 CPUs
+[06:01:35] Running: cat \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714\/KBS0714\.IS\.tmp\.396535\.faa | parallel --gnu --plain -j 8 --block 48258 --recstart '>' --pipe blastp -query - -db /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714\/KBS0714\.IS\.tmp\.396535\.blast 2> /dev/null
+[06:01:43] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.IS.tmp.396535.faa
+[06:01:43] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.IS.tmp.396535.blast
+[06:01:44] There are still 2199 unannotated CDS left (started with 2252)
+[06:01:44] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/AMR with 8 CPUs
+[06:01:44] Running: cat \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714\/KBS0714\.AMR\.tmp\.396535\.faa | parallel --gnu --plain -j 8 --block 47229 --recstart '>' --pipe blastp -query - -db /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714\/KBS0714\.AMR\.tmp\.396535\.blast 2> /dev/null
+[06:01:56] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.AMR.tmp.396535.faa
+[06:01:56] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.AMR.tmp.396535.blast
+[06:01:56] There are still 2196 unannotated CDS left (started with 2252)
+[06:01:56] Will use blast to search against /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/sprot with 8 CPUs
+[06:01:56] Running: cat \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714\/KBS0714\.sprot\.tmp\.396535\.faa | parallel --gnu --plain -j 8 --block 47055 --recstart '>' --pipe blastp -query - -db /225040511/miniconda3/envs/biomni_e1/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714\/KBS0714\.sprot\.tmp\.396535\.blast 2> /dev/null
+[06:02:36] Modify product: Probable hydrolase sll0100 => putative hydrolase
+[06:02:36] Modify product: Uncharacterized HTH-type transcriptional regulator YybR => putative HTH-type transcriptional regulator YybR
+[06:02:36] Modify product: Uncharacterized protein YihR => putative protein YihR
+[06:02:36] Modify product: Putative transport protein Rv0205 => Putative transport protein
+[06:02:37] Modify product: Uncharacterized metal-dependent hydrolase TatD => putative metal-dependent hydrolase TatD
+[06:02:37] Modify product: Probable phosphomannomutase => putative phosphomannomutase
+[06:02:37] Modify product: pH-sensitive adenylate cyclase Rv1264 => pH-sensitive adenylate cyclase
+[06:02:37] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
+[06:02:37] Modify product: Probable cation-transporting ATPase G => putative cation-transporting ATPase G
+[06:02:37] Modify product: Uncharacterized oxidoreductase YghA => putative oxidoreductase YghA
+[06:02:37] Modify product: Aldo-keto reductase MSMEG_2408/MSMEI_2347 => Aldo-keto reductase/MSMEI_2347
+[06:02:37] Modify product: Probable membrane transporter protein YfcA => putative membrane transporter protein YfcA
+[06:02:37] Modify product: Uncharacterized methyltransferase Rv3342 => putative methyltransferase
+[06:02:37] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
+[06:02:37] Modify product: Probable acetyl-CoA acetyltransferase => putative acetyl-CoA acetyltransferase
+[06:02:37] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit A => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit A
+[06:02:37] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit B => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit B
+[06:02:37] Modify product: UPF0053 protein Rv1842c => hypothetical protein
+[06:02:37] Modify product: Uncharacterized protein Rv1841c => putative protein
+[06:02:37] Modify product: Uncharacterized HIT-like protein Rv0759c => putative HIT-like protein
+[06:02:37] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ
+[06:02:37] Modify product: Uncharacterized protein Rv1324 => putative protein
+[06:02:37] Modify product: Uncharacterized protein Rv1339 => putative protein
+[06:02:37] Modify product: Probable malate:quinone oxidoreductase => putative malate:quinone oxidoreductase
+[06:02:37] Modify product: Putative peroxiredoxin Rv2521 => Putative peroxiredoxin
+[06:02:37] Modify product: Protein Rv2993c => Protein
+[06:02:37] Modify product: RNA/DNA methyltransferase Rv2966c => RNA/DNA methyltransferase
+[06:02:37] Modify product: Probable N-succinyldiaminopimelate aminotransferase DapC => putative N-succinyldiaminopimelate aminotransferase DapC
+[06:02:37] Modify product: Uncharacterized protein Rv2926c => putative protein
+[06:02:37] Modify product: Uncharacterized protein Rv2901c => putative protein
+[06:02:37] Modify product: Uncharacterized protein Rv2242 => putative protein
+[06:02:37] Modify product: Uncharacterized protein Rv2239c => putative protein
+[06:02:37] Modify product: GTP cyclohydrolase 1 type 2 homolog => GTP cyclohydrolase 1 type 2 
+[06:02:37] Modify product: Alpha-(1->6)-mannopyranosyltransferase Rv1459c => Alpha-(1->6)-mannopyranosyltransferase
+[06:02:37] Modify product: Thioredoxin-like reductase Rv2466c => Thioredoxin-like reductase
+[06:02:37] Modify product: Uncharacterized oxidoreductase Rv0484c => putative oxidoreductase
+[06:02:37] Modify product: Probable nicotinate-nucleotide adenylyltransferase => putative nicotinate-nucleotide adenylyltransferase
+[06:02:37] Modify product: Uncharacterized oxidoreductase YdgJ => putative oxidoreductase YdgJ
+[06:02:37] Modify product: Protein Rv0786c => Protein
+[06:02:37] Modify product: UPF0312 protein SA2479 => hypothetical protein
+[06:02:37] Modify product: Type I restriction enzyme BthVORF4518P methylase subunit => Type I restriction enzymeP methylase subunit
+[06:02:37] Modify product: Probable glycerophosphodiester phosphodiesterase 2 => putative glycerophosphodiester phosphodiesterase 2
+[06:02:37] Modify product: Putative low molecular weight protein-tyrosine-phosphatase slr0328 => Putative low molecular weight protein-tyrosine-phosphatase
+[06:02:37] Modify product: Putative 2-hydroxyacid dehydrogenase SA2098 => Putative 2-hydroxyacid dehydrogenase
+[06:02:37] Modify product: Probable glycerophosphodiester phosphodiesterase 1 => putative glycerophosphodiester phosphodiesterase 1
+[06:02:37] Modify product: UPF0045 protein Rv1898 => hypothetical protein
+[06:02:37] Modify product: Universal stress protein MT2698 => Universal stress protein
+[06:02:37] Modify product: Probable inactive lipase Rv1592c => putative inactive lipase
+[06:02:37] Modify product: Transcriptional repressor SmtB homolog => Transcriptional repressor SmtB 
+[06:02:37] Modify product: Acetyl- and succinyl-CoA transferase Rv0802c => Acetyl- and succinyl-CoA transferase
+[06:02:37] Modify product: Uncharacterized protein Rv2895c => putative protein
+[06:02:37] Modify product: Probable FMNH2-dependent monooxygenase SfnC => putative FMNH2-dependent monooxygenase SfnC
+[06:02:37] Modify product: Probable malonic semialdehyde reductase RutE => putative malonic semialdehyde reductase RutE
+[06:02:37] Modify product: Probable enoyl-CoA hydratase EchA8 => putative enoyl-CoA hydratase EchA8
+[06:02:37] Modify product: Probable 3-hydroxyisobutyrate dehydrogenase => putative 3-hydroxyisobutyrate dehydrogenase
+[06:02:37] Modify product: Uncharacterized oxidoreductase Rv1144 => putative oxidoreductase
+[06:02:37] Modify product: Probable glycine dehydrogenase (decarboxylating) => putative glycine dehydrogenase (decarboxylating)
+[06:02:37] Modify product: Uncharacterized SufE-like protein Rv3284 => putative SufE-like protein
+[06:02:37] Modify product: Putative methyltransferase Rv1407 => Putative methyltransferase
+[06:02:37] Modify product: Transcriptional repressor SmtB homolog => Transcriptional repressor SmtB 
+[06:02:37] Modify product: Uncharacterized protein Rv1841c => putative protein
+[06:02:37] Modify product: UPF0053 protein Rv1842c => hypothetical protein
+[06:02:37] Modify product: Uncharacterized membrane protein Rv2723 => putative membrane protein
+[06:02:37] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase
+[06:02:37] Modify product: Nucleotide-binding protein Rv1421 => Nucleotide-binding protein
+[06:02:37] Modify product: Probable cell division protein WhiA => putative cell division protein WhiA
+[06:02:37] Modify product: Iron-sulfur cluster assembly SufBD family protein SA0778 => Iron-sulfur cluster assembly SufBD family protein
+[06:02:37] Modify product: Iron-sulfur cluster assembly SufBD family protein Rv1462 => Iron-sulfur cluster assembly SufBD family protein
+[06:02:37] Modify product: Probable ATP-binding protein YheS => putative ATP-binding protein YheS
+[06:02:37] Modify product: Uncharacterized SURF1-like protein Rv2235 => putative SURF1-like protein
+[06:02:37] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA
+[06:02:37] Modify product: Uncharacterized protein Rv1276c => putative protein
+[06:02:37] Modify product: Phosphate-specific transport system accessory protein PhoU homolog 2 => Phosphate-specific transport system accessory protein PhoU 
+[06:02:37] Modify product: Uncharacterized tRNA/rRNA methyltransferase Rv3579c => putative tRNA/rRNA methyltransferase
+[06:02:37] Modify product: Probable transcriptional regulatory protein TcrX => putative transcriptional regulatory protein TcrX
+[06:02:37] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[06:02:37] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
+[06:02:37] Modify product: Uncharacterized HTH-type transcriptional regulator Rv0472c => putative HTH-type transcriptional regulator
+[06:02:37] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase
+[06:02:37] Modify product: Probable helicase HelY => putative helicase HelY
+[06:02:37] Modify product: Uncharacterized protein Rv1488 => putative protein
+[06:02:37] Modify product: Probable cytochrome c oxidase polypeptide 4 => putative cytochrome c oxidase polypeptide 4
+[06:02:37] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1
+[06:02:37] Modify product: Protein Rv2204c => Protein
+[06:02:37] Modify product: Uncharacterized protein Rv2206 => putative protein
+[06:02:37] Modify product: UPF0053 protein Rv2366c => hypothetical protein
+[06:02:37] Modify product: Probable DNA polymerase III subunit delta => putative DNA polymerase III subunit delta
+[06:02:37] Modify product: DegV domain-containing protein SA1258 => DegV domain-containing protein
+[06:02:37] Modify product: Probable replication restart protein PriA => putative replication restart protein PriA
+[06:02:37] Modify product: Uncharacterized AAA domain-containing protein Rv2559c => putative AAA domain-containing protein
+[06:02:37] Modify product: Uncharacterized transporter Rv1999c => putative transporter
+[06:02:37] Modify product: Uncharacterized protein MSMEG_2731/MSMEI_2664 => putative protein/MSMEI_2664
+[06:02:37] Modify product: Probable transcriptional regulatory protein Rv2603c => putative transcriptional regulatory protein
+[06:02:37] Modify product: Uncharacterized protein YdhK => putative protein YdhK
+[06:02:37] Modify product: Uncharacterized lipoprotein Rv2585c => putative lipoprotein
+[06:02:37] Modify product: Probable bacterial non-heme ferritin => putative bacterial non-heme ferritin
+[06:02:37] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating]
+[06:02:37] Modify product: Protein Rv2133c => Protein
+[06:02:38] Modify product: Uncharacterized protein YdhK => putative protein YdhK
+[06:02:38] Modify product: Macro domain-containing protein PG1779 => Macro domain-containing protein
+[06:02:38] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564
+[06:02:38] Modify product: Probable zinc-binding alcohol dehydrogenase Rv1895 => putative zinc-binding alcohol dehydrogenase
+[06:02:38] Modify product: Uncharacterized protein Rv3421c => putative protein
+[06:02:38] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX 
+[06:02:38] Modify product: Probable cytosol aminopeptidase => putative cytosol aminopeptidase
+[06:02:38] Modify product: Uncharacterized RNA pseudouridine synthase Rv1540 => putative RNA pseudouridine synthase
+[06:02:38] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW
+[06:02:38] Modify product: Uncharacterized HTH-type transcriptional regulator Rv1830 => putative HTH-type transcriptional regulator
+[06:02:38] Modify product: Uncharacterized protein Rv1829 => putative protein
+[06:02:38] Modify product: Uncharacterized HTH-type transcriptional regulator Rv1828 => putative HTH-type transcriptional regulator
+[06:02:38] Modify product: Uncharacterized protein Rv1708 => putative protein
+[06:02:38] Modify product: UPF0182 protein MSMEG_1959/MSMEI_1915 => hypothetical protein
+[06:02:38] Modify product: Uncharacterized protein YlbL => putative protein YlbL
+[06:02:38] Modify product: Probable O-methyltransferase Rv1220c => putative O-methyltransferase
+[06:02:38] Modify product: Probable aminotransferase Rv1178 => putative aminotransferase
+[06:02:38] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
+[06:02:38] Modify product: Putative hydro-lyase PSPTO_5379 => Putative hydro-lyase
+[06:02:38] Modify product: Probable cold shock protein A => putative cold shock protein A
+[06:02:38] Modify product: Probable enoyl-CoA hydratase EchA8 => putative enoyl-CoA hydratase EchA8
+[06:02:38] Modify product: UPF0371 protein DIP2346 => hypothetical protein
+[06:02:38] Modify product: Putative acyltransferase Rv0859 => Putative acyltransferase
+[06:02:38] Modify product: Acetyltransferase PA3944 => Acetyltransferase
+[06:02:38] Modify product: Uncharacterized protein Rv0088 => putative protein
+[06:02:38] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY
+[06:02:38] Modify product: UPF0336 protein Rv0637 => hypothetical protein
+[06:02:38] Modify product: Probable cystathionine beta-synthase Rv1077 => putative cystathionine beta-synthase
+[06:02:38] Modify product: Nucleotide-binding protein SCO4614 => Nucleotide-binding protein
+[06:02:38] Modify product: Uncharacterized oxidoreductase Rv1144 => putative oxidoreductase
+[06:02:38] Modify product: Probable enoyl-CoA hydratase EchA8 => putative enoyl-CoA hydratase EchA8
+[06:02:38] Modify product: Probable 2-succinylbenzoate--CoA ligase => putative 2-succinylbenzoate--CoA ligase
+[06:02:38] Modify product: Uncharacterized protein Rv0525 => putative protein
+[06:02:38] Modify product: Uncharacterized protein Rv0498 => putative protein
+[06:02:38] Modify product: Uncharacterized ATP-dependent helicase YprA => putative ATP-dependent helicase YprA
+[06:02:38] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[06:02:38] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein
+[06:02:38] Modify product: Probable lipoprotein aminopeptidase LpqL => putative lipoprotein aminopeptidase LpqL
+[06:02:38] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein
+[06:02:38] Modify product: Uncharacterized glycosyl hydrolase MT2062 => putative glycosyl hydrolase
+[06:02:38] Modify product: Uncharacterized ABC transporter ATP-binding protein YwjA => putative ABC transporter ATP-binding protein YwjA
+[06:02:38] Modify product: Probable transcriptional regulatory protein TcrX => putative transcriptional regulatory protein TcrX
+[06:02:38] Modify product: Probable siderophore transport system permease protein YfhA => putative siderophore transport system permease protein YfhA
+[06:02:38] Modify product: Probable siderophore transport system ATP-binding protein YusV => putative siderophore transport system ATP-binding protein YusV
+[06:02:38] Modify product: Uncharacterized sugar epimerase YhfK => putative sugar epimerase YhfK
+[06:02:38] Modify product: Uncharacterized N-acetyltransferase Rv2669 => putative N-acetyltransferase
+[06:02:38] Modify product: Uncharacterized oxidoreductase YghA => putative oxidoreductase YghA
+[06:02:38] Modify product: Probable ATP-binding protein YheS => putative ATP-binding protein YheS
+[06:02:38] Modify product: Probable zinc-binding alcohol dehydrogenase Rv1895 => putative zinc-binding alcohol dehydrogenase
+[06:02:38] Modify product: Probable glycerol uptake facilitator protein => putative glycerol uptake facilitator protein
+[06:02:38] Modify product: Probable zinc-binding alcohol dehydrogenase Rv1895 => putative zinc-binding alcohol dehydrogenase
+[06:02:38] Modify product: Probable M18 family aminopeptidase 2 => putative M18 family aminopeptidase 2
+[06:02:38] Cleaned 150 /product names
+[06:02:38] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.sprot.tmp.396535.faa
+[06:02:38] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.sprot.tmp.396535.blast
+[06:02:38] There are still 1075 unannotated CDS left (started with 2252)
+[06:02:38] Will use hmmer3 to search against /225040511/miniconda3/envs/biomni_e1/db/hmm/HAMAP.hmm with 8 CPUs
+[06:02:38] Running: cat \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714\/KBS0714\.HAMAP\.hmm\.tmp\.396535\.faa | parallel --gnu --plain -j 8 --block 20301 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /225040511/miniconda3/envs/biomni_e1/db/hmm/HAMAP.hmm /dev/stdin > \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714\/KBS0714\.HAMAP\.hmm\.tmp\.396535\.hmmer3 2> /dev/null
+[06:02:49] Modify product: Uncharacterized Nudix hydrolase NudL => putative Nudix hydrolase NudL
+[06:02:49] Modify product: Uncharacterized MFS-type transporter YfcJ => putative MFS-type transporter YfcJ
+[06:02:49] Modify product: Uncharacterized MFS-type transporter YfcJ => putative MFS-type transporter YfcJ
+[06:02:49] Cleaned 3 /product names
+[06:02:49] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.HAMAP.hmm.tmp.396535.faa
+[06:02:49] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.HAMAP.hmm.tmp.396535.hmmer3
+[06:02:49] Labelling remaining 903 proteins as 'hypothetical protein'
+[06:02:49] Possible /pseudo 'Serine/threonine-protein kinase PknD' at NZ_CP042169.1 position 20300
+[06:02:49] Possible /pseudo 'IS256 family transposase ISMlu1' at NZ_CP042169.1 position 663236
+[06:02:49] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP042169.1 position 1149627
+[06:02:49] Possible /pseudo 'Iron-sulfur cluster assembly SufBD family protein' at NZ_CP042169.1 position 1234071
+[06:02:49] Possible /pseudo 'IS5 family transposase ISBli8' at NZ_CP042169.1 position 1522733
+[06:02:49] Possible /pseudo 'IS256 family transposase ISMlu1' at NZ_CP042169.1 position 2261917
+[06:02:49] Found 1033 unique /gene codes.
+[06:02:49] Fixed 3 duplicate /gene - ywjA_1 ywjA_2 ywjA_3
+[06:02:49] Fixed 2 duplicate /gene - lnrK_1 lnrK_2
+[06:02:49] Fixed 2 duplicate /gene - fadB_1 fadB_2
+[06:02:49] Fixed 2 duplicate /gene - hutI_1 hutI_2
+[06:02:49] Fixed 2 duplicate /gene - rspR_1 rspR_2
+[06:02:49] Fixed 6 duplicate /gene - mshA_1 mshA_2 mshA_3 mshA_4 mshA_5 mshA_6
+[06:02:49] Fixed 2 duplicate /gene - ktrB_1 ktrB_2
+[06:02:49] Fixed 3 duplicate /gene - dinG_1 dinG_2 dinG_3
+[06:02:49] Fixed 2 duplicate /gene - acp_1 acp_2
+[06:02:49] Fixed 2 duplicate /gene - liaR_1 liaR_2
+[06:02:49] Fixed 6 duplicate /gene - btuD_1 btuD_2 btuD_3 btuD_4 btuD_5 btuD_6
+[06:02:49] Fixed 2 duplicate /gene - gyrA_1 gyrA_2
+[06:02:49] Fixed 2 duplicate /gene - lepB_1 lepB_2
+[06:02:49] Fixed 3 duplicate /gene - czcD_1 czcD_2 czcD_3
+[06:02:49] Fixed 2 duplicate /gene - lysG_1 lysG_2
+[06:02:49] Fixed 2 duplicate /gene - copA_1 copA_2
+[06:02:49] Fixed 2 duplicate /gene - resA_1 resA_2
+[06:02:49] Fixed 2 duplicate /gene - gatA_1 gatA_2
+[06:02:49] Fixed 6 duplicate /gene - mmgC_1 mmgC_2 mmgC_3 mmgC_4 mmgC_5 mmgC_6
+[06:02:49] Fixed 2 duplicate /gene - cobB_1 cobB_2
+[06:02:49] Fixed 4 duplicate /gene - cmtR_1 cmtR_2 cmtR_3 cmtR_4
+[06:02:49] Fixed 2 duplicate /gene - metB_1 metB_2
+[06:02:49] Fixed 4 duplicate /gene - pknD_1 pknD_2 pknD_3 pknD_4
+[06:02:49] Fixed 2 duplicate /gene - hin_1 hin_2
+[06:02:49] Fixed 2 duplicate /gene - yheS_1 yheS_2
+[06:02:49] Fixed 2 duplicate /gene - uup_1 uup_2
+[06:02:49] Fixed 2 duplicate /gene - yghA_1 yghA_2
+[06:02:49] Fixed 2 duplicate /gene - lepA_1 lepA_2
+[06:02:49] Fixed 2 duplicate /gene - ydhK_1 ydhK_2
+[06:02:49] Fixed 3 duplicate /gene - echA8_1 echA8_2 echA8_3
+[06:02:49] Fixed 2 duplicate /gene - copB_1 copB_2
+[06:02:49] Fixed 3 duplicate /gene - stp_1 stp_2 stp_3
+[06:02:49] Fixed 2 duplicate /gene - yfcJ_1 yfcJ_2
+[06:02:49] Fixed 2 duplicate /gene - mcr_1 mcr_2
+[06:02:49] Fixed 2 duplicate /gene - ydbD_1 ydbD_2
+[06:02:49] Fixed 5 duplicate /gene - acsA_1 acsA_2 acsA_3 acsA_4 acsA_5
+[06:02:49] Fixed 2 duplicate /gene - iscS_1 iscS_2
+[06:02:49] Fixed 2 duplicate /gene - acdA_1 acdA_2
+[06:02:49] Fixed 2 duplicate /gene - opuBB_1 opuBB_2
+[06:02:49] Fixed 3 duplicate /gene - pepN_1 pepN_2 pepN_3
+[06:02:49] Fixed 2 duplicate /gene - ziaR_1 ziaR_2
+[06:02:49] Fixed 2 duplicate /gene - citE_1 citE_2
+[06:02:49] Fixed 2 duplicate /gene - dnaJ_1 dnaJ_2
+[06:02:49] Fixed 2 duplicate /gene - mrpD_1 mrpD_2
+[06:02:49] Fixed 2 duplicate /gene - fprA_1 fprA_2
+[06:02:49] Fixed 2 duplicate /gene - trpB_1 trpB_2
+[06:02:49] Fixed 2 duplicate /gene - map_1 map_2
+[06:02:49] Fixed 2 duplicate /gene - tcrX_1 tcrX_2
+[06:02:49] Fixed 2 duplicate /gene - gyrB_1 gyrB_2
+[06:02:49] Fixed 2 duplicate /gene - pdhC_1 pdhC_2
+[06:02:49] Fixed 2 duplicate /gene - gabD1_1 gabD1_2
+[06:02:49] Fixed 2 duplicate /gene - lolD_1 lolD_2
+[06:02:49] Fixed 2 duplicate /gene - mca_1 mca_2
+[06:02:49] Fixed 2 duplicate /gene - fcs_1 fcs_2
+[06:02:49] Fixed 2 duplicate /gene - dapE_1 dapE_2
+[06:02:49] Fixed 2 duplicate /gene - xerC_1 xerC_2
+[06:02:49] Fixed 2 duplicate /gene - menB_1 menB_2
+[06:02:49] Fixed 4 duplicate /gene - sasA_1 sasA_2 sasA_3 sasA_4
+[06:02:49] Fixed 2 duplicate /gene - bkdA_1 bkdA_2
+[06:02:49] Fixed 2 duplicate /gene - kdgR_1 kdgR_2
+[06:02:49] Fixed 2 duplicate /gene - glgC_1 glgC_2
+[06:02:49] Fixed 2 duplicate /gene - dabB_1 dabB_2
+[06:02:49] Fixed 2 duplicate /gene - fgd_1 fgd_2
+[06:02:49] Fixed 3 duplicate /gene - tagU_1 tagU_2 tagU_3
+[06:02:49] Fixed 2 duplicate /gene - lspA_1 lspA_2
+[06:02:49] Fixed 2 duplicate /gene - rlmP_1 rlmP_2
+[06:02:49] Fixed 2 duplicate /gene - gloB_1 gloB_2
+[06:02:49] Fixed 2 duplicate /gene - def_1 def_2
+[06:02:49] Fixed 2 duplicate /gene - prmC_1 prmC_2
+[06:02:49] Fixed 2 duplicate /gene - idsA2_1 idsA2_2
+[06:02:49] Fixed 3 duplicate /gene - lcfB_1 lcfB_2 lcfB_3
+[06:02:49] Fixed 4 duplicate /gene - merA_1 merA_2 merA_3 merA_4
+[06:02:49] Fixed 2 duplicate /gene - bkdB_1 bkdB_2
+[06:02:49] Fixed 2 duplicate /gene - guaA_1 guaA_2
+[06:02:49] Fixed 2 duplicate /gene - hsdM_1 hsdM_2
+[06:02:49] Fixed 2 duplicate /gene - menE_1 menE_2
+[06:02:49] Fixed 2 duplicate /gene - nrtD_1 nrtD_2
+[06:02:49] Fixed 2 duplicate /gene - smc_1 smc_2
+[06:02:49] Fixed 2 duplicate /gene - glsA_1 glsA_2
+[06:02:49] Fixed 2 duplicate /gene - lysE_1 lysE_2
+[06:02:49] Fixed 2 duplicate /gene - mgtA_1 mgtA_2
+[06:02:49] Fixed 2 duplicate /gene - qorA_1 qorA_2
+[06:02:49] Fixed 2 duplicate /gene - atpH_1 atpH_2
+[06:02:49] Fixed 2 duplicate /gene - mshD_1 mshD_2
+[06:02:49] Fixed 2 duplicate /gene - sucD_1 sucD_2
+[06:02:49] Fixed 2 duplicate /gene - fadA6_1 fadA6_2
+[06:02:49] Fixed 2 duplicate /gene - pgsA_1 pgsA_2
+[06:02:49] Fixed 3 duplicate /gene - ettA_1 ettA_2 ettA_3
+[06:02:49] Fixed 2 duplicate /gene - accA3_1 accA3_2
+[06:02:49] Fixed 2 duplicate /gene - gabT_1 gabT_2
+[06:02:49] Fixed 90 colliding /gene names.
+[06:02:49] Adding /locus_tag identifiers
+[06:02:49] Assigned 2312 locus_tags to CDS and RNA features.
+[06:02:49] Writing outputs to /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/
+[06:02:50] Generating annotation statistics file
+[06:02:50] Generating Genbank and Sequin files
+[06:02:50] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.15.6 from https://github.com/tseemann/prokka' -Z \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714\/KBS0714\.err -i \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714\/KBS0714\.fsa 2> /dev/null
+[06:02:54] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/errorsummary.val
+[06:02:54] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.dr
+[06:02:54] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.fixedproducts
+[06:02:54] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.ecn
+[06:02:54] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.val
+[06:02:54] Repairing broken .GBK output that tbl2asn produces...
+[06:02:54] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714\/KBS0714\.gbf > \/225040511\/project\/Hypo_Bio_OS\/bioagent\-bench\-runs\/comparative\-genomics_20260514_055459\/prokka_annotations\/KBS0714\/KBS0714\.gbk
+[06:02:54] Deleting unwanted file: /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.gbf
+[06:02:54] Output files:
+[06:02:54] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.fsa
+[06:02:54] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.ffn
+[06:02:54] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.tsv
+[06:02:54] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.gff
+[06:02:54] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.sqn
+[06:02:54] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.txt
+[06:02:54] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.log
+[06:02:54] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.faa
+[06:02:54] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.gbk
+[06:02:54] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.err
+[06:02:54] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.tbl
+[06:02:54] /225040511/project/Hypo_Bio_OS/bioagent-bench-runs/comparative-genomics_20260514_055459/prokka_annotations/KBS0714/KBS0714.fna
+[06:02:54] Annotation finished successfully.
+[06:02:54] Walltime used: 1.58 minutes
+[06:02:54] If you use this result please cite the Prokka paper:
+[06:02:54] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
+[06:02:54] Type 'prokka --citation' for more details.
+[06:02:54] Share and enjoy!