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Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/final_answer.txt

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+The output file has been successfully created. Let me provide the final summary.
+
+## Final Summary
+
+**Task completed successfully!** Here's what was accomplished:
+
+### Analysis Steps:
+1. **Explored input data**: Examined count files (5xFAD, 3xTG-AD), DEA result files, and entrez gene ID mapping files for all three Alzheimer's mouse models.
+2. **Identified significant genes**:
+   - **5xFAD**: 916 significant genes (padj < 0.05)
+   - **3xTG-AD**: 578 significant genes (padj < 0.05)
+   - **PS3O1S**: 797 significant genes (pval < 0.05)
+3. **Mapped genes to symbols**: Used Ensembl-to-gene-symbol mapping from the PS3O1S DEA results to convert all significant genes to gene symbols for KEGG enrichment.
+4. **Performed KEGG pathway enrichment**: Used gseapy with the `KEGG_2019_Mouse` library for each model:
+   - **5xFAD**: 270 enriched pathways
+   - **3xTG-AD**: 221 enriched pathways
+   - **PS3O1S**: 253 enriched pathways
+5. **Merged results**: Created a comprehensive comparison with 294 unique pathways across all models, with 188 pathways shared by all three models.
+
+### Output File:
+- **`pathway_comparison.csv`** saved to the required output directory with columns:
+  - `pathway` - KEGG pathway name
+  - `5xFAD_pvalue` - enrichment p-value for 5xFAD model
+  - `3xTG_AD_pvalue` - enrichment p-value for 3xTG-AD model
+  - `PS3O1S_pvalue` - enrichment p-value for PS3O1S model
+
+### Key Finding Example:
+The **Phagosome** pathway (highlighted in the example) was found to be highly significant in the 5xFAD model (p = 5.64e-18) but not significant in 3xTG-AD (p = 0.89) or PS3O1S (p = 0.98), suggesting it may be a pathway specific to the 5xFAD model rather than shared across all three models.
+
+<solution>All deliverables have been completed successfully. The pathway_comparison.csv file has been saved to the required output path with the correct column names and format.</solution>

Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/output_validation.json

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+{
+  "postprocess": [
+    {
+      "file": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/pathway_comparison.csv",
+      "actions": [
+        "canonicalized_pathway_header"
+      ]
+    }
+  ],
+  "outputs": [
+    {
+      "path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/pathway_comparison.csv",
+      "exists": true,
+      "size_bytes": 22462
+    }
+  ]
+}

Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/pathway_comparison.csv

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+Pathway,5xFAD_pvalue,3xTG_AD_pvalue,PS3O1S_pvalue
+ABC transporters,0.3734951724540979,0.3982086454122566,0.8572677404245432
+AGE-RAGE signaling pathway in diabetic complications,0.0001876762433690555,,0.7699616525431697
+AMPK signaling pathway,0.8299784646011548,0.6994936073464167,0.7418407249595614
+Acute myeloid leukemia,5.824257657205522e-05,,0.9391894670565032
+Adherens junction,0.1086409878837307,0.8752999493958263,0.5487805982401147
+Adipocytokine signaling pathway,0.6320343242421363,0.8716350054205276,0.5392616314174665
+Adrenergic signaling in cardiomyocytes,0.3594597863572157,0.7964101258253508,0.7042081108149008
+African trypanosomiasis,0.2604835101591206,0.0242834828298966,0.7943131928270415
+"Alanine, aspartate and glutamate metabolism",0.2358223572090086,0.6566098436810323,0.7769204373512978
+Alcoholism,0.9510811498448736,0.3384187673624444,0.5362383217907123
+Aldosterone synthesis and secretion,0.6869057058370837,0.7908336671321714,0.9167981085973476
+Aldosterone-regulated sodium reabsorption,0.2481059618606755,,0.785793049845434
+Allograft rejection,1.026805922108731e-07,0.838168305656606,0.7196235651859002
+Alzheimer disease,0.8120602009792524,0.9937362878045384,0.920589266910598
+Amino sugar and nucleotide sugar metabolism,0.0015185660018933,,0.584625392855167
+Aminoacyl-tRNA biosynthesis,,,0.931303056893734
+Amoebiasis,0.0087737865302803,0.9534658649608524,0.797467591175662
+Amphetamine addiction,0.8212457712594252,0.1282364339718783,0.9366666363166524
+Amyotrophic lateral sclerosis (ALS),0.4230153454533441,,0.6171462096590109
+Antigen processing and presentation,1.1282436253974541e-12,0.7300273914947513,0.4817694108602536
+Apelin signaling pathway,0.1768325295494886,0.7560872798116083,0.644633304501988
+Apoptosis,2.159578775395238e-05,0.5722966489341726,0.9223577071736624
+Arachidonic acid metabolism,0.5804243489812264,0.01346400290366,0.973039861531982
+Arginine and proline metabolism,0.9025747039867544,0.4181672874809009,
+Arginine biosynthesis,0.2129323181469292,,
+Arrhythmogenic right ventricular cardiomyopathy (ARVC),0.8449962915575896,,0.7853579710904967
+Ascorbate and aldarate metabolism,0.7154211682778693,0.5415029955539521,
+Asthma,9.568817264651437e-06,,
+Autoimmune thyroid disease,3.534539825888963e-07,0.8951970615835416,0.9578249239415636
+Autophagy,0.0348303859055467,,0.5919154072524235
+Axon guidance,0.7152898802353675,0.9945847426337368,0.4235248933656133
+B cell receptor signaling pathway,1.09256102186713e-07,0.6114232484687668,0.7853579710904967
+Bacterial invasion of epithelial cells,0.1196964671483959,,0.7979875521465601
+Basal cell carcinoma,0.9468739948776976,0.838168305656606,0.9223952853228587
+Basal transcription factors,,,0.5136186434315607
+Base excision repair,0.8039619397164758,0.6361665165076187,0.1607832016867621
+Bile secretion,0.2289985964600332,0.6114232484687668,0.7853579710904967
+Biosynthesis of unsaturated fatty acids,0.0555709756124881,0.6032014043404286,0.7267391011634169
+Bladder cancer,0.5618297911010284,,
+Breast cancer,0.5046110005256168,0.9245176245947236,0.9974614456924362
+Butanoate metabolism,,,0.6652868233851852
+C-type lectin receptor signaling pathway,4.6118638518955e-05,0.9609023879067096,0.989430177993062
+Calcium signaling pathway,0.357175367265085,0.4511245469770473,0.8744851293034686
+Carbohydrate digestion and absorption,0.0125658337330266,,
+Cardiac muscle contraction,0.8752750028227865,0.8951970615835416,0.8212850478463981
+Cell adhesion molecules (CAMs),3.192918699970801e-11,0.956384784700632,0.9919772114630284
+Cell cycle,0.3264290109904464,0.6838819605102117,0.7246257326245588
+Cellular senescence,0.0046768196498642,0.9953183904033032,0.7478192115948229
+Central carbon metabolism in cancer,0.0082115864204126,0.8427869182672838,0.925485849363174
+Chagas disease (American trypanosomiasis),1.692626014828807e-10,0.9492338827262312,0.3889181271848207
+Chemical carcinogenesis,0.8065016413901517,0.5028386619067495,
+Chemokine signaling pathway,5.880515224210386e-09,0.3292165057941231,0.5247063660060708
+Cholesterol metabolism,0.0015185660018933,0.7573135920330686,0.3081479395235083
+Choline metabolism in cancer,0.294709795673692,0.1517306276917983,0.7581347954192857
+Cholinergic synapse,0.4084354930071912,0.4015823192639477,0.6611653572286089
+Chronic myeloid leukemia,0.0570563761514604,,0.9542513631223596
+Circadian entrainment,0.4702272446098515,0.776874954611114,0.5569928197426123
+Circadian rhythm,,,0.3355306737678538
+Citrate cycle (TCA cycle),,,0.7267391011634169
+Cocaine addiction,0.6480239698879974,0.0114523843548001,0.5733406062096127
+Collecting duct acid secretion,0.3490748716080725,,0.6652868233851852
+Colorectal cancer,0.3710261880718421,0.4592416569125473,0.9719202615848072
+Complement and coagulation cascades,1.883654665018678e-09,0.9215666263421688,0.9719202615848072
+Cortisol synthesis and secretion,0.6126526797032542,0.3131268264958325,0.5198837553116666
+Cushing syndrome,0.4358754907502958,0.4741667461695822,0.7612834437258328
+Cysteine and methionine metabolism,0.9025747039867544,,
+Cytokine-cytokine receptor interaction,1.4833571798834152e-13,0.5928651991207703,0.9766203689430262
+Cytosolic DNA-sensing pathway,8.361353162582018e-05,,0.7028892152636298
+DNA replication,0.8039619397164758,,0.758058954332533
+Dilated cardiomyopathy (DCM),0.3892378290132526,0.7300273914947513,0.4817694108602536
+Dopaminergic synapse,0.5806169786399643,0.3394920083621832,0.6253708733432658
+Drug metabolism,0.5959305806801,0.4080130508140198,
+ECM-receptor interaction,0.3255957429166209,0.2110098856942028,0.8470008029436239
+Endocrine and other factor-regulated calcium reabsorption,0.7202029069450163,0.7959954243050831,0.8925884203658613
+Endocytosis,0.0058380751075481,0.9499651199322736,0.8420080565102842
+Endometrial cancer,0.747104231708447,0.4943619520448446,
+Epstein-Barr virus infection,1.867815297151293e-18,0.8939712158127048,0.952175372311086
+ErbB signaling pathway,0.1825384513077233,0.9119240163176464,0.9669578426537668
+Estrogen signaling pathway,0.1567495046430888,0.7382467232871458,0.9051701870163528
+Ether lipid metabolism,0.1640959031248951,0.1490507750838108,0.5618341678521759
+Fanconi anemia pathway,,0.1767700117228449,0.330102729560645
+Fat digestion and absorption,0.8447101362684128,,
+Fatty acid degradation,,0.7642349351581245,0.8684020418177673
+Fatty acid elongation,0.0407954082480255,,
+Fc epsilon RI signaling pathway,0.0002295278870491026,0.3053067310563251,0.9366666363166524
+Fc gamma R-mediated phagocytosis,5.7546931347283456e-08,0.7126525672296605,0.2635116067051573
+Ferroptosis,0.1068787567122705,0.6851448261068036,0.8024948513857095
+Fluid shear stress and atherosclerosis,0.0008006170881466081,0.5834566377274996,0.9792301983786712
+Focal adhesion,0.2959957988560507,0.9250153268815444,0.95834038509844
+Folate biosynthesis,0.7018528020553783,,0.6514306598053069
+FoxO signaling pathway,0.3935426365892228,0.8930115121394787,0.77379552923939
+Fructose and mannose metabolism,0.2116079994207596,,
+GABAergic synapse,0.1149620272013041,0.9259851593973384,0.4817694108602536
+Galactose metabolism,0.0555709756124881,,0.7267391011634169
+Gap junction,0.3528167519260489,0.22910734315518,0.9695398234980942
+Gastric acid secretion,0.4355738992665367,0.6263530688961628,0.9503754043961108
+Gastric cancer,0.2433020311904404,0.8037714809871142,0.9402643346688224
+Glioma,0.2545906053611015,,0.952352732064606
+Glucagon signaling pathway,0.9494526045485092,,0.9167981085973476
+Glutamatergic synapse,0.034812089358029,0.4080130508140198,0.0839412377138514
+Glutathione metabolism,0.794280037235346,0.8427869182672838,0.925485849363174
+Glycerolipid metabolism,0.7717534060636356,0.5212662856034557,
+Glycerophospholipid metabolism,0.6483470188604411,0.1428558800486901,0.3413465697418953
+"Glycine, serine and threonine metabolism",,0.6851448261068036,0.4752279474852387
+Glycolysis / Gluconeogenesis,0.3630792809897446,0.8558680802224687,0.934039274709356
+Glycosaminoglycan biosynthesis,0.4351968776599302,,0.3520379800652464
+Glycosaminoglycan degradation,0.0002613138253093437,0.1190261564829761,
+Glycosphingolipid biosynthesis,0.0008517662411013396,0.7275397842706464,0.5381607227996654
+Glycosylphosphatidylinositol (GPI)-anchor biosynthesis,,,0.6370016401563485
+Glyoxylate and dicarboxylate metabolism,0.7638000891264057,,0.3501481587884255
+GnRH signaling pathway,0.22537234927445,0.253800720891804,0.8773629908528048
+Graft-versus-host disease,1.8243886405577303e-08,0.8427869182672838,0.925485849363174
+HIF-1 signaling pathway,0.00025652857833940383,0.9506855941232908,0.9853593727508416
+Hedgehog signaling pathway,0.8711255507979093,,0.8320973993299161
+Hematopoietic cell lineage,4.0777868201448543e-13,0.7517999858682484,
+Hepatitis B,0.001232078997628,0.8463402254260931,0.9897105480724842
+Hepatitis C,3.5083762511635564e-09,0.9903083875136752,0.9885577258770644
+Hepatocellular carcinoma,0.0903016968147951,0.8683548342514004,0.911906185124888
+Herpes simplex virus 1 infection,8.430392304971093e-08,0.7911096233867867,0.9793491804525208
+Hippo signaling pathway,0.4358754907502958,0.9431962582602328,0.1819166179042629
+Histidine metabolism,0.6727467869611315,0.4999784841151393,
+Human T-cell leukemia virus 1 infection,6.7084229518505995e-09,0.8298956553463598,0.9683839815514867
+Human cytomegalovirus infection,2.0199205993291227e-07,0.934506291699727,0.8839742474646106
+Human immunodeficiency virus 1 infection,1.3731729229401338e-06,0.8107382541076694,0.6065418510564768
+Human papillomavirus infection,0.0002435676862209852,0.8900298808200845,0.7714452897529168
+Huntington disease,0.9770475275624316,0.9961817491207158,0.7785574336046389
+Hypertrophic cardiomyopathy (HCM),0.5531000747189112,0.9168847986542256,0.2559423525857411
+IL-17 signaling pathway,0.3983323198126799,0.9281003429162302,0.8812165381472914
+Inflammatory bowel disease (IBD),2.858744056701845e-07,,0.6853320825488993
+Inflammatory mediator regulation of TRP channels,0.2209176415970789,0.1542755954901461,0.8846130732782835
+Influenza A,1.1980324749353736e-16,0.9542276521446252,0.9048493258444028
+Inositol phosphate metabolism,0.2374469640359056,0.8788604325038609,0.7917572586609677
+Insulin resistance,0.127829461999632,0.8243532144631156,0.6403081889219072
+Insulin secretion,0.7556153409518007,0.7066562985348247,0.8607689802493782
+Insulin signaling pathway,0.6092239703652477,0.9821523615910084,0.9761384099044492
+Intestinal immune network for IgA production,3.333605446491324e-08,0.7113124198149073,0.5136186434315607
+JAK-STAT signaling pathway,1.5191940296994322e-06,0.9496038146002916,0.998730543253102
+Kaposi sarcoma-associated herpesvirus infection,1.3918207194182026e-08,0.8664248772044295,0.974159313919616
+Legionellosis,9.327022492388878e-06,,0.6762387905131497
+Leishmaniasis,4.012247013443773e-18,0.8558680802224687,0.5000717646329553
+Leukocyte transendothelial migration,2.2309504700371857e-07,0.9641630402918362,0.8400369507873777
+Linoleic acid metabolism,,0.0534263330101907,0.8684020418177673
+Long-term depression,0.0580291768456571,0.5212662856034557,0.7028892152636298
+Long-term potentiation,0.5925965771933602,,
+Longevity regulating pathway,0.8481574467682668,0.9477395112252992,0.9167981085973476
+Lysine degradation,,0.5034365194349372,0.6853320825488993
+Lysosome,1.236646420206176e-20,0.2781979322067384,0.2229203791880803
+MAPK signaling pathway,0.0020564137288393,0.734785078058778,0.9777813078692807
+Malaria,0.0015185660018933,0.0502348608800661,0.584625392855167
+Mannose type O-glycan biosynthesis,0.2812469128468413,,0.2315799652394364
+Maturity onset diabetes of the young,0.7154211682778693,0.5415029955539521,
+Measles,7.3105976295860585e-09,0.780996189106052,0.9288116240750004
+Melanogenesis,0.6718507961795477,0.9446177455928872,0.7641084136126405
+Melanoma,0.6414692503378052,,
+Metabolism of xenobiotics by cytochrome P450,0.5823196899584273,0.5639268792335304,
+MicroRNAs in cancer,0.5141546608208084,0.9973472144473514,0.9991372274938484
+Mineral absorption,0.000728970464072021,,0.5259970939221404
+Mismatch repair,,0.4702304761909727,0.5900360033380718
+Mitophagy,0.7869987731210207,,0.9223952853228587
+Morphine addiction,0.2403282300686285,0.2663479873337597,0.15883331435568
+Mucin type O-glycan biosynthesis,0.3657294653268459,,0.306023837082694
+N-Glycan biosynthesis,0.9025747039867544,,0.5956879709979176
+NF-kappa B signaling pathway,8.547284589338923e-10,0.5580112557165765,0.9167981085973476
+NOD-like receptor signaling pathway,2.341357195543686e-10,0.9337936020439612,0.9997600808366974
+Natural killer cell mediated cytotoxicity,7.405220050595797e-08,0.9671521817563892,0.9917221345822612
+Necroptosis,0.0011264076468827,0.5640874569770989,0.9727581648668564
+"Neomycin, kanamycin and gentamicin biosynthesis",0.0188261968901867,,
+Neuroactive ligand-receptor interaction,0.0750239757331225,0.1232881073086274,0.7312686567410913
+Neurotrophin signaling pathway,0.1854919652232887,0.4525600167913193,0.8639216943031445
+Nicotinate and nicotinamide metabolism,0.8128874175359724,0.6465356880657994,0.7676807931158754
+Nicotine addiction,0.5483479954695247,0.6851448261068036,0.4752279474852387
+Nitrogen metabolism,0.5466458664937254,,0.4978930787706773
+Non-alcoholic fatty liver disease (NAFLD),0.5332073785878096,0.987408507229352,0.8547046130193011
+Non-homologous end-joining,,,0.4094992507369164
+Non-small cell lung cancer,0.5823196899584273,0.8516331158851426,0.931303056893734
+Notch signaling pathway,0.8979240420960097,0.7573135920330686,0.584625392855167
+Nucleotide excision repair,,,0.8251405883943322
+Olfactory transduction,0.9999944555955632,0.9999951511964408,0.999994660071484
+One carbon pool by folate,0.2129323181469292,,
+Oocyte meiosis,0.2755986519637982,0.4208314973734192,0.4903497765054139
+Osteoclast differentiation,1.958533326958932e-16,0.0300150868001105,0.9944925408651863
+Other glycan degradation,8.017904871422696e-06,0.4053301868395954,0.5178436354613557
+Other types of O-glycan biosynthesis,0.2641270153797711,0.4702304761909727,0.0101887780324461
+Ovarian steroidogenesis,0.2596830780263931,0.2206471005570144,0.9009702536041344
+Oxidative phosphorylation,0.98572602438564,,0.9051701870163528
+Oxytocin signaling pathway,0.7061274453227522,0.6417087027080524,0.7364406152928616
+PI3K-Akt signaling pathway,0.0036954024906438,0.942752353606112,0.9744743596103924
+PPAR signaling pathway,0.7485508635690783,0.9144402912110756,0.4378706250898923
+Pancreatic cancer,0.12542565782948,,0.8040521635143886
+Pancreatic secretion,0.5223236187500635,0.9520958611491486,0.9246043789066708
+Pantothenate and CoA biosynthesis,0.5672682866057815,,
+"Parathyroid hormone synthesis, secretion and action",0.2138148226125825,0.3627949446841116,0.8026263639959617
+Parkinson disease,0.9620068027558384,0.588973234124182,0.8282758015349989
+Pathways in cancer,0.0026040530034102,0.7574088953163731,0.9981427591113704
+Pentose and glucuronate interconversions,0.199714076226302,,0.7480391324212297
+Pentose phosphate pathway,,,0.7267391011634169
+Peroxisome,,0.9119240163176464,0.8517222944985142
+Pertussis,8.49151167238353e-10,0.8889444202932038,0.8099544085577488
+Phagosome,5.643221206791418e-18,0.8897560424203869,0.975935402241498
+Phenylalanine metabolism,0.2812469128468413,,
+"Phenylalanine, tyrosine and tryptophan biosynthesis",0.310775334509711,,
+Phosphatidylinositol signaling system,0.2867797947448608,0.9413098408058346,0.905204796300897
+Phospholipase D signaling pathway,0.0080487305547025,0.8001191681903398,0.8475294838001037
+Phototransduction,0.7154211682778693,0.5415029955539521,
+Platelet activation,0.00017426810715829024,0.4775291921049847,0.961418185735801
+Porphyrin and chlorophyll metabolism,0.2854528156911962,,0.8103514563677723
+Primary bile acid biosynthesis,0.0336560048576978,,0.4771180925215306
+Primary immunodeficiency,0.0224700349472553,0.6465356880657994,
+Prion diseases,0.0039135901861884,,0.3932743392123864
+Progesterone-mediated oocyte maturation,0.052019863010597,0.7300273914947513,0.8773629908528048
+Prolactin signaling pathway,0.1086409878837307,0.8752999493958263,
+Propanoate metabolism,0.7638000891264057,,0.7154239493547337
+Prostate cancer,0.2788967120498453,,0.9805318456285708
+Proteasome,0.6248568267801495,,0.5501070596308211
+Protein digestion and absorption,0.7822831438602025,0.473964193866013,0.9741148703913364
+Protein export,,,0.6785928466633031
+Protein processing in endoplasmic reticulum,0.942020437724576,0.9483800776808436,0.0605571508429523
+Proteoglycans in cancer,0.00039007410820779984,0.9972285291050184,0.7000727022670568
+Proximal tubule bicarbonate reclamation,0.0758189306419275,,
+Purine metabolism,0.7457666077984797,0.5436836890683961,0.9735320494532615
+Pyrimidine metabolism,0.747104231708447,0.8129625589303786,0.9049128964621872
+Pyruvate metabolism,0.5205214063149609,0.2944712989426278,0.4486332443933831
+RIG-I-like receptor signaling pathway,0.0035314187643366,,0.7580051179117162
+RNA degradation,,0.9093338706294674,0.8470008029436239
+RNA polymerase,,0.5545648345235226,0.6785928466633031
+RNA transport,0.9963053195585172,0.5173666427427686,0.998876630022096
+Rap1 signaling pathway,0.0149329740880335,0.8491930785126062,0.72818678889946
+Ras signaling pathway,0.2629765313449747,0.7960305777119534,0.9568181925792916
+Regulation of actin cytoskeleton,0.1194036450603661,0.9863303921628542,0.7627703469064105
+Regulation of lipolysis in adipocytes,0.249620696283607,0.8018153144163448,0.657411737820988
+Relaxin signaling pathway,0.1424604460202219,0.7241999581944403,0.5987375750491811
+Renal cell carcinoma,0.8212457712594252,0.8599823669280198,0.9366666363166524
+Renin secretion,0.0570563761514604,0.6408341031891823,0.9542513631223596
+Renin-angiotensin system,0.2236503161956788,0.6465356880657994,0.421294100864465
+Retinol metabolism,0.9230738806360156,0.7356177441526812,0.9751470620719322
+Retrograde endocannabinoid signaling,0.6819777379018304,0.9296674856964344,0.7152468966596092
+Rheumatoid arthritis,1.8185744393533968e-12,0.6943509328946099,0.6534192208178323
+Riboflavin metabolism,,0.2062135711270461,0.2768463670886862
+Ribosome,,0.9927550970670898,0.9672381027240664
+Ribosome biogenesis in eukaryotes,,0.9641630402918362,0.9906460266240952
+SNARE interactions in vesicular transport,0.7848149376308632,,0.7376048873356247
+Salivary secretion,0.1433887118975166,0.6548696346761385,0.9578249239415636
+Salmonella infection,4.605730028899655e-05,0.8951970615835416,0.8212850478463981
+Selenocompound metabolism,,,0.1447181568869057
+Serotonergic synapse,0.7219660657691114,0.1746430475799498,0.6054951726182619
+Signaling pathways regulating pluripotency of stem cells,0.751475406220763,0.7517212143507535,0.912920166743514
+Small cell lung cancer,0.6067651031115721,0.7411092316713952,0.8849579008583652
+Sphingolipid metabolism,0.1730351369800772,0.0114523843548001,
+Sphingolipid signaling pathway,0.0257870601743318,0.6891519312145487,0.8746450339745783
+Spliceosome,0.9978865459142592,0.5201036721865451,0.8996624032423824
+Staphylococcus aureus infection,4.042269692320453e-12,0.7570014829911564,
+Starch and sucrose metabolism,0.4461365712979102,,
+Steroid biosynthesis,0.2129323181469292,,
+Steroid hormone biosynthesis,0.9842209701756964,0.9238078608327468,0.973039861531982
+Synaptic vesicle cycle,0.8706389004582772,0.6479073093224752,0.365750760311565
+Systemic lupus erythematosus,0.0021994652380578,0.9170970445302004,0.8241917241439921
+T cell receptor signaling pathway,0.0165120422793559,0.786268528752333,0.7699616525431697
+TGF-beta signaling pathway,0.3983323198126799,0.9281003429162302,0.8812165381472914
+TNF signaling pathway,0.00013509504801267517,0.6093407703848268,
+Taste transduction,0.9834663046711432,0.7185458375142267,0.2711312790029847
+Terpenoid backbone biosynthesis,0.6571462010109316,,
+Th1 and Th2 cell differentiation,0.0019187760233029,0.9192595819250462,0.6766847540983636
+Th17 cell differentiation,7.128875380389324e-07,0.9477395112252992,0.5807356024263919
+Thermogenesis,0.9985050464231616,0.9619234238488394,0.8153961825172849
+Thiamine metabolism,0.5024093701692232,0.3514986189780421,0.4554846530609762
+Thyroid cancer,0.821406946905836,0.6566098436810323,
+Thyroid hormone signaling pathway,0.1527665542601775,0.9641630402918362,0.945920630191421
+Thyroid hormone synthesis,0.4253255625603916,0.6189444177316381,0.5581829047285021
+Tight junction,0.1397122323505674,0.8577194898517353,0.6551734498152928
+Toll-like receptor signaling pathway,2.8429305085541117e-09,0.3110160835545683,0.5569928197426123
+Toxoplasmosis,4.632840809304179e-10,0.8164568059217981,0.4284085297130833
+Transcriptional misregulation in cancer,9.942138629058674e-06,0.9682076448229572,0.8563768802440082
+Tryptophan metabolism,0.6480239698879974,0.7501894252824993,0.8572677404245432
+Tuberculosis,2.3888119476946656e-17,0.9640793997748062,0.926589874793279
+Type I diabetes mellitus,5.771512924926477e-08,0.5881828057305921,0.7651132084399163
+Type II diabetes mellitus,0.0657643556159768,0.7501894252824993,
+Tyrosine metabolism,0.5483479954695247,,
+Ubiquinone and other terpenoid-quinone biosynthesis,0.4005830361831431,,0.0682762332440027
+Ubiquitin mediated proteolysis,0.7570882660634862,0.9068572962404412,0.469333850960332
+VEGF signaling pathway,0.122801025868957,0.4943619520448446,0.6762387905131497
+"Valine, leucine and isoleucine degradation",0.9263555476250656,0.4759009060698196,0.896864345623378
+Vascular smooth muscle contraction,0.7680278087553132,0.1051518629203765,0.9200901618264052
+Vasopressin-regulated water reabsorption,0.5879191701727197,,0.5136186434315607
+Viral carcinogenesis,0.00032372540186051765,0.9987006678988628,0.6929303723667709
+Viral myocarditis,9.664088472155295e-09,0.9192595819250462,0.8651003634451919
+Vitamin digestion and absorption,0.6727467869611315,0.4999784841151393,0.6219761119567314
+Wnt signaling pathway,0.1929035095066998,0.6711411886850801,0.8835350255051094
+alpha-Linolenic acid metabolism,,0.0331053669197804,0.2613631306402563
+beta-Alanine metabolism,0.7745519727836904,0.6032014043404286,
+cAMP signaling pathway,0.2532168938335664,0.0179979932450931,0.4611821014332201
+cGMP-PKG signaling pathway,0.3812149838902618,0.8709017906437516,0.9925297125109196
+mRNA surveillance pathway,0.9363695824486508,0.7621085726753557,0.5325469270201381
+mTOR signaling pathway,0.8343097004118427,,0.8649282169130451
+p53 signaling pathway,0.0420009467710441,,

Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/retrieval_plan.json

@@ -0,0 +1,708 @@
+{
+  "query": "You are running a bioagent-bench task with local files already prepared.\n\nTask ID: alzheimer-mouse\nTask name: Alzheimer Mouse Models: Comparative Pathway Analysis\nBenchmark prompt:\nPerform 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\nPhagosome Homo sapiens hsa04145,1.5045916403148935e-09,0.3102788532065793,0.4443015705596512\n</example> \nData background:\nAnalyze 5xFAD, 3xTG-AD, and PS301S mouse models: normalize counts, perform differential expression, run KEGG pathway enrichment, and compare shared pathways across models.\n\nConstraints:\n1. Use only the benchmark inputs and references explicitly listed below.\n2. Save the required final deliverables exactly to the paths listed below.\n3. Save all intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658\n4. Keep final deliverables in the same schema/format requested by the benchmark prompt.\n5. Return a concise final summary after writing the required files.\n\nTask-specific instruction:\nUse the provided mouse count and DEA files as inputs. Report the shared/comparative KEGG pathway set supported by the three model analyses, with the requested pathway and p-value columns.\n\nBenchmark data policy:\n- Allowed input data directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data\n- Allowed reference directory: <none>\n- Allowed scratch/output directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658\n- Forbidden truth/results directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/results\n- Forbidden sibling benchmark task directories: /225040511/project/bioagent-bench/dataset/<any task other than alzheimer-mouse>\n- Do not inspect previous bioagent-bench-runs or sibling task outputs as data sources.\n- Do not download external databases or install new packages during the benchmark run.\n\nInput data directory:\n/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data\nVisible input files:\n- 3xtgad_counts_clean.csv\n- 5xfad_counts_clean.csv\n- 5xfad_counts_integer.csv\n- DEA_3xTGAD.csv\n- DEA_5xFAD.csv\n- DEA_PS3O1S.csv\n- GSE161904_Raw_gene_counts_cortex.txt\n- GSE168137_countList.txt\n- entrez_3xtgad.txt\n- entrez_5xfad.txt\n- entrez_ps301s.txt\n- run_deseq2_5xfad.R\n\nReference data directory:\n<none>\nVisible reference files:\n- <none>\n\nRequired final output paths:\n- pathway_comparison.csv: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/pathway_comparison.csv",
+  "query_context": {},
+  "mcp_enabled": true,
+  "mcp_config": "/225040511/project/Biomni/experiments/bioagent_bench/configs/mcp_scale_100.yaml",
+  "planning_context_text": "{\"prompt\": \"You are running a bioagent-bench task with local files already prepared.\\n\\nTask ID: alzheimer-mouse\\nTask name: Alzheimer Mouse Models: Comparative Pathway Analysis\\nBenchmark prompt:\\nPerform 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\\nPhagosome Homo sapiens hsa04145,1.5045916403148935e-09,0.3102788532065793,0.4443015705596512\\n</example> \\nData background:\\nAnalyze 5xFAD, 3xTG-AD, and PS301S mouse models: normalize counts, perform differential expression, run KEGG pathway enrichment, and compare shared pathways across models.\\n\\nConstraints:\\n1. Use only the benchmark inputs and references explicitly listed below.\\n2. Save the required final deliverables exactly to the paths listed below.\\n3. Save all intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658\\n4. Keep final deliverables in the same schema/format requested by the benchmark prompt.\\n5. Return a concise final summary after writing the required files.\\n\\nTask-specific instruction:\\nUse the provided mouse count and DEA files as inputs. Report the shared/comparative KEGG pathway set supported by the three model analyses, with the requested pathway and p-value columns.\\n\\nBenchmark data policy:\\n- Allowed input data directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data\\n- Allowed reference directory: <none>\\n- Allowed scratch/output directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658\\n- Forbidden truth/results directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/results\\n- Forbidden sibling benchmark task directories: /225040511/project/bioagent-bench/dataset/<any task other than alzheimer-mouse>\\n- Do not inspect previous bioagent-bench-runs or sibling task outputs as data sources.\\n- Do not download external databases or install new packages during the benchmark run.\\n\\nInput data directory:\\n/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data\\nVisible input files:\\n- 3xtgad_counts_clean.csv\\n- 5xfad_counts_clean.csv\\n- 5xfad_counts_integer.csv\\n- DEA_3xTGAD.csv\\n- DEA_5xFAD.csv\\n- DEA_PS3O1S.csv\\n- GSE161904_Raw_gene_counts_cortex.txt\\n- GSE168137_countList.txt\\n- entrez_3xtgad.txt\\n- entrez_5xfad.txt\\n- entrez_ps301s.txt\\n- run_deseq2_5xfad.R\\n\\nReference data directory:\\n<none>\\nVisible reference files:\\n- <none>\\n\\nRequired final output paths:\\n- pathway_comparison.csv: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/pathway_comparison.csv\", \"selected_resources_names\": {\"tools\": [{\"description\": \"Executes the provided Python command in the notebook environment and returns the output.\", \"name\": \"run_python_repl\", \"optional_parameters\": [], \"required_parameters\": [{\"default\": null, \"description\": \"Python command to execute in the notebook environment\", \"name\": \"command\", \"type\": \"str\"}], \"id\": 174}, {\"description\": \"Take a natural language prompt and convert it to a structured KEGG API query.\", \"name\": \"query_kegg\", \"optional_parameters\": [{\"name\": \"endpoint\", \"type\": \"str\", \"description\": \"Direct KEGG endpoint to query\", \"default\": null}, {\"name\": \"verbose\", \"type\": \"bool\", \"description\": \"Return detailed results\", \"default\": true}], \"required_parameters\": [{\"name\": \"prompt\", \"type\": \"str\", \"description\": \"Natural language query about KEGG data\", \"default\": null}], \"id\": 182}, {\"description\": \"Query the Reactome database using natural language or a direct endpoint; optionally download pathway diagrams.\", \"name\": \"query_reactome\", \"optional_parameters\": [{\"name\": \"endpoint\", \"type\": \"str\", \"description\": \"Direct endpoint or full URL\", \"default\": null}, {\"name\": \"download\", \"type\": \"bool\", \"description\": \"Download pathway diagram if available\", \"default\": false}, {\"name\": \"output_dir\", \"type\": \"str\", \"description\": \"Directory to save downloads\", \"default\": null}, {\"name\": \"verbose\", \"type\": \"bool\", \"description\": \"Return detailed results\", \"default\": true}], \"required_parameters\": [{\"name\": \"prompt\", \"type\": \"str\", \"description\": \"Natural language query about biological pathways\", \"default\": null}], \"id\": 200}, {\"description\": \"Returns a list of supported databases for gene set enrichment analysis.\", \"name\": \"get_gene_set_enrichment_analysis_supported_database_list\", \"optional_parameters\": [], \"required_parameters\": [], \"id\": 82}, {\"description\": \"Perform enrichment analysis for a list of genes, with optional background gene set and plotting functionality.\", \"name\": \"gene_set_enrichment_analysis\", \"optional_parameters\": [{\"default\": 10, \"description\": \"Number of top pathways to return\", \"name\": \"top_k\", \"type\": \"int\"}, {\"default\": \"ontology\", \"description\": \"Database to use for enrichment analysis (e.g., pathway, transcription, ontology)\", \"name\": \"database\", \"type\": \"str\"}, {\"default\": null, \"description\": \"List of background genes to use for enrichment analysis\", \"name\": \"background_list\", \"type\": \"list\"}, {\"default\": false, \"description\": \"Generate a bar plot of the top K enrichment results\", \"name\": \"plot\", \"type\": \"bool\"}], \"required_parameters\": [{\"default\": null, \"description\": \"List of gene symbols to analyze\", \"name\": \"genes\", \"type\": \"list\"}], \"id\": 83}, {\"description\": \"Analyze chromatin interactions from Hi-C data to identify enhancer-promoter interactions and TADs.\", \"name\": \"analyze_chromatin_interactions\", \"optional_parameters\": [{\"default\": \"./output\", \"description\": \"Directory to save output files\", \"name\": \"output_dir\", \"type\": \"str\"}], \"required_parameters\": [{\"default\": null, \"description\": \"Path to the Hi-C data file (.cool or .hic format)\", \"name\": \"hic_file_path\", \"type\": \"str\"}, {\"default\": null, \"description\": \"Path to BED file containing genomic coordinates of regulatory elements (enhancers, promoters, CTCF sites, etc.)\", \"name\": \"regulatory_elements_bed\", \"type\": \"str\"}], \"id\": 84}, {\"name\": \"csvtk_headers\", \"description\": \"Print headers of a CSV/TSV file.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9c23507ba0>\", \"id\": 237}, {\"name\": \"csvtk_dim\", \"description\": \"Dimensions of CSV file (rows and columns).\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9c23507b00>\", \"id\": 238}, {\"name\": \"csvtk_ncol\", \"description\": \"Print number of columns.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804040>\", \"id\": 239}, {\"name\": \"csvtk_nrow\", \"description\": \"Print number of records (rows).\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba18040e0>\", \"id\": 240}, {\"name\": \"csvtk_corr\", \"description\": \"Calculate Pearson correlation between two columns.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"ignore_illegal_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"ignore_illegal_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804180>\", \"id\": 241}, {\"name\": \"csvtk_summary\", \"description\": \"Summary statistics of selected numeric or text fields (groupby group fields).\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"groups\": {\"type\": \"string\", \"description\": \"\", \"default\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"groups\", \"type\": \"string\", \"description\": \"\", \"default\": \"\"}, {\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804220>\", \"id\": 242}, {\"name\": \"csvtk_cut\", \"description\": \"Select and arrange fields/columns.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba18042c0>\", \"id\": 243}, {\"name\": \"csvtk_grep\", \"description\": \"Grep data by selected fields with patterns/regular expressions.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"pattern\": {\"type\": \"string\", \"description\": \"\"}, \"ignore_case\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"invert_match\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"use_regexp\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"pattern\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"ignore_case\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"invert_match\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"use_regexp\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804360>\", \"id\": 244}, {\"name\": \"csvtk_filter\", \"description\": \"Filter rows by values of selected fields with arithmetic expression (e.g., \\\"col1 > 10\\\").\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"filter_expr\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"filter_expr\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804400>\", \"id\": 245}, {\"name\": \"csvtk_filter2\", \"description\": \"Filter rows by awk-like arithmetic/string expressions (e.g., '$1 > 10 && $2 == \\\"A\\\"').\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"expression\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"expression\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba18044a0>\", \"id\": 246}, {\"name\": \"csvtk_sort\", \"description\": \"Sort by selected fields. Keys format: 1:n (numeric), 2:r (reverse).\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"keys\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"keys\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804540>\", \"id\": 247}, {\"name\": \"csvtk_join\", \"description\": \"Join files by selected fields.\", \"parameters\": {\"file1\": {\"type\": \"string\", \"description\": \"\"}, \"file2\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"left_join\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"outer_join\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"file1\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"file2\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"left_join\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"outer_join\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba18045e0>\", \"id\": 248}, {\"name\": \"csvtk_concat\", \"description\": \"Concatenate CSV/TSV files by rows.\", \"parameters\": {\"files\": {\"type\": \"array\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"files\", \"type\": \"array\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804680>\", \"id\": 249}, {\"name\": \"csvtk_uniq\", \"description\": \"Unique data without sorting.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804720>\", \"id\": 250}, {\"name\": \"csvtk_freq\", \"description\": \"Frequencies of selected fields.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"sort_by_freq\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"sort_by_freq\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba18047c0>\", \"id\": 251}, {\"name\": \"csvtk_mutate\", \"description\": \"Create new column from selected fields by regular expression.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"name\": {\"type\": \"string\", \"description\": \"\"}, \"pattern\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"name\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"pattern\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804860>\", \"id\": 252}, {\"name\": \"csvtk_mutate2\", \"description\": \"Create a new column from selected fields by awk-like arithmetic/string expressions.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"name\": {\"type\": \"string\", \"description\": \"\"}, \"expression\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"name\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"expression\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804900>\", \"id\": 253}, {\"name\": \"csvtk_rename\", \"description\": \"Rename column names with new names.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"names\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"names\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba18049a0>\", \"id\": 254}, {\"name\": \"csvtk_replace\", \"description\": \"Replace data of selected fields by regular expression.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"pattern\": {\"type\": \"string\", \"description\": \"\"}, \"replacement\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"pattern\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"replacement\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804a40>\", \"id\": 255}, {\"name\": \"csvtk_round\", \"description\": \"Round float to n decimal places.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"decimal_places\": {\"type\": \"number\", \"description\": \"\", \"default\": 2}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"decimal_places\", \"type\": \"number\", \"description\": \"\", \"default\": 2}, {\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804ae0>\", \"id\": 256}, {\"name\": \"csvtk_transpose\", \"description\": \"Transpose CSV data.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804b80>\", \"id\": 257}, {\"name\": \"csvtk_sep\", \"description\": \"Separate column into multiple columns.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"sep_char\": {\"type\": \"string\", \"description\": \"\"}, \"names\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"sep_char\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"names\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804c20>\", \"id\": 258}, {\"name\": \"csvtk_gather\", \"description\": \"Gather columns into key-value pairs (pivot_longer).\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"key_col\": {\"type\": \"string\", \"description\": \"\"}, \"value_col\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"key_col\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"value_col\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804cc0>\", \"id\": 259}, {\"name\": \"csvtk_spread\", \"description\": \"Spread a key-value pair across multiple columns (pivot_wider).\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"key_col\": {\"type\": \"string\", \"description\": \"\"}, \"value_col\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"key_col\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"value_col\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804d60>\", \"id\": 260}, {\"name\": \"csvtk_pretty\", \"description\": \"Convert CSV to a readable aligned table.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804e00>\", \"id\": 261}, {\"name\": \"csvtk_csv2md\", \"description\": \"Convert CSV to markdown format.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804ea0>\", \"id\": 262}, {\"name\": \"csvtk_csv2json\", \"description\": \"Convert CSV to JSON format.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804f40>\", \"id\": 263}, {\"name\": \"csvtk_xlsx2csv\", \"description\": \"Convert XLSX to CSV format.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"sheet_index\": {\"type\": \"number\", \"description\": \"\", \"default\": 1}, \"sheet_name\": {\"type\": \"string\", \"description\": \"\", \"default\": \"\"}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"sheet_index\", \"type\": \"number\", \"description\": \"\", \"default\": 1}, {\"name\": \"sheet_name\", \"type\": \"string\", \"description\": \"\", \"default\": \"\"}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1804fe0>\", \"id\": 264}, {\"name\": \"csvtk_fix\", \"description\": \"Fix CSV/TSV with different numbers of columns in rows.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1805080>\", \"id\": 265}, {\"name\": \"csvtk_fix_quotes\", \"description\": \"Fix malformed CSV/TSV caused by double-quotes.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1805120>\", \"id\": 266}, {\"name\": \"csvtk_del_quotes\", \"description\": \"Remove extra double quotes added by 'fix-quotes'.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba18051c0>\", \"id\": 267}, {\"name\": \"csvtk_head\", \"description\": \"Print first N records.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"number\": {\"type\": \"number\", \"description\": \"\", \"default\": 10}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"number\", \"type\": \"number\", \"description\": \"\", \"default\": 10}, {\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1805260>\", \"id\": 268}, {\"name\": \"csvtk_sample\", \"description\": \"Sampling by proportion.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"proportion\": {\"type\": \"number\", \"description\": \"\", \"default\": 0.1}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"proportion\", \"type\": \"number\", \"description\": \"\", \"default\": 0.1}, {\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1805300>\", \"id\": 269}, {\"name\": \"csvtk_split\", \"description\": \"Split CSV/TSV into multiple files according to column values.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"out_dir\": {\"type\": \"string\", \"description\": \"\", \"default\": \".\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"out_dir\", \"type\": \"string\", \"description\": \"\", \"default\": \".\"}, {\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba18053a0>\", \"id\": 270}, {\"name\": \"csvtk_comb\", \"description\": \"Compute combinations of items at every row.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"number\": {\"type\": \"number\", \"description\": \"\", \"default\": 2}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"number\", \"type\": \"number\", \"description\": \"\", \"default\": 2}, {\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1805440>\", \"id\": 271}, {\"name\": \"csvtk_fmtdate\", \"description\": \"Format date of selected fields.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"format_str\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"format_str\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba18054e0>\", \"id\": 272}, {\"name\": \"csvtk_fold\", \"description\": \"Fold multiple values of a field into cells of groups.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"groups\": {\"type\": \"string\", \"description\": \"\", \"default\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"groups\", \"type\": \"string\", \"description\": \"\", \"default\": \"\"}, {\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1805580>\", \"id\": 273}, {\"name\": \"csvtk_unfold\", \"description\": \"Unfold multiple values in cells of a field.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"sep_char\": {\"type\": \"string\", \"description\": \"\", \"default\": \",\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"sep_char\", \"type\": \"string\", \"description\": \"\", \"default\": \",\"}, {\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1805620>\", \"id\": 274}, {\"name\": \"csvtk_plot\", \"description\": \"Plot common figures (line, hist, box, etc.).\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"plot_type\": {\"type\": \"string\", \"description\": \"\"}, \"x_field\": {\"type\": \"string\", \"description\": \"\"}, \"y_field\": {\"type\": \"string\", \"description\": \"\", \"default\": \"\"}, \"title\": {\"type\": \"string\", \"description\": \"\", \"default\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"plot.png\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"plot_type\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"x_field\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"y_field\", \"type\": \"string\", \"description\": \"\", \"default\": \"\"}, {\"name\": \"title\", \"type\": \"string\", \"description\": \"\", \"default\": \"\"}, {\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"plot.png\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba18056c0>\", \"id\": 275}, {\"name\": \"csvtk_version\", \"description\": \"Print version information.\", \"parameters\": {}, \"required_parameters\": [], \"optional_parameters\": [], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7f9ba1805760>\", \"id\": 276}], \"data_lake\": [], \"libraries\": [\"pandas\", \"numpy\", \"scipy\", \"scikit-learn\", \"matplotlib\", \"seaborn\", \"statsmodels\", \"gseapy\", \"biopython\", \"DESeq2\", \"clusterProfiler\", \"edgeR\", \"limma\"], \"know_how\": []}}",
+  "planning_context_tokens": 12881,
+  "planning_context_chars": 45691,
+  "planning_latency_seconds": 3.106582012027502,
+  "total_runtime_seconds": 1676.0743004567921,
+  "token_usage": {
+    "prompt_tokens": 917883,
+    "completion_tokens": 15996,
+    "total_tokens": 933879,
+    "llm_call_count": 40
+  },
+  "selected_resources": {
+    "tools": [
+      {
+        "name": "run_python_repl",
+        "module": "biomni.tool.support_tools",
+        "description": "Executes the provided Python command in the notebook environment and returns the output."
+      },
+      {
+        "name": "query_kegg",
+        "module": "biomni.tool.database",
+        "description": "Take a natural language prompt and convert it to a structured KEGG API query."
+      },
+      {
+        "name": "query_reactome",
+        "module": "biomni.tool.database",
+        "description": "Query the Reactome database using natural language or a direct endpoint; optionally download pathway diagrams."
+      },
+      {
+        "name": "get_gene_set_enrichment_analysis_supported_database_list",
+        "module": "biomni.tool.genomics",
+        "description": "Returns a list of supported databases for gene set enrichment analysis."
+      },
+      {
+        "name": "gene_set_enrichment_analysis",
+        "module": "biomni.tool.genomics",
+        "description": "Perform enrichment analysis for a list of genes, with optional background gene set and plotting functionality."
+      },
+      {
+        "name": "analyze_chromatin_interactions",
+        "module": "biomni.tool.genomics",
+        "description": "Analyze chromatin interactions from Hi-C data to identify enhancer-promoter interactions and TADs."
+      },
+      {
+        "name": "csvtk_headers",
+        "module": "mcp_servers.csvtk",
+        "description": "Print headers of a CSV/TSV file."
+      },
+      {
+        "name": "csvtk_dim",
+        "module": "mcp_servers.csvtk",
+        "description": "Dimensions of CSV file (rows and columns)."
+      },
+      {
+        "name": "csvtk_ncol",
+        "module": "mcp_servers.csvtk",
+        "description": "Print number of columns."
+      },
+      {
+        "name": "csvtk_nrow",
+        "module": "mcp_servers.csvtk",
+        "description": "Print number of records (rows)."
+      },
+      {
+        "name": "csvtk_corr",
+        "module": "mcp_servers.csvtk",
+        "description": "Calculate Pearson correlation between two columns."
+      },
+      {
+        "name": "csvtk_summary",
+        "module": "mcp_servers.csvtk",
+        "description": "Summary statistics of selected numeric or text fields (groupby group fields)."
+      },
+      {
+        "name": "csvtk_cut",
+        "module": "mcp_servers.csvtk",
+        "description": "Select and arrange fields/columns."
+      },
+      {
+        "name": "csvtk_grep",
+        "module": "mcp_servers.csvtk",
+        "description": "Grep data by selected fields with patterns/regular expressions."
+      },
+      {
+        "name": "csvtk_filter",
+        "module": "mcp_servers.csvtk",
+        "description": "Filter rows by values of selected fields with arithmetic expression (e.g., \"col1 > 10\")."
+      },
+      {
+        "name": "csvtk_filter2",
+        "module": "mcp_servers.csvtk",
+        "description": "Filter rows by awk-like arithmetic/string expressions (e.g., '$1 > 10 && $2 == \"A\"')."
+      },
+      {
+        "name": "csvtk_sort",
+        "module": "mcp_servers.csvtk",
+        "description": "Sort by selected fields. Keys format: 1:n (numeric), 2:r (reverse)."
+      },
+      {
+        "name": "csvtk_join",
+        "module": "mcp_servers.csvtk",
+        "description": "Join files by selected fields."
+      },
+      {
+        "name": "csvtk_concat",
+        "module": "mcp_servers.csvtk",
+        "description": "Concatenate CSV/TSV files by rows."
+      },
+      {
+        "name": "csvtk_uniq",
+        "module": "mcp_servers.csvtk",
+        "description": "Unique data without sorting."
+      },
+      {
+        "name": "csvtk_freq",
+        "module": "mcp_servers.csvtk",
+        "description": "Frequencies of selected fields."
+      },
+      {
+        "name": "csvtk_mutate",
+        "module": "mcp_servers.csvtk",
+        "description": "Create new column from selected fields by regular expression."
+      },
+      {
+        "name": "csvtk_mutate2",
+        "module": "mcp_servers.csvtk",
+        "description": "Create a new column from selected fields by awk-like arithmetic/string expressions."
+      },
+      {
+        "name": "csvtk_rename",
+        "module": "mcp_servers.csvtk",
+        "description": "Rename column names with new names."
+      },
+      {
+        "name": "csvtk_replace",
+        "module": "mcp_servers.csvtk",
+        "description": "Replace data of selected fields by regular expression."
+      },
+      {
+        "name": "csvtk_round",
+        "module": "mcp_servers.csvtk",
+        "description": "Round float to n decimal places."
+      },
+      {
+        "name": "csvtk_transpose",
+        "module": "mcp_servers.csvtk",
+        "description": "Transpose CSV data."
+      },
+      {
+        "name": "csvtk_sep",
+        "module": "mcp_servers.csvtk",
+        "description": "Separate column into multiple columns."
+      },
+      {
+        "name": "csvtk_gather",
+        "module": "mcp_servers.csvtk",
+        "description": "Gather columns into key-value pairs (pivot_longer)."
+      },
+      {
+        "name": "csvtk_spread",
+        "module": "mcp_servers.csvtk",
+        "description": "Spread a key-value pair across multiple columns (pivot_wider)."
+      },
+      {
+        "name": "csvtk_pretty",
+        "module": "mcp_servers.csvtk",
+        "description": "Convert CSV to a readable aligned table."
+      },
+      {
+        "name": "csvtk_csv2md",
+        "module": "mcp_servers.csvtk",
+        "description": "Convert CSV to markdown format."
+      },
+      {
+        "name": "csvtk_csv2json",
+        "module": "mcp_servers.csvtk",
+        "description": "Convert CSV to JSON format."
+      },
+      {
+        "name": "csvtk_xlsx2csv",
+        "module": "mcp_servers.csvtk",
+        "description": "Convert XLSX to CSV format."
+      },
+      {
+        "name": "csvtk_fix",
+        "module": "mcp_servers.csvtk",
+        "description": "Fix CSV/TSV with different numbers of columns in rows."
+      },
+      {
+        "name": "csvtk_fix_quotes",
+        "module": "mcp_servers.csvtk",
+        "description": "Fix malformed CSV/TSV caused by double-quotes."
+      },
+      {
+        "name": "csvtk_del_quotes",
+        "module": "mcp_servers.csvtk",
+        "description": "Remove extra double quotes added by 'fix-quotes'."
+      },
+      {
+        "name": "csvtk_head",
+        "module": "mcp_servers.csvtk",
+        "description": "Print first N records."
+      },
+      {
+        "name": "csvtk_sample",
+        "module": "mcp_servers.csvtk",
+        "description": "Sampling by proportion."
+      },
+      {
+        "name": "csvtk_split",
+        "module": "mcp_servers.csvtk",
+        "description": "Split CSV/TSV into multiple files according to column values."
+      },
+      {
+        "name": "csvtk_comb",
+        "module": "mcp_servers.csvtk",
+        "description": "Compute combinations of items at every row."
+      },
+      {
+        "name": "csvtk_fmtdate",
+        "module": "mcp_servers.csvtk",
+        "description": "Format date of selected fields."
+      },
+      {
+        "name": "csvtk_fold",
+        "module": "mcp_servers.csvtk",
+        "description": "Fold multiple values of a field into cells of groups."
+      },
+      {
+        "name": "csvtk_unfold",
+        "module": "mcp_servers.csvtk",
+        "description": "Unfold multiple values in cells of a field."
+      },
+      {
+        "name": "csvtk_plot",
+        "module": "mcp_servers.csvtk",
+        "description": "Plot common figures (line, hist, box, etc.)."
+      },
+      {
+        "name": "csvtk_version",
+        "module": "mcp_servers.csvtk",
+        "description": "Print version information."
+      }
+    ],
+    "data_lake": [],
+    "libraries": [
+      {
+        "name": "pandas",
+        "description": "[Python Package] A fast, powerful, and flexible data analysis and manipulation library for Python."
+      },
+      {
+        "name": "numpy",
+        "description": "[Python Package] The fundamental package for scientific computing with Python, providing support for arrays, matrices, and mathematical functions."
+      },
+      {
+        "name": "scipy",
+        "description": "[Python Package] A Python library for scientific and technical computing, including modules for optimization, linear algebra, integration, and statistics."
+      },
+      {
+        "name": "scikit-learn",
+        "description": "[Python Package] A machine learning library featuring various classification, regression, and clustering algorithms."
+      },
+      {
+        "name": "matplotlib",
+        "description": "[Python Package] A comprehensive library for creating static, animated, and interactive visualizations in Python."
+      },
+      {
+        "name": "seaborn",
+        "description": "[Python Package] A statistical data visualization library based on matplotlib with a high-level interface for drawing attractive statistical graphics."
+      },
+      {
+        "name": "statsmodels",
+        "description": "[Python Package] A Python module for statistical modeling and econometrics, including descriptive statistics and estimation of statistical models."
+      },
+      {
+        "name": "gseapy",
+        "description": "[Python Package] A Python wrapper for Gene Set Enrichment Analysis (GSEA) and visualization."
+      },
+      {
+        "name": "biopython",
+        "description": "[Python Package] A set of tools for biological computation including parsers for bioinformatics files, access to online services, and interfaces to common bioinformatics programs."
+      },
+      {
+        "name": "DESeq2",
+        "description": "[R Package] Differential gene expression analysis based on the negative binomial distribution. Use with subprocess.run(['Rscript', '-e', 'library(DESeq2); ...'])."
+      },
+      {
+        "name": "clusterProfiler",
+        "description": "[R Package] A package for statistical analysis and visualization of functional profiles for genes and gene clusters. Use with subprocess calls."
+      },
+      {
+        "name": "edgeR",
+        "description": "[R Package] Empirical Analysis of Digital Gene Expression Data in R, for differential expression analysis. Use with subprocess calls."
+      },
+      {
+        "name": "limma",
+        "description": "[R Package] Linear Models for Microarray Data, for differential expression analysis. Use with subprocess calls."
+      }
+    ],
+    "know_how": []
+  },
+  "selected_resource_names": {
+    "tools": [
+      "run_python_repl",
+      "query_kegg",
+      "query_reactome",
+      "get_gene_set_enrichment_analysis_supported_database_list",
+      "gene_set_enrichment_analysis",
+      "analyze_chromatin_interactions",
+      "csvtk_headers",
+      "csvtk_dim",
+      "csvtk_ncol",
+      "csvtk_nrow",
+      "csvtk_corr",
+      "csvtk_summary",
+      "csvtk_cut",
+      "csvtk_grep",
+      "csvtk_filter",
+      "csvtk_filter2",
+      "csvtk_sort",
+      "csvtk_join",
+      "csvtk_concat",
+      "csvtk_uniq",
+      "csvtk_freq",
+      "csvtk_mutate",
+      "csvtk_mutate2",
+      "csvtk_rename",
+      "csvtk_replace",
+      "csvtk_round",
+      "csvtk_transpose",
+      "csvtk_sep",
+      "csvtk_gather",
+      "csvtk_spread",
+      "csvtk_pretty",
+      "csvtk_csv2md",
+      "csvtk_csv2json",
+      "csvtk_xlsx2csv",
+      "csvtk_fix",
+      "csvtk_fix_quotes",
+      "csvtk_del_quotes",
+      "csvtk_head",
+      "csvtk_sample",
+      "csvtk_split",
+      "csvtk_comb",
+      "csvtk_fmtdate",
+      "csvtk_fold",
+      "csvtk_unfold",
+      "csvtk_plot",
+      "csvtk_version"
+    ],
+    "data_lake": [],
+    "libraries": [
+      "pandas",
+      "numpy",
+      "scipy",
+      "scikit-learn",
+      "matplotlib",
+      "seaborn",
+      "statsmodels",
+      "gseapy",
+      "biopython",
+      "DESeq2",
+      "clusterProfiler",
+      "edgeR",
+      "limma"
+    ],
+    "know_how": []
+  },
+  "registered_tool_count": 331,
+  "registered_tool_names": [
+    "fetch_supplementary_info_from_doi",
+    "query_arxiv",
+    "query_scholar",
+    "query_pubmed",
+    "search_google",
+    "extract_url_content",
+    "extract_pdf_content",
+    "advanced_web_search_claude",
+    "analyze_circular_dichroism_spectra",
+    "analyze_rna_secondary_structure_features",
+    "analyze_protease_kinetics",
+    "analyze_enzyme_kinetics_assay",
+    "analyze_itc_binding_thermodynamics",
+    "analyze_protein_conservation",
+    "split_modalities",
+    "prepare_input_for_nnunet",
+    "segment_with_nn_unet",
+    "create_segmentation_visualization",
+    "quick_rigid_registration",
+    "quick_affine_registration",
+    "quick_deformable_registration",
+    "batch_register_images",
+    "calculate_similarity_metrics",
+    "create_registration_visualization",
+    "analyze_cell_migration_metrics",
+    "perform_crispr_cas9_genome_editing",
+    "analyze_calcium_imaging_data",
+    "analyze_in_vitro_drug_release_kinetics",
+    "analyze_myofiber_morphology",
+    "decode_behavior_from_neural_trajectories",
+    "simulate_whole_cell_ode_model",
+    "predict_protein_disorder_regions",
+    "analyze_cell_morphology_and_cytoskeleton",
+    "analyze_tissue_deformation_flow",
+    "find_n_glycosylation_motifs",
+    "predict_o_glycosylation_hotspots",
+    "list_glycoengineering_resources",
+    "analyze_ddr_network_in_cancer",
+    "analyze_cell_senescence_and_apoptosis",
+    "detect_and_annotate_somatic_mutations",
+    "detect_and_characterize_structural_variations",
+    "perform_gene_expression_nmf_analysis",
+    "analyze_copy_number_purity_ploidy_and_focal_events",
+    "quantify_cell_cycle_phases_from_microscopy",
+    "quantify_and_cluster_cell_motility",
+    "perform_facs_cell_sorting",
+    "analyze_flow_cytometry_immunophenotyping",
+    "analyze_mitochondrial_morphology_and_potential",
+    "annotate_open_reading_frames",
+    "annotate_plasmid",
+    "get_gene_coding_sequence",
+    "get_plasmid_sequence",
+    "align_sequences",
+    "pcr_simple",
+    "digest_sequence",
+    "find_restriction_sites",
+    "find_restriction_enzymes",
+    "find_sequence_mutations",
+    "design_knockout_sgrna",
+    "get_oligo_annealing_protocol",
+    "get_golden_gate_assembly_protocol",
+    "get_bacterial_transformation_protocol",
+    "design_primer",
+    "design_verification_primers",
+    "design_golden_gate_oligos",
+    "golden_gate_assembly",
+    "liftover_coordinates",
+    "bayesian_finemapping_with_deep_vi",
+    "analyze_cas9_mutation_outcomes",
+    "analyze_crispr_genome_editing",
+    "simulate_demographic_history",
+    "identify_transcription_factor_binding_sites",
+    "fit_genomic_prediction_model",
+    "perform_pcr_and_gel_electrophoresis",
+    "analyze_protein_phylogeny",
+    "annotate_celltype_scRNA",
+    "annotate_celltype_with_panhumanpy",
+    "create_scvi_embeddings_scRNA",
+    "create_harmony_embeddings_scRNA",
+    "get_uce_embeddings_scRNA",
+    "map_to_ima_interpret_scRNA",
+    "get_rna_seq_archs4",
+    "get_gene_set_enrichment_analysis_supported_database_list",
+    "gene_set_enrichment_analysis",
+    "analyze_chromatin_interactions",
+    "analyze_comparative_genomics_and_haplotypes",
+    "perform_chipseq_peak_calling_with_macs2",
+    "find_enriched_motifs_with_homer",
+    "analyze_genomic_region_overlap",
+    "unsupervised_celltype_transfer_between_scRNA_datasets",
+    "generate_embeddings_with_state",
+    "interspecies_gene_conversion",
+    "generate_gene_embeddings_with_ESM_models",
+    "generate_transcriptformer_embeddings",
+    "analyze_atac_seq_differential_accessibility",
+    "analyze_bacterial_growth_curve",
+    "isolate_purify_immune_cells",
+    "estimate_cell_cycle_phase_durations",
+    "track_immune_cells_under_flow",
+    "analyze_cfse_cell_proliferation",
+    "analyze_cytokine_production_in_cd4_tcells",
+    "analyze_ebv_antibody_titers",
+    "analyze_cns_lesion_histology",
+    "analyze_immunohistochemistry_image",
+    "optimize_anaerobic_digestion_process",
+    "analyze_arsenic_speciation_hplc_icpms",
+    "count_bacterial_colonies",
+    "annotate_bacterial_genome",
+    "enumerate_bacterial_cfu_by_serial_dilution",
+    "model_bacterial_growth_dynamics",
+    "quantify_biofilm_biomass_crystal_violet",
+    "segment_and_analyze_microbial_cells",
+    "segment_cells_with_deep_learning",
+    "simulate_generalized_lotka_volterra_dynamics",
+    "predict_rna_secondary_structure",
+    "simulate_microbial_population_dynamics",
+    "analyze_aortic_diameter_and_geometry",
+    "analyze_atp_luminescence_assay",
+    "analyze_thrombus_histology",
+    "analyze_intracellular_calcium_with_rhod2",
+    "quantify_corneal_nerve_fibers",
+    "segment_and_quantify_cells_in_multiplexed_images",
+    "analyze_bone_microct_morphometry",
+    "run_diffdock_with_smiles",
+    "docking_autodock_vina",
+    "run_autosite",
+    "retrieve_topk_repurposing_drugs_from_disease_txgnn",
+    "predict_admet_properties",
+    "predict_binding_affinity_protein_1d_sequence",
+    "analyze_accelerated_stability_of_pharmaceutical_formulations",
+    "run_3d_chondrogenic_aggregate_assay",
+    "grade_adverse_events_using_vcog_ctcae",
+    "analyze_radiolabeled_antibody_biodistribution",
+    "estimate_alpha_particle_radiotherapy_dosimetry",
+    "perform_mwas_cyp2c19_metabolizer_status",
+    "calculate_physicochemical_properties",
+    "analyze_xenograft_tumor_growth_inhibition",
+    "analyze_pixel_distribution",
+    "find_roi_from_image",
+    "analyze_western_blot",
+    "query_drug_interactions",
+    "check_drug_combination_safety",
+    "analyze_interaction_mechanisms",
+    "find_alternative_drugs_ddinter",
+    "query_fda_adverse_events",
+    "get_fda_drug_label_info",
+    "check_fda_drug_recalls",
+    "analyze_fda_safety_signals",
+    "reconstruct_3d_face_from_mri",
+    "analyze_abr_waveform_p1_metrics",
+    "analyze_ciliary_beat_frequency",
+    "analyze_protein_colocalization",
+    "perform_cosinor_analysis",
+    "calculate_brain_adc_map",
+    "analyze_endolysosomal_calcium_dynamics",
+    "analyze_fatty_acid_composition_by_gc",
+    "analyze_hemodynamic_data",
+    "simulate_thyroid_hormone_pharmacokinetics",
+    "quantify_amyloid_beta_plaques",
+    "engineer_bacterial_genome_for_therapeutic_delivery",
+    "analyze_bacterial_growth_rate",
+    "analyze_barcode_sequencing_data",
+    "analyze_bifurcation_diagram",
+    "create_biochemical_network_sbml_model",
+    "optimize_codons_for_heterologous_expression",
+    "simulate_gene_circuit_with_growth_feedback",
+    "identify_fas_functional_domains",
+    "perform_flux_balance_analysis",
+    "model_protein_dimerization_network",
+    "simulate_metabolic_network_perturbation",
+    "simulate_protein_signaling_network",
+    "compare_protein_structures",
+    "simulate_renin_angiotensin_system_dynamics",
+    "query_chatnt",
+    "run_python_repl",
+    "read_function_source_code",
+    "download_synapse_data",
+    "query_uniprot",
+    "query_alphafold",
+    "query_interpro",
+    "query_pdb",
+    "query_pdb_identifiers",
+    "query_kegg",
+    "query_stringdb",
+    "query_iucn",
+    "query_paleobiology",
+    "query_jaspar",
+    "query_worms",
+    "query_cbioportal",
+    "query_clinvar",
+    "query_geo",
+    "query_dbsnp",
+    "query_ucsc",
+    "query_ensembl",
+    "query_opentarget",
+    "query_monarch",
+    "query_openfda",
+    "query_gwas_catalog",
+    "query_gnomad",
+    "blast_sequence",
+    "query_reactome",
+    "query_regulomedb",
+    "query_pride",
+    "query_gtopdb",
+    "query_remap",
+    "query_mpd",
+    "query_emdb",
+    "query_synapse",
+    "query_pubchem",
+    "query_chembl",
+    "query_unichem",
+    "query_clinicaltrials",
+    "query_dailymed",
+    "query_quickgo",
+    "query_encode",
+    "region_to_ccre_screen",
+    "get_genes_near_ccre",
+    "test_pylabrobot_script",
+    "get_pylabrobot_documentation_liquid",
+    "get_pylabrobot_documentation_material",
+    "search_protocols",
+    "get_protocol_details",
+    "list_local_protocols",
+    "read_local_protocol",
+    "kallisto_index",
+    "kallisto_quant",
+    "kallisto_bus",
+    "kallisto_quant_tcc",
+    "kallisto_h5dump",
+    "kallisto_inspect",
+    "kallisto_version",
+    "kallisto_cite",
+    "kallisto_bus_list_technologies",
+    "kallisto_merge",
+    "kraken2_classify",
+    "kraken2_build_db",
+    "kraken2_inspect_db",
+    "csvtk_headers",
+    "csvtk_dim",
+    "csvtk_ncol",
+    "csvtk_nrow",
+    "csvtk_corr",
+    "csvtk_summary",
+    "csvtk_cut",
+    "csvtk_grep",
+    "csvtk_filter",
+    "csvtk_filter2",
+    "csvtk_sort",
+    "csvtk_join",
+    "csvtk_concat",
+    "csvtk_uniq",
+    "csvtk_freq",
+    "csvtk_mutate",
+    "csvtk_mutate2",
+    "csvtk_rename",
+    "csvtk_replace",
+    "csvtk_round",
+    "csvtk_transpose",
+    "csvtk_sep",
+    "csvtk_gather",
+    "csvtk_spread",
+    "csvtk_pretty",
+    "csvtk_csv2md",
+    "csvtk_csv2json",
+    "csvtk_xlsx2csv",
+    "csvtk_fix",
+    "csvtk_fix_quotes",
+    "csvtk_del_quotes",
+    "csvtk_head",
+    "csvtk_sample",
+    "csvtk_split",
+    "csvtk_comb",
+    "csvtk_fmtdate",
+    "csvtk_fold",
+    "csvtk_unfold",
+    "csvtk_plot",
+    "csvtk_version",
+    "megahit_assemble",
+    "megahit_core_contig2fastg",
+    "kaiju_classify",
+    "kaiju_makedb",
+    "kaiju_mkbwt",
+    "kaiju_mkfmi",
+    "kaiju_multi_classify",
+    "kaiju2krona",
+    "kaiju2table",
+    "kaiju_add_taxon_names",
+    "kaiju_merge_outputs",
+    "kaijux_search",
+    "kaijup_search",
+    "fastp_tool",
+    "spades_py",
+    "metaspades_py",
+    "rnaspades_py",
+    "plasmidspades_py",
+    "metaviralspades_py",
+    "coronaspades_py",
+    "biosyntheticspades_py",
+    "spades_test",
+    "spades_kmercount",
+    "spades_hammer",
+    "settings",
+    "scanpy_filter",
+    "scanpy_norm",
+    "scanpy_log1p",
+    "scanpy_hvg",
+    "scanpy_scale",
+    "scanpy_pca",
+    "scanpy_neighbors",
+    "scanpy_umap",
+    "scanpy_tsne",
+    "scanpy_diffexp",
+    "scanpy_louvain",
+    "scanpy_leiden",
+    "scanpy_paga",
+    "scanpy_cli_read",
+    "scanpy_cli_filter",
+    "scanpy_cli_norm",
+    "scanpy_cli_hvg",
+    "scanpy_cli_scale",
+    "scanpy_cli_regress",
+    "scanpy_cli_pca",
+    "scanpy_cli_neighbor",
+    "scanpy_cli_embed",
+    "scanpy_cli_cluster",
+    "scanpy_cli_diffexp",
+    "scanpy_cli_paga",
+    "scanpy_cli_dpt",
+    "scanpy_cli_integrate",
+    "scanpy_cli_multiplet",
+    "scanpy_cli_plot"
+  ]
+}

Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/run_metadata.json

@@ -0,0 +1,43 @@
+{
+  "task_id": "alzheimer-mouse",
+  "task_name": "Alzheimer Mouse Models: Comparative Pathway Analysis",
+  "run_dir": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658",
+  "dataset_dir": "/225040511/project/bioagent-bench/dataset/alzheimer-mouse",
+  "data_dir": "/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data",
+  "reference_dir": "/225040511/project/bioagent-bench/dataset/alzheimer-mouse/reference",
+  "agent_runtime_dir": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/agent_runtime",
+  "output_paths": [
+    "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/pathway_comparison.csv"
+  ],
+  "mcp_enabled": true,
+  "mcp_config": "/225040511/project/Biomni/experiments/bioagent_bench/configs/mcp_scale_100.yaml",
+  "agent_kwargs": {
+    "path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/agent_runtime",
+    "expected_data_lake_files": [],
+    "use_tool_retriever": true,
+    "timeout_seconds": 1200,
+    "llm": "deepseek-chat",
+    "source": "Custom",
+    "base_url": "https://api.deepseek.com/v1",
+    "api_key": "sk-06e6154722b84e89b081b1c9571838ef"
+  },
+  "query": "You are running a bioagent-bench task with local files already prepared.\n\nTask ID: alzheimer-mouse\nTask name: Alzheimer Mouse Models: Comparative Pathway Analysis\nBenchmark prompt:\nPerform 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\nPhagosome Homo sapiens hsa04145,1.5045916403148935e-09,0.3102788532065793,0.4443015705596512\n</example> \nData background:\nAnalyze 5xFAD, 3xTG-AD, and PS301S mouse models: normalize counts, perform differential expression, run KEGG pathway enrichment, and compare shared pathways across models.\n\nConstraints:\n1. Use only the benchmark inputs and references explicitly listed below.\n2. Save the required final deliverables exactly to the paths listed below.\n3. Save all intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658\n4. Keep final deliverables in the same schema/format requested by the benchmark prompt.\n5. Return a concise final summary after writing the required files.\n\nTask-specific instruction:\nUse the provided mouse count and DEA files as inputs. Report the shared/comparative KEGG pathway set supported by the three model analyses, with the requested pathway and p-value columns.\n\nBenchmark data policy:\n- Allowed input data directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data\n- Allowed reference directory: <none>\n- Allowed scratch/output directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658\n- Forbidden truth/results directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/results\n- Forbidden sibling benchmark task directories: /225040511/project/bioagent-bench/dataset/<any task other than alzheimer-mouse>\n- Do not inspect previous bioagent-bench-runs or sibling task outputs as data sources.\n- Do not download external databases or install new packages during the benchmark run.\n\nInput data directory:\n/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data\nVisible input files:\n- 3xtgad_counts_clean.csv\n- 5xfad_counts_clean.csv\n- 5xfad_counts_integer.csv\n- DEA_3xTGAD.csv\n- DEA_5xFAD.csv\n- DEA_PS3O1S.csv\n- GSE161904_Raw_gene_counts_cortex.txt\n- GSE168137_countList.txt\n- entrez_3xtgad.txt\n- entrez_5xfad.txt\n- entrez_ps301s.txt\n- run_deseq2_5xfad.R\n\nReference data directory:\n<none>\nVisible reference files:\n- <none>\n\nRequired final output paths:\n- pathway_comparison.csv: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/pathway_comparison.csv",
+  "timestamp_utc": "20260523_124658",
+  "runtime_environment": {
+    "execution_env_prefix": "/225040511/miniconda3/envs/biomni_e1",
+    "execution_python": "/225040511/miniconda3/envs/biomni_e1/bin/python",
+    "conda_default_env": "biomni_e1",
+    "conda_prefix": "/225040511/miniconda3/envs/biomni_e1"
+  },
+  "biomni_root": "/225040511/project/Biomni",
+  "post_run_metrics": {
+    "planning_latency_seconds": 3.106582012027502,
+    "total_runtime_seconds": 1676.0743004567921,
+    "planning_context_tokens": 12881,
+    "planning_context_chars": 45691,
+    "prompt_tokens": 917883,
+    "completion_tokens": 15996,
+    "total_tokens": 933879,
+    "llm_call_count": 40
+  }
+}

Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/run_summary.json

@@ -0,0 +1,23 @@
+{
+  "task_id": "alzheimer-mouse",
+  "run_dir": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658",
+  "outputs": [
+    {
+      "path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/pathway_comparison.csv",
+      "exists": true,
+      "size_bytes": 22462
+    }
+  ],
+  "planning_latency_seconds": 3.106582012027502,
+  "total_runtime_seconds": 1676.0743004567921,
+  "planning_context_tokens": 12881,
+  "planning_context_chars": 45691,
+  "prompt_tokens": 917883,
+  "completion_tokens": 15996,
+  "total_tokens": 933879,
+  "llm_call_count": 40,
+  "final_answer_path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/final_answer.txt",
+  "metadata_path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/run_metadata.json",
+  "retrieval_plan_path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/retrieval_plan.json",
+  "output_validation_path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/output_validation.json"
+}

Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/task_query.txt

@@ -0,0 +1,53 @@
+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. Save the required final deliverables exactly to the paths listed below.
+3. Save all intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658
+4. Keep final deliverables in the same schema/format requested by the benchmark prompt.
+5. Return a concise final summary after writing the required files.
+
+Task-specific instruction:
+Use the provided mouse count and DEA files as inputs. Report the shared/comparative KEGG pathway set supported by the three model analyses, with the requested pathway and p-value columns.
+
+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/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658
+- 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>
+- Do not inspect previous bioagent-bench-runs or sibling task outputs as data sources.
+- Do not download external databases or install new packages during the benchmark run.
+
+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/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/alzheimer-mouse_20260523_124658/pathway_comparison.csv

Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/comparative-genomics_20260523_124658/Micrococcus_luteus_AS2_db.pjs

@@ -0,0 +1,24 @@
+{
+  "version": "1.2",
+  "dbname": "Micrococcus_luteus_AS2_db",
+  "dbtype": "Protein",
+  "db-version": 5,
+  "description": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/comparative-genomics_20260523_124658/Micrococcus_luteus_AS2_proteins_clean.faa",
+  "number-of-letters": 1513041,
+  "number-of-sequences": 4885,
+  "last-updated": "2026-05-23T12:59:00",
+  "number-of-volumes": 1,
+  "bytes-total": 2618039,
+  "bytes-to-cache": 1557287,
+  "files": [
+    "Micrococcus_luteus_AS2_db.pdb",
+    "Micrococcus_luteus_AS2_db.phr",
+    "Micrococcus_luteus_AS2_db.pin",
+    "Micrococcus_luteus_AS2_db.pog",
+    "Micrococcus_luteus_AS2_db.pos",
+    "Micrococcus_luteus_AS2_db.pot",
+    "Micrococcus_luteus_AS2_db.psq",
+    "Micrococcus_luteus_AS2_db.ptf",
+    "Micrococcus_luteus_AS2_db.pto"
+  ]
+}

Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/comparative-genomics_20260523_124658/Micrococcus_luteus_SA211_db.pjs

@@ -0,0 +1,24 @@
+{
+  "version": "1.2",
+  "dbname": "Micrococcus_luteus_SA211_db",
+  "dbtype": "Protein",
+  "db-version": 5,
+  "description": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/comparative-genomics_20260523_124658/Micrococcus_luteus_SA211_proteins_clean.faa",
+  "number-of-letters": 1381861,
+  "number-of-sequences": 4364,
+  "last-updated": "2026-05-23T12:58:00",
+  "number-of-volumes": 1,
+  "bytes-total": 2407400,
+  "bytes-to-cache": 1421426,
+  "files": [
+    "Micrococcus_luteus_SA211_db.pdb",
+    "Micrococcus_luteus_SA211_db.phr",
+    "Micrococcus_luteus_SA211_db.pin",
+    "Micrococcus_luteus_SA211_db.pog",
+    "Micrococcus_luteus_SA211_db.pos",
+    "Micrococcus_luteus_SA211_db.pot",
+    "Micrococcus_luteus_SA211_db.psq",
+    "Micrococcus_luteus_SA211_db.ptf",
+    "Micrococcus_luteus_SA211_db.pto"
+  ]
+}

Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/comparative-genomics_20260523_124658/Micrococcus_sp_KBS0714_db.pjs

@@ -0,0 +1,24 @@
+{
+  "version": "1.2",
+  "dbname": "Micrococcus_sp_KBS0714_db",
+  "dbtype": "Protein",
+  "db-version": 5,
+  "description": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/comparative-genomics_20260523_124658/Micrococcus_sp_KBS0714_proteins_clean.faa",
+  "number-of-letters": 1398311,
+  "number-of-sequences": 4433,
+  "last-updated": "2026-05-23T12:56:00",
+  "number-of-volumes": 1,
+  "bytes-total": 2403137,
+  "bytes-to-cache": 1438489,
+  "files": [
+    "Micrococcus_sp_KBS0714_db.pdb",
+    "Micrococcus_sp_KBS0714_db.phr",
+    "Micrococcus_sp_KBS0714_db.pin",
+    "Micrococcus_sp_KBS0714_db.pog",
+    "Micrococcus_sp_KBS0714_db.pos",
+    "Micrococcus_sp_KBS0714_db.pot",
+    "Micrococcus_sp_KBS0714_db.psq",
+    "Micrococcus_sp_KBS0714_db.ptf",
+    "Micrococcus_sp_KBS0714_db.pto"
+  ]
+}

Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/comparative-genomics_20260523_124658/Micrococcus_sp_KD337_db.pjs

@@ -0,0 +1,24 @@
+{
+  "version": "1.2",
+  "dbname": "Micrococcus_sp_KD337_db",
+  "dbtype": "Protein",
+  "db-version": 5,
+  "description": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/comparative-genomics_20260523_124658/Micrococcus_sp_KD337_proteins_clean.faa",
+  "number-of-letters": 1450126,
+  "number-of-sequences": 4666,
+  "last-updated": "2026-05-23T13:01:00",
+  "number-of-volumes": 1,
+  "bytes-total": 2466803,
+  "bytes-to-cache": 1492393,
+  "files": [
+    "Micrococcus_sp_KD337_db.pdb",
+    "Micrococcus_sp_KD337_db.phr",
+    "Micrococcus_sp_KD337_db.pin",
+    "Micrococcus_sp_KD337_db.pog",
+    "Micrococcus_sp_KD337_db.pos",
+    "Micrococcus_sp_KD337_db.pot",
+    "Micrococcus_sp_KD337_db.psq",
+    "Micrococcus_sp_KD337_db.ptf",
+    "Micrococcus_sp_KD337_db.pto"
+  ]
+}

Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/comparative-genomics_20260523_124658/cluster_annotation_mapping.csv

@@ -0,0 +1,1157 @@
+cluster_number,consensus_annotation
+1,"K02038  pstA, phosphate transport system permease protein"
+2,"K01153  hsdR, type I restriction enzyme, R subunit [EC:3.1.21.3]"
+3,"K01153  hsdR, type I restriction enzyme, R subunit [EC:3.1.21.3]"
+4,"K01153  hsdR, type I restriction enzyme, R subunit [EC:3.1.21.3]"
+5,"K21791  redJ, thioesterase"
+6,"K02335  polA, DNA polymerase I [EC:2.7.7.7]"
+7,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+8,"K02036  pstB, phosphate transport system ATP-binding protein [EC:7.3.2.1]"
+9,"K02945  RP-S1, rpsA, small subunit ribosomal protein S1"
+10,"K16168  bpsB, srsB, methyltransferase"
+11,"K00859  coaE, dephospho-CoA kinase [EC:2.7.1.24]"
+12,"K00859  coaE, dephospho-CoA kinase [EC:2.7.1.24]"
+13,"K03702  uvrB, excinuclease ABC subunit B"
+14,"K02199  ccmG, dsbE, cytochrome c biogenesis protein CcmG, thiol:disulfide interchange protein DsbE"
+15,"K03306  TC.PIT, inorganic phosphate transporter, PiT family"
+16,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+17,"K06877  , DEAD/DEAH box helicase domain-containing protein"
+18,"K00595  cobL-cbiET, precorrin-6B C5,15-methyltransferase / cobalt-precorrin-6B C5,C15-methyltransferase [EC:2.1.1.132 2.1.1.289 2.1.1.196]"
+19,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+20,"K03701  uvrA, excinuclease ABC subunit A"
+21,"K00655  plsC, 1-acyl-sn-glycerol-3-phosphate acyltransferase [EC:2.3.1.51]"
+22,"K03703  uvrC, excinuclease ABC subunit C"
+23,"K06958  rapZ, RNase adapter protein RapZ"
+24,uridine diphosphate-N-acetylglucosamine-binding protein YvcK
+25,"K09762  whiA, cell division protein WhiA"
+26,"K04564  SOD2, superoxide dismutase, Fe-Mn family [EC:1.15.1.1]"
+27,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+28,"K00927  PGK, pgk, phosphoglycerate kinase [EC:2.7.2.3]"
+29,"K01803  TPI, tpiA, triosephosphate isomerase (TIM) [EC:5.3.1.1]"
+30,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+31,"K00036  G6PD, zwf, glucose-6-phosphate 1-dehydrogenase [EC:1.1.1.49 1.1.1.363]"
+32,"K01810  GPI, pgi, glucose-6-phosphate isomerase [EC:5.3.1.9]"
+33,"K00616  E2.2.1.2, talA, talB, transaldolase [EC:2.2.1.2]"
+34,"K02257  COX10, ctaB, cyoE, heme o synthase [EC:2.5.1.141]"
+35,"K02259  COX15, ctaA, heme a synthase [EC:1.17.99.9]"
+36,ABC transporter permease
+37,ABC transporter ATP-binding protein
+38,"K09014  sufB, Fe-S cluster assembly protein SufB"
+39,"K09015  sufD, Fe-S cluster assembly protein SufD"
+40,"K09013  sufC, Fe-S cluster assembly ATP-binding protein"
+41,metal-sulfur cluster assembly factor
+42,"K06147  ABCB-BAC, ATP-binding cassette, subfamily B, bacterial"
+43,"K14998  SURF1, SHY1, surfeit locus 1 family protein"
+44,beta-ketoacyl-ACP reductase
+45,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+46,"K01079  serB, PSPH, phosphoserine phosphatase [EC:3.1.3.3]"
+47,ABC transporter ATP-binding protein
+48,"K03437  spoU, RNA methyltransferase, TrmH family"
+49,"K01910  citC, [citrate (pro-3S)-lyase] ligase [EC:6.2.1.22]"
+50,"K01256  pepN, aminopeptidase N [EC:3.4.11.2]"
+51,"K00975  glgC, glucose-1-phosphate adenylyltransferase [EC:2.7.7.27]"
+52,"K16150  , glycogen synthase [EC:2.4.1.11]"
+53,"K02167  betI, TetR/AcrR family transcriptional regulator, transcriptional repressor of bet genes"
+54,3-oxoacyl-ACP reductase
+55,"K00705  malQ, 4-alpha-glucanotransferase [EC:2.4.1.25]"
+56,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+57,undecaprenyl-diphosphate phosphatase
+58,"K15526  mshC, L-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase [EC:6.3.1.13]"
+59,HAD family phosphatase
+60,"K16168  bpsB, srsB, methyltransferase"
+61,proteasome ATPase
+62,proteasome accessory factor PafA2
+63,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+64,"K07503  nucS, endonuclease [EC:3.1.-.-]"
+65,"K13571  pafA, proteasome accessory factor A [EC:6.3.1.19]"
+66,"K03772  fkpA, FKBP-type peptidyl-prolyl cis-trans isomerase FkpA [EC:5.2.1.8]"
+67,"K03772  fkpA, FKBP-type peptidyl-prolyl cis-trans isomerase FkpA [EC:5.2.1.8]"
+68,"K03118  tatC, sec-independent protein translocase protein TatC"
+69,"K06877  , DEAD/DEAH box helicase domain-containing protein"
+70,RNA polymerase-binding protein RbpA
+71,SPFH/Band 7/PHB domain protein
+72,"K00219  fadH, 2,4-dienoyl-CoA reductase (NADPH2) [EC:1.3.1.34]"
+73,"K00766  trpD, anthranilate phosphoribosyltransferase [EC:2.4.2.18]"
+74,heme-copper oxidase subunit III
+75,"K08738  CYC, cytochrome c"
+76,Rieske (2Fe-2S) protein
+77,cytochrome bc complex cytochrome b subunit
+78,"K02274  coxA, ctaD, cytochrome c oxidase subunit I [EC:7.1.1.9]"
+79,"K02275  coxB, ctaC, cytochrome c oxidase subunit II [EC:7.1.1.9]"
+80,iron-sulfur cluster assembly accessory protein
+81,"K08659  pepDA, pepDB, dipeptidase [EC:3.4.-.-]"
+82,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+83,isoprenyl transferase
+84,"K03584  recO, DNA repair protein RecO (recombination protein O)"
+85,"K01649  leuA, IMS, 2-isopropylmalate synthase [EC:2.3.3.13]"
+86,"K03595  era, ERAL1, GTPase"
+87,"K06075  slyA, MarR family transcriptional regulator, transcriptional regulator for hemolysin"
+88,"K07042  ybeY, yqfG, probable rRNA maturation factor"
+89,"K01519  rdgB, ITPA, XTP/dITP diphosphohydrolase [EC:3.6.1.66]"
+90,"K16168  bpsB, srsB, methyltransferase"
+91,"K03686  dnaJ, molecular chaperone DnaJ"
+92,"K03705  hrcA, heat-inducible transcriptional repressor"
+93,"K03596  lepA, GTP-binding protein LepA"
+94,type II toxin-antitoxin system PemK/MazF family toxin
+95,"K02237  comEA, competence protein ComEA"
+96,"K01869  LARS, leuS, leucyl-tRNA synthetase [EC:6.1.1.4]"
+97,"K00789  metK, MAT, S-adenosylmethionine synthetase [EC:2.5.1.6]"
+98,"K13038  coaBC, dfp, phosphopantothenoylcysteine decarboxylase / phosphopantothenate---cysteine ligase [EC:4.1.1.36 6.3.2.5]"
+99,"K00942  gmk, GUK1, guanylate kinase [EC:2.7.4.8]"
+100,"K01591  pyrF, orotidine-5'-phosphate decarboxylase [EC:4.1.1.23]"
+101,"K01955  carB, CPA2, carbamoyl-phosphate synthase large subunit [EC:6.3.5.5]"
+102,"K01956  carA, CPA1, carbamoyl-phosphate synthase small subunit [EC:6.3.5.5]"
+103,"K01465  URA4, pyrC, dihydroorotase [EC:3.5.2.3]"
+104,"K00609  pyrB, PYR2, aspartate carbamoyltransferase catalytic subunit [EC:2.1.3.2]"
+105,"K02825  pyrR, pyrimidine operon attenuation protein / uracil phosphoribosyltransferase [EC:2.4.2.9]"
+106,"K03625  nusB, transcription antitermination protein NusB"
+107,"K02356  efp, elongation factor P"
+108,"K00891  aroK, aroL, shikimate kinase [EC:2.7.1.71]"
+109,"K01736  aroC, chorismate synthase [EC:4.2.3.5]"
+110,endolytic transglycosylase MltG
+111,"K00643  E2.3.1.37, ALAS, 5-aminolevulinate synthase [EC:2.3.1.37]"
+112,"K02986  RP-S4, rpsD, small subunit ribosomal protein S4"
+113,"K01175  ybfF, esterase [EC:3.1.-.-]"
+114,replication-associated recombination protein A
+115,"K07560  dtd, DTD, D-aminoacyl-tRNA deacylase [EC:3.1.1.96]"
+116,"K01876  DARS2, aspS, aspartyl-tRNA synthetase [EC:6.1.1.12]"
+117,APC family permease
+118,"K21138  HDDC3, guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase [EC:3.1.7.2]"
+119,"K03074  secF, preprotein translocase subunit SecF"
+120,"K03072  secD, preprotein translocase subunit SecD"
+121,"K03210  yajC, preprotein translocase subunit YajC"
+122,"K03551  ruvB, holliday junction DNA helicase RuvB [EC:5.6.2.4]"
+123,M3 family metallopeptidase
+124,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+125,"K07305  msrB, peptide-methionine (R)-S-oxide reductase [EC:1.8.4.12]"
+126,"K03684  rnd, ribonuclease D [EC:3.1.13.5]"
+127,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+128,"K01848  E5.4.99.2A, mcmA1, methylmalonyl-CoA mutase, N-terminal domain [EC:5.4.99.2]"
+129,aldo/keto reductase
+130,"K01662  dxs, 1-deoxy-D-xylulose-5-phosphate synthase [EC:2.2.1.7]"
+131,glycerophosphodiester phosphodiesterase
+132,heavy metal translocating P-type ATPase
+133,"K07734  paiB, transcriptional regulator"
+134,"K01681  ACO, acnA, aconitate hydratase [EC:4.2.1.3]"
+135,"K16168  bpsB, srsB, methyltransferase"
+136,ABC transporter substrate-binding protein
+137,TrkA family potassium uptake protein
+138,"K01077  E3.1.3.1, phoA, phoB, alkaline phosphatase [EC:3.1.3.1]"
+139,ABC transporter permease
+140,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+141,"K00394  aprA, adenylylsulfate reductase, subunit A [EC:1.8.99.2]"
+142,"K16012  cydC, ATP-binding cassette, subfamily C, bacterial CydC"
+143,"K00426  cydB, cytochrome bd ubiquinol oxidase subunit II [EC:7.1.1.7]"
+144,3-oxoacyl-ACP synthase III
+145,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+146,"K14627  actVI3, dehydratase [EC:4.2.1.-]"
+147,"K00395  aprB, adenylylsulfate reductase, subunit B [EC:1.8.99.2]"
+148,"K01255  CARP, pepA, leucyl aminopeptidase [EC:3.4.11.1]"
+149,"K23842  lpdA, NAD(P)H dehydrogenase (quinone) [EC:1.6.5.2]"
+150,"K00658  DLST, sucB, 2-oxoglutarate dehydrogenase E2 component (dihydrolipoamide succinyltransferase) [EC:2.3.1.61]"
+151,"K04757  rsbW, serine/threonine-protein kinase RsbW [EC:2.7.11.1]"
+152,"K03801  lipB, lipoyl(octanoyl) transferase [EC:2.3.1.181]"
+153,"K03644  lipA, LIAS, LIP1, LIP5, lipoyl synthase [EC:2.8.1.8]"
+154,"K01915  glnA, GLUL, glutamine synthetase [EC:6.3.1.2]"
+155,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+156,"K01915  glnA, GLUL, glutamine synthetase [EC:6.3.1.2]"
+157,"K01915  glnA, GLUL, glutamine synthetase [EC:6.3.1.2]"
+158,"K00606  panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase [EC:2.1.2.11]"
+159,"K01265  map, methionyl aminopeptidase [EC:3.4.11.18]"
+160,"K13570  pup, prokaryotic ubiquitin-like protein Pup"
+161,"K07738  nrdR, transcriptional repressor NrdR"
+162,"K02337  dnaE, DNA polymerase III subunit alpha [EC:2.7.7.7]"
+163,RluA family pseudouridine synthase
+164,"K03101  lspA, signal peptidase II [EC:3.4.23.36]"
+165,"K03531  ftsZ, cell division protein FtsZ"
+166,"K01924  murC, UDP-N-acetylmuramate--alanine ligase [EC:6.3.2.8]"
+167,"K02563  murG, UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase [EC:2.4.1.227]"
+168,"K03588  ftsW, spoVE, cell division protein FtsW"
+169,"K01925  murD, UDP-N-acetylmuramoylalanine--D-glutamate ligase [EC:6.3.2.9]"
+170,"K01000  mraY, phospho-N-acetylmuramoyl-pentapeptide-transferase [EC:2.7.8.13]"
+171,"K01929  murF, UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase [EC:6.3.2.10]"
+172,"K01928  murE, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase [EC:6.3.2.13]"
+173,"K05515  mrdA, penicillin-binding protein 2 [EC:3.4.16.4]"
+174,Nramp family divalent metal transporter
+175,"K03438  mraW, rsmH, 16S rRNA (cytosine1402-N4)-methyltransferase [EC:2.1.1.199]"
+176,"K02346  dinB, DNA polymerase IV [EC:2.7.7.7]"
+177,Rv2175c family DNA-binding protein
+178,Stk1 family PASTA domain-containing Ser/Thr kinase
+179,"K01626  E2.5.1.54, aroF, aroG, aroH, 3-deoxy-7-phosphoheptulonate synthase [EC:2.5.1.54]"
+180,thiamine-binding protein
+181,"K00655  plsC, 1-acyl-sn-glycerol-3-phosphate acyltransferase [EC:2.3.1.51]"
+182,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+183,"K01910  citC, [citrate (pro-3S)-lyase] ligase [EC:6.2.1.22]"
+184,"K17883  mtr, mycothione reductase [EC:1.8.1.15]"
+185,"K01958  PC, pyc, pyruvate carboxylase [EC:6.4.1.1]"
+186,"K02437  gcvH, GCSH, glycine cleavage system H protein"
+187,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+188,"K01802  E5.2.1.8, peptidylprolyl isomerase [EC:5.2.1.8]"
+189,"K00797  speE, SRM, SPE3, spermidine synthase [EC:2.5.1.16]"
+190,"K03977  engA, der, GTPase"
+191,"K04517  tyrA2, prephenate dehydrogenase [EC:1.3.1.12]"
+192,rRNA pseudouridine synthase
+193,"K03301  TC.AAA, ATP:ADP antiporter, AAA family"
+194,"K06149  uspA, universal stress protein A"
+195,AMP-binding protein
+196,"K02043  phnF, GntR family transcriptional regulator, phosphonate transport system regulatory protein"
+197,"K03417  prpB, methylisocitrate lyase [EC:4.1.3.30]"
+198,"K01647  CS, gltA, citrate synthase [EC:2.3.3.1]"
+199,"K13522  , nadM, bifunctional NMN adenylyltransferase/nudix hydrolase [EC:2.7.7.1 3.6.1.-]"
+200,"K03631  recN, DNA repair protein RecN (Recombination protein N)"
+201,NAD kinase
+202,"K01866  YARS, tyrS, tyrosyl-tRNA synthetase [EC:6.1.1.1]"
+203,"K03301  TC.AAA, ATP:ADP antiporter, AAA family"
+204,"K01755  argH, ASL, argininosuccinate lyase [EC:4.3.2.1]"
+205,"K21140  mec, [CysO sulfur-carrier protein]-S-L-cysteine hydrolase [EC:3.13.1.6]"
+206,"K01940  argG, ASS1, argininosuccinate synthase [EC:6.3.4.5]"
+207,"K08309  slt, soluble lytic murein transglycosylase [EC:4.2.2.-]"
+208,"K03402  argR, ahrC, transcriptional regulator of arginine metabolism"
+209,"K00611  OTC, argF, argI, ornithine carbamoyltransferase [EC:2.1.3.3]"
+210,acetylornithine transaminase
+211,"K00930  argB, acetylglutamate kinase [EC:2.7.2.8]"
+212,"K00620  argJ, glutamate N-acetyltransferase / amino-acid N-acetyltransferase [EC:2.3.1.35 2.3.1.1]"
+213,"K00145  argC, N-acetyl-gamma-glutamyl-phosphate reductase [EC:1.2.1.38]"
+214,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+215,non-ribosomal peptide synthetase
+216,M1 family metallopeptidase
+217,"K01890  FARSB, pheT, phenylalanyl-tRNA synthetase beta chain [EC:6.1.1.20]"
+218,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+219,"K03451  TC.BCT, betaine/carnitine transporter, BCCT family"
+220,"K03437  spoU, RNA methyltransferase, TrmH family"
+221,"K02520  infC, MTIF3, translation initiation factor IF-3"
+222,"K10819  E2.7.13.3, histidine kinase [EC:2.7.13.3]"
+223,"K16237  aroP, aromatic amino acid permease"
+224,"K04061  flhB2, flagellar biosynthesis protein"
+225,"K03070  secA, preprotein translocase subunit SecA [EC:7.4.2.8]"
+226,ribosome-associated translation inhibitor RaiA
+227,"K02240  comFA, competence protein ComFA"
+228,"K07654  mtrB, two-component system, OmpR family, sensor histidine kinase MtrB [EC:2.7.13.3]"
+229,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+230,"K07670  mtrA, two-component system, OmpR family, response regulator MtrA"
+231,"K04092  tyrA1, chorismate mutase [EC:5.4.99.5]"
+232,"K04487  iscS, NFS1, cysteine desulfurase [EC:2.8.1.7]"
+233,TrkH family potassium uptake protein
+234,"K00796  folP, dihydropteroate synthase [EC:2.5.1.15]"
+235,"K03686  dnaJ, molecular chaperone DnaJ"
+236,"K20978  hsbA, HptB-dependent secretion and biofilm anti anti-sigma factor"
+237,PIG-L family deacetylase
+238,sodium:glutamate symporter
+239,"K01142  E3.1.11.2, xthA, exodeoxyribonuclease III [EC:3.1.11.2]"
+240,ThiF family adenylyltransferase
+241,"K03726  helS, ATP-dependent DNA helicase [EC:5.6.2.4]"
+242,"K06877  , DEAD/DEAH box helicase domain-containing protein"
+243,"K03578  hrpA, ATP-dependent helicase HrpA [EC:3.6.4.13]"
+244,3'-5' exonuclease
+245,"K01845  hemL, glutamate-1-semialdehyde 2,1-aminomutase [EC:5.4.3.8]"
+246,"K14645  , serine protease [EC:3.4.21.-]"
+247,"K01916  nadE, NAD+ synthase [EC:6.3.1.5]"
+248,"K01698  hemB, ALAD, porphobilinogen synthase [EC:4.2.1.24]"
+249,branched-chain amino acid transport system II carrier protein
+250,"K01719  hemD, UROS, uroporphyrinogen-III synthase [EC:4.2.1.75]"
+251,"K01749  hemC, HMBS, hydroxymethylbilane synthase [EC:2.5.1.61]"
+252,"K01772  hemH, FECH, protoporphyrin/coproporphyrin ferrochelatase [EC:4.98.1.1 4.99.1.9]"
+253,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+254,"K07734  paiB, transcriptional regulator"
+255,"K02167  betI, TetR/AcrR family transcriptional regulator, transcriptional repressor of bet genes"
+256,RNB domain-containing ribonuclease
+257,"K06877  , DEAD/DEAH box helicase domain-containing protein"
+258,"K01269  yhfE, aminopeptidase [EC:3.4.11.-]"
+259,"K00873  PK, pyk, pyruvate kinase [EC:2.7.1.40]"
+260,"K00762  pyrE, orotate phosphoribosyltransferase [EC:2.4.2.10]"
+261,Mrp/NBP35 family ATP-binding protein
+262,preprotein translocase subunit TatA
+263,"K16168  bpsB, srsB, methyltransferase"
+264,TIGR00730 family Rossman fold protein
+265,amino acid ABC transporter ATP-binding protein
+266,glutamate ABC transporter substrate-binding protein
+267,magnesium and cobalt transport protein CorA
+268,ABC transporter permease subunit
+269,amino acid ABC transporter permease
+270,"K01439  dapE, succinyl-diaminopimelate desuccinylase [EC:3.5.1.18]"
+271,"K00674  dapD, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase [EC:2.3.1.117]"
+272,"K01647  CS, gltA, citrate synthase [EC:2.3.3.1]"
+273,"K14267  dapC, N-succinyldiaminopimelate aminotransferase [EC:2.6.1.17]"
+274,"K00169  porA, pyruvate ferredoxin oxidoreductase alpha subunit [EC:1.2.7.1]"
+275,"K06207  typA, bipA, GTP-binding protein"
+276,ABC transporter ATP-binding protein
+277,ABC transporter permease
+278,ABC transporter permease subunit
+279,ABC transporter family substrate-binding protein
+280,"K07238  TC.ZIP, zupT, ZRT3, ZIP2, zinc transporter, ZIP family"
+281,"K14645  , serine protease [EC:3.4.21.-]"
+282,"K11065  tpx, thioredoxin-dependent peroxiredoxin [EC:1.11.1.24]"
+283,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+284,"K13522  , nadM, bifunctional NMN adenylyltransferase/nudix hydrolase [EC:2.7.7.1 3.6.1.-]"
+285,"K03517  nadA, quinolinate synthase [EC:2.5.1.72]"
+286,"K00767  nadC, QPRT, nicotinate-nucleotide pyrophosphorylase (carboxylating) [EC:2.4.2.19]"
+287,"K04487  iscS, NFS1, cysteine desulfurase [EC:2.8.1.7]"
+288,"K01077  E3.1.3.1, phoA, phoB, alkaline phosphatase [EC:3.1.3.1]"
+289,glycine betaine ABC transporter substrate-binding protein
+290,ABC transporter permease
+291,"K01053  gnl, RGN, gluconolactonase [EC:3.1.1.17]"
+292,"K06147  ABCB-BAC, ATP-binding cassette, subfamily B, bacterial"
+293,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+294,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+295,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+296,organic hydroperoxide resistance protein
+297,"K03712  marR, MarR family transcriptional regulator, multiple antibiotic resistance protein MarR"
+298,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+299,"K14244  oxyD, amidotransferase [EC:6.3.5.-]"
+300,"K06147  ABCB-BAC, ATP-binding cassette, subfamily B, bacterial"
+301,"K01624  FBA, fbaA, fructose-bisphosphate aldolase, class II [EC:4.1.2.13]"
+302,MSMEG_4193 family putative phosphomutase
+303,"K07481  , transposase, IS5 family"
+304,"K06942  ychF, ribosome-binding ATPase"
+305,"K01637  E4.1.3.1, aceA, isocitrate lyase [EC:4.1.3.1]"
+306,"K02168  betT, betS, choline/glycine/proline betaine transport protein"
+307,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+308,"K13993  HSP20, HSP20 family protein"
+309,"K23518  MACROD, ymdB, O-acetyl-ADP-ribose deacetylase [EC:3.1.1.106]"
+310,"K09760  rmuC, DNA recombination protein RmuC"
+311,4-hydroxy-3-methylbut-2-enyl diphosphate reductase
+312,"K01638  aceB, glcB, malate synthase [EC:2.3.3.9]"
+313,"K14244  oxyD, amidotransferase [EC:6.3.5.-]"
+314,"K00937  ppk1, polyphosphate kinase [EC:2.7.4.1]"
+315,"K00841  patA, aminotransferase [EC:2.6.1.-]"
+316,"K02203  thrH, phosphoserine / homoserine phosphotransferase [EC:3.1.3.3 2.7.1.39]"
+317,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+318,"K01934  MTHFS, 5-formyltetrahydrofolate cyclo-ligase [EC:6.3.3.2]"
+319,"K01951  guaA, GMPS, GMP synthase (glutamine-hydrolysing) [EC:6.3.5.2]"
+320,"K00088  IMPDH, guaB, IMP dehydrogenase [EC:1.1.1.205]"
+321,"K00088  IMPDH, guaB, IMP dehydrogenase [EC:1.1.1.205]"
+322,"K03451  TC.BCT, betaine/carnitine transporter, BCCT family"
+323,"K04077  groEL, HSPD1, chaperonin GroEL [EC:5.6.1.7]"
+324,"K06147  ABCB-BAC, ATP-binding cassette, subfamily B, bacterial"
+325,iron chelate uptake ABC transporter family permease subunit
+326,iron chelate uptake ABC transporter family permease subunit
+327,ABC transporter substrate-binding protein
+328,"K16168  bpsB, srsB, methyltransferase"
+329,"K01919  gshA, glutamate--cysteine ligase [EC:6.3.2.2]"
+330,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+331,"K03311  TC.LIVCS, branched-chain amino acid:cation transporter, LIVCS family"
+332,"K25706  tsaD, tRNA N6-adenosine threonylcarbamoyltransferase [EC:2.3.1.234]"
+333,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+334,"K14742  tsaB, tRNA threonylcarbamoyladenosine biosynthesis protein TsaB"
+335,"K06925  tsaE, tRNA threonylcarbamoyladenosine biosynthesis protein TsaE"
+336,"K01775  alr, alanine racemase [EC:5.1.1.1]"
+337,"K14627  actVI3, dehydratase [EC:4.2.1.-]"
+338,"K02438  glgX, glycogen debranching enzyme [EC:3.2.1.196]"
+339,"K00820  glmS, GFPT, glutamine---fructose-6-phosphate transaminase (isomerizing) [EC:2.6.1.16]"
+340,"K01784  galE, GALE, UDP-glucose 4-epimerase [EC:5.1.3.2]"
+341,"K03431  glmM, phosphoglucosamine mutase [EC:5.4.2.10]"
+342,"K02996  RP-S9, MRPS9, rpsI, small subunit ribosomal protein S9"
+343,"K02871  RP-L13, MRPL13, rplM, large subunit ribosomal protein L13"
+344,"K06173  truA, PUS1, tRNA pseudouridine38-40 synthase [EC:5.4.99.12]"
+345,"K02879  RP-L17, MRPL17, rplQ, large subunit ribosomal protein L17"
+346,"K03040  rpoA, DNA-directed RNA polymerase subunit alpha [EC:2.7.7.6]"
+347,"K02952  RP-S13, rpsM, small subunit ribosomal protein S13"
+348,"K01265  map, methionyl aminopeptidase [EC:3.4.11.18]"
+349,"K00939  adk, AK, adenylate kinase [EC:2.7.4.3]"
+350,"K02876  RP-L15, MRPL15, rplO, large subunit ribosomal protein L15"
+351,"K02881  RP-L18, MRPL18, rplR, large subunit ribosomal protein L18"
+352,"K02933  RP-L6, MRPL6, rplF, large subunit ribosomal protein L6"
+353,"K02994  RP-S8, rpsH, small subunit ribosomal protein S8"
+354,"K02931  RP-L5, MRPL5, rplE, large subunit ribosomal protein L5"
+355,"K02895  RP-L24, MRPL24, rplX, large subunit ribosomal protein L24"
+356,"K02878  RP-L16, MRPL16, rplP, large subunit ribosomal protein L16"
+357,"K02982  RP-S3, rpsC, small subunit ribosomal protein S3"
+358,"K02890  RP-L22, MRPL22, rplV, large subunit ribosomal protein L22"
+359,"K02886  RP-L2, MRPL2, rplB, large subunit ribosomal protein L2"
+360,"K02926  RP-L4, MRPL4, rplD, large subunit ribosomal protein L4"
+361,"K02906  RP-L3, MRPL3, rplC, large subunit ribosomal protein L3"
+362,"K02946  RP-S10, MRPS10, rpsJ, small subunit ribosomal protein S10"
+363,"K01657  trpE, anthranilate synthase component I [EC:4.1.3.27]"
+364,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+365,"K02358  tuf, TUFM, elongation factor Tu"
+366,"K02355  fusA, GFM, EFG, elongation factor G"
+367,"K02992  RP-S7, MRPS7, rpsG, small subunit ribosomal protein S7"
+368,"K03046  rpoC, DNA-directed RNA polymerase subunit beta' [EC:2.7.7.6]"
+369,"K03043  rpoB, DNA-directed RNA polymerase subunit beta [EC:2.7.7.6]"
+370,"K02935  RP-L7, MRPL12, rplL, large subunit ribosomal protein L7/L12"
+371,"K02864  RP-L10, MRPL10, rplJ, large subunit ribosomal protein L10"
+372,"K02863  RP-L1, MRPL1, rplA, large subunit ribosomal protein L1"
+373,"K02867  RP-L11, MRPL11, rplK, large subunit ribosomal protein L11"
+374,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+375,"K02601  nusG, transcription termination/antitermination protein NusG"
+376,"K01552  ecfA, energy-coupling factor transport system ATP-binding protein [EC:7.-.-.-]"
+377,"K00847  E2.7.1.4, scrK, fructokinase [EC:2.7.1.4]"
+378,folate-binding protein YgfZ
+379,"K13522  , nadM, bifunctional NMN adenylyltransferase/nudix hydrolase [EC:2.7.7.1 3.6.1.-]"
+380,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+381,"K00560  thyA, TYMS, thymidylate synthase [EC:2.1.1.45]"
+382,"K00287  DHFR, folA, dihydrofolate reductase [EC:1.5.1.3]"
+383,"K00133  asd, aspartate-semialdehyde dehydrogenase [EC:1.2.1.11]"
+384,"K00075  murB, UDP-N-acetylmuramate dehydrogenase [EC:1.3.1.98]"
+385,"K01012  bioB, biotin synthase [EC:2.8.1.6]"
+386,"K06877  , DEAD/DEAH box helicase domain-containing protein"
+387,"K01436  yhaA, amidohydrolase [EC:3.5.1.-]"
+388,"K01739  metB, cystathionine gamma-synthase [EC:2.5.1.48]"
+389,pyridoxal-phosphate dependent enzyme
+390,3-methyladenine DNA glycosylase
+391,AMP-binding protein
+392,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+393,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+394,"K05786  rarD, chloramphenicol-sensitive protein RarD"
+395,"K01233  csn, chitosanase [EC:3.2.1.132]"
+396,"K02551  menD, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase [EC:2.2.1.9]"
+397,PhoX family phosphatase
+398,"K02549  menC, o-succinylbenzoate synthase [EC:4.2.1.113]"
+399,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+400,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+401,thiamine pyrophosphate-dependent enzyme
+402,"K03718  asnC, Lrp/AsnC family transcriptional regulator, regulator for asnA, asnC and gidA"
+403,"K10215  ethA, monooxygenase [EC:1.14.13.-]"
+404,S9 family peptidase
+405,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+406,1%2C4-dihydroxy-2-naphthoyl-CoA synthase
+407,YidE/YbjL duplication
+408,c-type cytochrome biogenesis protein CcsB
+409,"K07399  resB, ccs1, cytochrome c biogenesis protein"
+410,"K07399  resB, ccs1, cytochrome c biogenesis protein"
+411,"K04768  acuC, acetoin utilization protein AcuC"
+412,potassium transporter Trk
+413,"K00286  proC, pyrroline-5-carboxylate reductase [EC:1.5.1.2]"
+414,sugar phosphate isomerase/epimerase
+415,"K03168  topA, DNA topoisomerase I [EC:5.6.2.1]"
+416,"K16168  bpsB, srsB, methyltransferase"
+417,rhodanese-related sulfurtransferase
+418,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+419,"K03781  katE, CAT, catB, srpA, catalase [EC:1.11.1.6]"
+420,"K02283  cpaF, tadA, pilus assembly protein CpaF [EC:7.4.2.8]"
+421,"K18568  thnR, CoA pyrophosphatase [EC:3.6.1.-]"
+422,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+423,"K01762  ACS, 1-aminocyclopropane-1-carboxylate synthase [EC:4.4.1.14]"
+424,"K02043  phnF, GntR family transcriptional regulator, phosphonate transport system regulatory protein"
+425,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+426,"K01420  fnr, CRP/FNR family transcriptional regulator, anaerobic regulatory protein"
+427,"K13522  , nadM, bifunctional NMN adenylyltransferase/nudix hydrolase [EC:2.7.7.1 3.6.1.-]"
+428,"K08309  slt, soluble lytic murein transglycosylase [EC:4.2.2.-]"
+429,metallophosphoesterase
+430,ABC transporter ATP-binding protein/permease
+431,"K15466  rifF, asm9, amide synthase"
+432,"K01945  purD, phosphoribosylamine---glycine ligase [EC:6.3.4.13]"
+433,"K02475  , two-component system, CitB family, response regulator"
+434,"K10819  E2.7.13.3, histidine kinase [EC:2.7.13.3]"
+435,ABC transporter ATP-binding protein
+436,"K01424  E3.5.1.1, ansA, ansB, L-asparaginase [EC:3.5.1.1]"
+437,"K00764  purF, PPAT, amidophosphoribosyltransferase [EC:2.4.2.14]"
+438,"K01933  purM, phosphoribosylformylglycinamidine cyclo-ligase [EC:6.3.3.1]"
+439,"K03695  clpB, ATP-dependent Clp protease ATP-binding subunit ClpB"
+440,"K03810  mviM, virulence factor"
+441,ABC transporter substrate-binding protein
+442,amino acid ABC transporter permease
+443,amino acid ABC transporter ATP-binding protein
+444,"K03439  trmB, METTL1, TRM8, tRNA (guanine-N7-)-methyltransferase [EC:2.1.1.33]"
+445,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+446,"K08365  merR, MerR family transcriptional regulator, mercuric resistance operon regulatory protein"
+447,"K00123  fdoG, fdhF, fdwA, formate dehydrogenase major subunit [EC:1.17.1.9]"
+448,nucleotide exchange factor GrpE
+449,"K04043  dnaK, HSPA9, molecular chaperone DnaK"
+450,"K07734  paiB, transcriptional regulator"
+451,MMPL family transporter
+452,"K00841  patA, aminotransferase [EC:2.6.1.-]"
+453,"K05571  mnhG, mrpG, multicomponent Na+:H+ antiporter subunit G"
+454,monovalent cation/H+ antiporter complex subunit F
+455,"K01153  hsdR, type I restriction enzyme, R subunit [EC:3.1.21.3]"
+456,"K01468  hutI, AMDHD1, imidazolonepropionase [EC:3.5.2.7]"
+457,"K01153  hsdR, type I restriction enzyme, R subunit [EC:3.1.21.3]"
+458,"K00340  nuoK, NADH-quinone oxidoreductase subunit K [EC:7.1.1.2]"
+459,"K00394  aprA, adenylylsulfate reductase, subunit A [EC:1.8.99.2]"
+460,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+461,"K01494  dcd, dCTP deaminase [EC:3.5.4.13]"
+462,"K00528  fpr, ferredoxin/flavodoxin---NADP+ reductase [EC:1.18.1.2 1.19.1.1]"
+463,"K08738  CYC, cytochrome c"
+464,"K19511  PXDN, VPO1, peroxidase [EC:1.11.1.7]"
+465,"K07213  ATOX1, ATX1, copZ, golB, copper chaperone"
+466,"K07156  copC, pcoC, copper resistance protein C"
+467,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+468,"K02954  RP-S14, MRPS14, rpsN, small subunit ribosomal protein S14"
+469,"K02043  phnF, GntR family transcriptional regulator, phosphonate transport system regulatory protein"
+470,"K00799  GST, gst, glutathione S-transferase [EC:2.5.1.18]"
+471,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+472,"K06149  uspA, universal stress protein A"
+473,mechanosensitive ion channel
+474,"K00013  hisD, histidinol dehydrogenase [EC:1.1.1.23]"
+475,type I restriction-modification system subunit M
+476,"K00284  GLU, gltS, glutamate synthase (ferredoxin) [EC:1.4.7.1]"
+477,iron ABC transporter permease
+478,ABC transporter ATP-binding protein
+479,"K02167  betI, TetR/AcrR family transcriptional regulator, transcriptional repressor of bet genes"
+480,"K04757  rsbW, serine/threonine-protein kinase RsbW [EC:2.7.11.1]"
+481,"K03469  rnhA, RNASEH1, ribonuclease HI [EC:3.1.26.4]"
+482,"K00626  ACAT, atoB, acetyl-CoA C-acetyltransferase [EC:2.3.1.9]"
+483,"K12507  fadK, acyl-CoA synthetase [EC:6.2.1.-]"
+484,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+485,"K03712  marR, MarR family transcriptional regulator, multiple antibiotic resistance protein MarR"
+486,"K01692  paaF, echA, enoyl-CoA hydratase [EC:4.2.1.17]"
+487,"K07503  nucS, endonuclease [EC:3.1.-.-]"
+488,type I restriction-modification system subunit M
+489,"K01458  hutG, N-formylglutamate deformylase [EC:3.5.1.68]"
+490,"K01077  E3.1.3.1, phoA, phoB, alkaline phosphatase [EC:3.1.3.1]"
+491,"K09181  yfiQ, acetyltransferase"
+492,"K08762  DBI, ACBP, diazepam-binding inhibitor (GABA receptor modulator, acyl-CoA-binding protein)"
+493,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+494,LutB/LldF family L-lactate oxidation iron-sulfur protein
+495,(Fe-S)-binding protein
+496,"K01738  cysK, cysteine synthase [EC:2.5.1.47]"
+497,"K00259  ald, alanine dehydrogenase [EC:1.4.1.1]"
+498,"K06215  pdxS, pdx1, pyridoxal 5'-phosphate synthase pdxS subunit [EC:4.3.3.6]"
+499,"K00841  patA, aminotransferase [EC:2.6.1.-]"
+500,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+501,"K02043  phnF, GntR family transcriptional regulator, phosphonate transport system regulatory protein"
+502,"K00151  hpaE, hpcC, 5-carboxymethyl-2-hydroxymuconic-semialdehyde dehydrogenase [EC:1.2.1.60]"
+503,"K00455  hpaD, hpcB, 3,4-dihydroxyphenylacetate 2,3-dioxygenase [EC:1.13.11.15]"
+504,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+505,"K01028  scoA, 3-oxoacid CoA-transferase subunit A [EC:2.8.3.5]"
+506,"K07549  bbsA, benzoylsuccinyl-CoA thiolase BbsA subunit [EC:2.3.1.310]"
+507,"K10215  ethA, monooxygenase [EC:1.14.13.-]"
+508,histidinol-phosphate transaminase
+509,"K10215  ethA, monooxygenase [EC:1.14.13.-]"
+510,"K02609  paaA, ring-1,2-phenylacetyl-CoA epoxidase subunit PaaA [EC:1.14.13.149]"
+511,"K02610  paaB, ring-1,2-phenylacetyl-CoA epoxidase subunit PaaB"
+512,"K02611  paaC, ring-1,2-phenylacetyl-CoA epoxidase subunit PaaC [EC:1.14.13.149]"
+513,EamA family transporter
+514,"K15927  jadF, oxygenase"
+515,"K01912  paaK, phenylacetate-CoA ligase [EC:6.2.1.30]"
+516,"K01692  paaF, echA, enoyl-CoA hydratase [EC:4.2.1.17]"
+517,"K02625  pcaT, MFS transporter, MHS family, dicarboxylic acid transporter PcaT"
+518,"K07549  bbsA, benzoylsuccinyl-CoA thiolase BbsA subunit [EC:2.3.1.310]"
+519,"K01692  paaF, echA, enoyl-CoA hydratase [EC:4.2.1.17]"
+520,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+521,"K01579  panD, aspartate 1-decarboxylase [EC:4.1.1.11]"
+522,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+523,"K02618  paaZ, oxepin-CoA hydrolase / 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase [EC:3.3.2.12 1.2.1.91]"
+524,"K00022  HADH, 3-hydroxyacyl-CoA dehydrogenase [EC:1.1.1.35]"
+525,"K02167  betI, TetR/AcrR family transcriptional regulator, transcriptional repressor of bet genes"
+526,AMP-binding protein
+527,"K21791  redJ, thioesterase"
+528,TM0106 family RecB-like putative nuclease
+529,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+530,"K02625  pcaT, MFS transporter, MHS family, dicarboxylic acid transporter PcaT"
+531,"K01756  purB, ADSL, adenylosuccinate lyase [EC:4.3.2.2]"
+532,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+533,"K21191  mdpB2, CoA ligase [EC:6.2.1.-]"
+534,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+535,"K01041  gcdG, caiB, glutaryl-CoA transferase [EC:2.8.3.-]"
+536,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+537,"K00626  ACAT, atoB, acetyl-CoA C-acetyltransferase [EC:2.3.1.9]"
+538,"K21191  mdpB2, CoA ligase [EC:6.2.1.-]"
+539,HAD-IC family P-type ATPase
+540,"K07058  , membrane protein"
+541,biotin transporter BioY
+542,aldo/keto reductase
+543,M20 family metallopeptidase
+544,metalloregulator ArsR/SmtB family transcription factor
+545,metalloregulator ArsR/SmtB family transcription factor
+546,"K08738  CYC, cytochrome c"
+547,metalloregulator ArsR/SmtB family transcription factor
+548,cation diffusion facilitator family transporter
+549,"K01762  ACS, 1-aminocyclopropane-1-carboxylate synthase [EC:4.4.1.14]"
+550,"K00384  trxB, TRR, thioredoxin reductase (NADPH) [EC:1.8.1.9]"
+551,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+552,"K02167  betI, TetR/AcrR family transcriptional regulator, transcriptional repressor of bet genes"
+553,"K03712  marR, MarR family transcriptional regulator, multiple antibiotic resistance protein MarR"
+554,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+555,"K07734  paiB, transcriptional regulator"
+556,"K00249  ACADM, acd, acyl-CoA dehydrogenase [EC:1.3.8.7]"
+557,"K06895  lysE, argO, L-lysine exporter family protein LysE/ArgO"
+558,"K24042  yitJ, methionine synthase / methylenetetrahydrofolate reductase (NADH) [EC:2.1.1.13 1.5.1.54]"
+559,"K01739  metB, cystathionine gamma-synthase [EC:2.5.1.48]"
+560,PLP-dependent transferase
+561,"K16168  bpsB, srsB, methyltransferase"
+562,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+563,ABC transporter permease
+564,PQQ-binding-like beta-propeller repeat protein
+565,"K00249  ACADM, acd, acyl-CoA dehydrogenase [EC:1.3.8.7]"
+566,"K00841  patA, aminotransferase [EC:2.6.1.-]"
+567,"K06877  , DEAD/DEAH box helicase domain-containing protein"
+568,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+569,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+570,"K10027  crtI, phytoene desaturase [EC:1.3.99.26 1.3.99.28 1.3.99.29 1.3.99.31]"
+571,Tat (twin-arginine translocation) pathway signal sequence
+572,"K01823  idi, IDI, isopentenyl-diphosphate Delta-isomerase [EC:5.3.3.2]"
+573,"K03671  trxA, thioredoxin 1"
+574,"K05558  , pyridoxamine 5'-phosphate oxidase family protein"
+575,"K06941  rlmN, 23S rRNA (adenine2503-C2)-methyltransferase [EC:2.1.1.192]"
+576,chorismate-binding protein
+577,protein-tyrosine-phosphatase
+578,"K07734  paiB, transcriptional regulator"
+579,"K03588  ftsW, spoVE, cell division protein FtsW"
+580,heavy metal translocating P-type ATPase
+581,"K21791  redJ, thioesterase"
+582,"K13953  adhP, alcohol dehydrogenase, propanol-preferring [EC:1.1.1.1]"
+583,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+584,thiamine pyrophosphate-binding protein
+585,"K00016  LDH, ldh, L-lactate dehydrogenase [EC:1.1.1.27]"
+586,"K03327  TC.MATE, SLC47A, norM, mdtK, dinF, multidrug resistance protein, MATE family"
+587,CPBP family intramembrane metalloprotease
+588,"K01759  GLO1, gloA, lactoylglutathione lyase [EC:4.4.1.5]"
+589,"K03321  TC.SULP, sulfate permease, SulP family"
+590,"K01992  ABC-2.P, ABC-2 type transport system permease protein"
+591,ABC transporter ATP-binding protein
+592,ABC transporter ATP-binding protein/permease
+593,ABC transporter ATP-binding protein/permease
+594,"K07734  paiB, transcriptional regulator"
+595,"K23265  purQ, phosphoribosylformylglycinamidine synthase subunit PurQ / glutaminase [EC:6.3.5.3 3.5.1.2]"
+596,"K01073  E3.1.2.20, acyl-CoA hydrolase [EC:3.1.2.20]"
+597,"K16168  bpsB, srsB, methyltransferase"
+598,"K01838  pgmB, beta-phosphoglucomutase [EC:5.4.2.6]"
+599,"K10819  E2.7.13.3, histidine kinase [EC:2.7.13.3]"
+600,"K02475  , two-component system, CitB family, response regulator"
+601,"K00459  ncd2, npd, nitronate monooxygenase [EC:1.13.12.16]"
+602,"K10819  E2.7.13.3, histidine kinase [EC:2.7.13.3]"
+603,"K02475  , two-component system, CitB family, response regulator"
+604,ABC transporter ATP-binding protein
+605,ABC transporter permease
+606,ABC transporter ATP-binding protein/permease
+607,"K13522  , nadM, bifunctional NMN adenylyltransferase/nudix hydrolase [EC:2.7.7.1 3.6.1.-]"
+608,LysE family transporter
+609,"K07734  paiB, transcriptional regulator"
+610,"K10819  E2.7.13.3, histidine kinase [EC:2.7.13.3]"
+611,"K02475  , two-component system, CitB family, response regulator"
+612,YchJ family metal-binding protein
+613,"K16168  bpsB, srsB, methyltransferase"
+614,iron-siderophore ABC transporter substrate-binding protein
+615,iron ABC transporter permease
+616,iron ABC transporter permease
+617,ABC transporter ATP-binding protein
+618,siderophore-interacting protein
+619,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+620,"K01425  glsA, GLS, glutaminase [EC:3.5.1.2]"
+621,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+622,FAD-binding protein
+623,"K02614  paaI, acyl-CoA thioesterase [EC:3.1.2.-]"
+624,"K07816  E2.7.6.5, GTP pyrophosphokinase [EC:2.7.6.5]"
+625,"K02167  betI, TetR/AcrR family transcriptional regulator, transcriptional repressor of bet genes"
+626,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+627,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+628,"K09684  pucR, PucR family transcriptional regulator, purine catabolism regulatory protein"
+629,"K00529  hcaD, 3-phenylpropionate/trans-cinnamate dioxygenase ferredoxin reductase component [EC:1.18.1.3]"
+630,"K00797  speE, SRM, SPE3, spermidine synthase [EC:2.5.1.16]"
+631,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+632,DMT family transporter
+633,"K01696  trpB, tryptophan synthase beta chain [EC:4.2.1.20]"
+634,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+635,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+636,"K01436  yhaA, amidohydrolase [EC:3.5.1.-]"
+637,"K01758  CTH, cystathionine gamma-lyase [EC:4.4.1.1]"
+638,"K06147  ABCB-BAC, ATP-binding cassette, subfamily B, bacterial"
+639,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+640,"K21191  mdpB2, CoA ligase [EC:6.2.1.-]"
+641,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+642,"K05339  lrgB, holin-like protein LrgB"
+643,"K02043  phnF, GntR family transcriptional regulator, phosphonate transport system regulatory protein"
+644,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+645,S8 family serine peptidase
+646,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+647,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+648,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+649,"K00864  glpK, GK, glycerol kinase [EC:2.7.1.30]"
+650,"K00928  lysC, aspartate kinase [EC:2.7.2.4]"
+651,ABC transporter ATP-binding protein
+652,"K06147  ABCB-BAC, ATP-binding cassette, subfamily B, bacterial"
+653,"K02314  dnaB, replicative DNA helicase [EC:5.6.2.3]"
+654,"K01041  gcdG, caiB, glutaryl-CoA transferase [EC:2.8.3.-]"
+655,"K05844  rimK, ribosomal protein S6--L-glutamate ligase [EC:6.3.2.-]"
+656,"K07263  pqqL, zinc protease [EC:3.4.24.-]"
+657,"K02939  RP-L9, MRPL9, rplI, large subunit ribosomal protein L9"
+658,single-stranded DNA-binding protein
+659,"K02990  RP-S6, MRPS6, rpsF, small subunit ribosomal protein S6"
+660,"K01269  yhfE, aminopeptidase [EC:3.4.11.-]"
+661,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+662,inositol-3-phosphate synthase
+663,"K13522  , nadM, bifunctional NMN adenylyltransferase/nudix hydrolase [EC:2.7.7.1 3.6.1.-]"
+664,murein biosynthesis protein MurJ
+665,"K00305  soxG, sarcosine oxidase, subunit gamma [EC:1.5.3.24 1.5.3.1]"
+666,"K00384  trxB, TRR, thioredoxin reductase (NADPH) [EC:1.8.1.9]"
+667,"K03671  trxA, thioredoxin 1"
+668,"K03497  parB, spo0J, ParB family transcriptional regulator, chromosome partitioning protein"
+669,"K01424  E3.5.1.1, ansA, ansB, L-asparaginase [EC:3.5.1.1]"
+670,"K03501  gidB, rsmG, 16S rRNA (guanine527-N7)-methyltransferase [EC:2.1.1.170]"
+671,"K03217  yidC, spoIIIJ, OXA1, ccfA, YidC/Oxa1 family membrane protein insertase"
+672,"K07058  , membrane protein"
+673,tRNA glutamyl-Q(34) synthetase GluQRS
+674,"K00156  poxB, pyruvate dehydrogenase (quinone) [EC:1.2.5.1]"
+675,"K01560  E3.8.1.2, 2-haloacid dehalogenase [EC:3.8.1.2]"
+676,tryptophan-rich sensory protein
+677,"K03810  mviM, virulence factor"
+678,L-serine ammonia-lyase
+679,"K13522  , nadM, bifunctional NMN adenylyltransferase/nudix hydrolase [EC:2.7.7.1 3.6.1.-]"
+680,"K00303  soxB, sarcosine oxidase, subunit beta [EC:1.5.3.24 1.5.3.1]"
+681,"K00302  soxA, sarcosine oxidase, subunit alpha [EC:1.5.3.24 1.5.3.1]"
+682,"K01692  paaF, echA, enoyl-CoA hydratase [EC:4.2.1.17]"
+683,"K01692  paaF, echA, enoyl-CoA hydratase [EC:4.2.1.17]"
+684,"K00020  HIBADH, mmsB, 3-hydroxyisobutyrate dehydrogenase [EC:1.1.1.31]"
+685,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+686,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+687,"K03712  marR, MarR family transcriptional regulator, multiple antibiotic resistance protein MarR"
+688,AMP-binding protein
+689,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+690,"K00281  GLDC, gcvP, glycine dehydrogenase [EC:1.4.4.2]"
+691,"K00605  gcvT, AMT, aminomethyltransferase [EC:2.1.2.10]"
+692,"K02475  , two-component system, CitB family, response regulator"
+693,"K10819  E2.7.13.3, histidine kinase [EC:2.7.13.3]"
+694,"K00941  thiD, hydroxymethylpyrimidine/phosphomethylpyrimidine kinase [EC:2.7.1.49 2.7.4.7]"
+695,"K02167  betI, TetR/AcrR family transcriptional regulator, transcriptional repressor of bet genes"
+696,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+697,"K00773  tgt, queuine tRNA-ribosyltransferase [EC:2.4.2.29]"
+698,"K18802  DUG3, glutamine amidotransferase"
+699,"K13522  , nadM, bifunctional NMN adenylyltransferase/nudix hydrolase [EC:2.7.7.1 3.6.1.-]"
+700,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+701,AMP-binding protein
+702,"K00059  fabG, OAR1, 3-oxoacyl-[acyl-carrier protein] reductase [EC:1.1.1.100]"
+703,"K00626  ACAT, atoB, acetyl-CoA C-acetyltransferase [EC:2.3.1.9]"
+704,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+705,sugar phosphate nucleotidyltransferase
+706,"K10563  mutM, fpg, formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18]"
+707,"K03578  hrpA, ATP-dependent helicase HrpA [EC:3.6.4.13]"
+708,"K16168  bpsB, srsB, methyltransferase"
+709,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+710,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+711,"K00761  upp, UPRT, uracil phosphoribosyltransferase [EC:2.4.2.9]"
+712,"K08296  sixA, phosphohistidine phosphatase [EC:3.1.3.-]"
+713,"K01596  E4.1.1.32, pckA, PCK, phosphoenolpyruvate carboxykinase (GTP) [EC:4.1.1.32]"
+714,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+715,"K13643  iscR, Rrf2 family transcriptional regulator, iron-sulfur cluster assembly transcription factor"
+716,"K03726  helS, ATP-dependent DNA helicase [EC:5.6.2.4]"
+717,"K01835  pgm, phosphoglucomutase [EC:5.4.2.2]"
+718,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+719,FAD/NAD(P)-binding protein
+720,"K07503  nucS, endonuclease [EC:3.1.-.-]"
+721,"K01081  E3.1.3.5, 5'-nucleotidase [EC:3.1.3.5]"
+722,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+723,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+724,"K02341  holB, DNA polymerase III subunit delta' [EC:2.7.7.7]"
+725,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+726,phosphoglyceromutase
+727,"K02039  phoU, phosphate transport system protein"
+728,"K01552  ecfA, energy-coupling factor transport system ATP-binding protein [EC:7.-.-.-]"
+729,"K02475  , two-component system, CitB family, response regulator"
+730,"K07736  carD, CarD family transcriptional regulator, regulator of rRNA transcription"
+731,"K01770  ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [EC:4.6.1.12]"
+732,"K01883  CARS, cysS, cysteinyl-tRNA synthetase [EC:6.1.1.16]"
+733,"K03218  rlmB, 23S rRNA (guanosine2251-2'-O)-methyltransferase [EC:2.1.1.185]"
+734,"K00700  GBE1, glgB, 1,4-alpha-glucan branching enzyme [EC:2.4.1.18]"
+735,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+736,"K01607  pcaC, 4-carboxymuconolactone decarboxylase [EC:4.1.1.44]"
+737,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+738,aldo/keto reductase
+739,"K13057  treT, trehalose synthase [EC:2.4.1.245]"
+740,"K01236  treZ, glgZ, maltooligosyltrehalose trehalohydrolase [EC:3.2.1.141]"
+741,"K00384  trxB, TRR, thioredoxin reductase (NADPH) [EC:1.8.1.9]"
+742,"K03648  UNG, UDG, uracil-DNA glycosylase [EC:3.2.2.27]"
+743,"K01849  E5.4.99.2B, mcmA2, methylmalonyl-CoA mutase, C-terminal domain [EC:5.4.99.2]"
+744,"K04077  groEL, HSPD1, chaperonin GroEL [EC:5.6.1.7]"
+745,"K10819  E2.7.13.3, histidine kinase [EC:2.7.13.3]"
+746,"K02475  , two-component system, CitB family, response regulator"
+747,carbohydrate kinase
+748,"K07734  paiB, transcriptional regulator"
+749,"K07503  nucS, endonuclease [EC:3.1.-.-]"
+750,ABC transporter ATP-binding protein/permease
+751,"K03657  uvrD, pcrA, ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]"
+752,"K01903  sucC, succinyl-CoA synthetase beta subunit [EC:6.2.1.5]"
+753,"K01902  sucD, succinyl-CoA synthetase alpha subunit [EC:6.2.1.5]"
+754,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+755,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+756,thiamine pyrophosphate-binding protein
+757,"K05558  , pyridoxamine 5'-phosphate oxidase family protein"
+758,inositol monophosphatase
+759,"K02614  paaI, acyl-CoA thioesterase [EC:3.1.2.-]"
+760,"K00262  E1.4.1.4, gdhA, glutamate dehydrogenase (NADP+) [EC:1.4.1.4]"
+761,aldo/keto reductase
+762,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+763,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+764,"K16168  bpsB, srsB, methyltransferase"
+765,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+766,"K01425  glsA, GLS, glutaminase [EC:3.5.1.2]"
+767,"K03579  hrpB, ATP-dependent helicase HrpB [EC:3.6.4.13]"
+768,extracellular solute-binding protein
+769,sugar ABC transporter permease
+770,carbohydrate ABC transporter permease
+771,"K05816  ugpC, sn-glycerol 3-phosphate transport system ATP-binding protein [EC:7.6.2.10]"
+772,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+773,"K01673  cynT, can, carbonic anhydrase [EC:4.2.1.1]"
+774,"K16237  aroP, aromatic amino acid permease"
+775,"K03781  katE, CAT, catB, srpA, catalase [EC:1.11.1.6]"
+776,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+777,ABC transporter ATP-binding protein
+778,ABC transporter permease
+779,ABC transporter permease
+780,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+781,"K01620  ltaE, threonine aldolase [EC:4.1.2.48]"
+782,"K01142  E3.1.11.2, xthA, exodeoxyribonuclease III [EC:3.1.11.2]"
+783,"K01867  WARS, trpS, tryptophanyl-tRNA synthetase [EC:6.1.1.2]"
+784,ABC transporter ATP-binding protein
+785,ABC transporter permease
+786,"K00240  sdhB, frdB, succinate dehydrogenase iron-sulfur subunit [EC:1.3.5.1]"
+787,"K00239  sdhA, frdA, succinate dehydrogenase flavoprotein subunit [EC:1.3.5.1]"
+788,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+789,"K00241  sdhC, frdC, succinate dehydrogenase cytochrome b subunit"
+790,"K00966  GMPP, mannose-1-phosphate guanylyltransferase [EC:2.7.7.13]"
+791,"K01436  yhaA, amidohydrolase [EC:3.5.1.-]"
+792,BMP family ABC transporter substrate-binding protein
+793,ABC transporter ATP-binding protein
+794,ABC transporter permease
+795,ABC transporter permease
+796,"K00758  deoA, TYMP, thymidine phosphorylase [EC:2.4.2.4]"
+797,"K01488  add, ADA, adenosine deaminase [EC:3.5.4.4]"
+798,"K16168  bpsB, srsB, methyltransferase"
+799,"K01689  ENO, eno, enolase [EC:4.2.1.11]"
+800,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+801,"K03718  asnC, Lrp/AsnC family transcriptional regulator, regulator for asnA, asnC and gidA"
+802,"K01754  E4.3.1.19, ilvA, tdcB, threonine dehydratase [EC:4.3.1.19]"
+803,GPP34 family phosphoprotein
+804,"K03624  greA, transcription elongation factor GreA"
+805,"K18455  mca, mycothiol S-conjugate amidase [EC:3.5.1.115]"
+806,"K11068  hlyIII, hemolysin III"
+807,isoprenyl transferase
+808,"K01519  rdgB, ITPA, XTP/dITP diphosphohydrolase [EC:3.6.1.66]"
+809,glycerophosphodiester phosphodiesterase
+810,"K01676  E4.2.1.2A, fumA, fumB, fumarate hydratase, class I [EC:4.2.1.2]"
+811,"K01673  cynT, can, carbonic anhydrase [EC:4.2.1.1]"
+812,"K01809  manA, MPI, mannose-6-phosphate isomerase [EC:5.3.1.8]"
+813,5-(carboxyamino)imidazole ribonucleotide synthase
+814,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+815,"K01251  AHCY, ahcY, adenosylhomocysteinase [EC:3.13.2.1]"
+816,"K07058  , membrane protein"
+817,"K01910  citC, [citrate (pro-3S)-lyase] ligase [EC:6.2.1.22]"
+818,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+819,"K07056  rsmI, 16S rRNA (cytidine1402-2'-O)-methyltransferase [EC:2.1.1.198]"
+820,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+821,"K01835  pgm, phosphoglucomutase [EC:5.4.2.2]"
+822,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+823,ABC transporter ATP-binding protein/permease
+824,"K00862  eryA, erythritol kinase (D-erythritol 1-phosphate-forming) [EC:2.7.1.215]"
+825,"K06147  ABCB-BAC, ATP-binding cassette, subfamily B, bacterial"
+826,"K19428  epsL, sugar transferase EpsL [EC:2.-.-.-]"
+827,"K04042  glmU, bifunctional UDP-N-acetylglucosamine pyrophosphorylase / glucosamine-1-phosphate N-acetyltransferase [EC:2.7.7.23 2.3.1.157]"
+828,ribose-phosphate diphosphokinase
+829,"K03100  lepB, signal peptidase I [EC:3.4.21.89]"
+830,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+831,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+832,"K01654  neuB, nnaB, N-acetylneuraminate synthase [EC:2.5.1.56]"
+833,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+834,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+835,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+836,"K00973  rfbA, rmlA, rffH, glucose-1-phosphate thymidylyltransferase [EC:2.7.7.24]"
+837,"K02470  gyrB, DNA gyrase subunit B [EC:5.6.2.2]"
+838,PIG-L family deacetylase
+839,"K01710  rfbB, rmlB, rffG, dTDP-glucose 4,6-dehydratase [EC:4.2.1.46]"
+840,sugar nucleotide-binding protein
+841,polysaccharide biosynthesis tyrosine autokinase
+842,"K02847  waaL, rfaL, O-antigen ligase [EC:2.4.1.-]"
+843,50S ribosomal protein L25/general stress protein Ctc
+844,"K01056  PTH1, PTRH1, pth, spoVC, peptidyl-tRNA hydrolase, PTH1 family [EC:3.1.1.29]"
+845,phosphotyrosine protein phosphatase
+846,"K03723  mfd, transcription-repair coupling factor (superfamily II helicase) [EC:5.6.2.4]"
+847,"K00962  pnp, PNPT1, polyribonucleotide nucleotidyltransferase [EC:2.7.7.8]"
+848,polysaccharide biosynthesis tyrosine autokinase
+849,"K02847  waaL, rfaL, O-antigen ligase [EC:2.4.1.-]"
+850,"K01619  deoC, DERA, deoxyribose-phosphate aldolase [EC:4.1.2.4]"
+851,"K01426  E3.5.1.4, amiE, amidase [EC:3.5.1.4]"
+852,phospho-sugar mutase
+853,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+854,"K02625  pcaT, MFS transporter, MHS family, dicarboxylic acid transporter PcaT"
+855,"K20859  phnPP, phosphoribosyl 1,2-cyclic phosphate 1,2-diphosphodiesterase [EC:3.1.4.57]"
+856,"K05555  actIV, cyclase [EC:4.-.-.-]"
+857,"K01972  E6.5.1.2, ligA, ligB, DNA ligase (NAD+) [EC:6.5.1.2]"
+858,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+859,"K02433  gatA, QRSL1, aspartyl-tRNA(Asn)/glutamyl-tRNA(Gln) amidotransferase subunit A [EC:6.3.5.6 6.3.5.7]"
+860,"K02434  gatB, PET112, aspartyl-tRNA(Asn)/glutamyl-tRNA(Gln) amidotransferase subunit B [EC:6.3.5.6 6.3.5.7]"
+861,CPBP family intramembrane metalloprotease
+862,bifunctional o-acetylhomoserine/o-acetylserine sulfhydrylase
+863,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+864,"K01048  pldB, lysophospholipase [EC:3.1.1.5]"
+865,"K14680  E6.5.1.3, RNA ligase [EC:6.5.1.3]"
+866,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+867,sphingosine kinase
+868,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+869,"K21442  ANKRD54, ankyrin repeat domain-containing protein 54"
+870,"K05540  dusB, tRNA-dihydrouridine synthase B [EC:1.-.-.-]"
+871,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+872,ABC transporter ATP-binding protein
+873,NAD-dependent deacylase
+874,"K01875  SARS, serS, seryl-tRNA synthetase [EC:6.1.1.11]"
+875,"K01657  trpE, anthranilate synthase component I [EC:4.1.3.27]"
+876,"K02316  dnaG, DNA primase [EC:2.7.7.101]"
+877,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+878,"K07481  , transposase, IS5 family"
+879,"K14059  int, integrase"
+880,copper-translocating P-type ATPase
+881,"K10819  E2.7.13.3, histidine kinase [EC:2.7.13.3]"
+882,"K02475  , two-component system, CitB family, response regulator"
+883,"K07481  , transposase, IS5 family"
+884,"K01425  glsA, GLS, glutaminase [EC:3.5.1.2]"
+885,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+886,"K01250  rihA, pyrimidine-specific ribonucleoside hydrolase [EC:3.2.2.-]"
+887,aldo/keto reductase
+888,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+889,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+890,"K02357  tsf, TSFM, elongation factor Ts"
+891,"K02469  gyrA, DNA gyrase subunit A [EC:5.6.2.2]"
+892,"K01286  E3.4.16.4, D-alanyl-D-alanine carboxypeptidase [EC:3.4.16.4]"
+893,"K02838  frr, MRRF, RRF, ribosome recycling factor"
+894,"K00981  E2.7.7.41, CDS1, CDS2, cdsA, phosphatidate cytidylyltransferase [EC:2.7.7.41]"
+895,"K04074  divIVA, cell division initiation protein"
+896,"K00161  PDHA, pdhA, pyruvate dehydrogenase E1 component alpha subunit [EC:1.2.4.1]"
+897,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+898,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+899,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+900,zinc-dependent metalloprotease
+901,"K00099  dxr, 1-deoxy-D-xylulose-5-phosphate reductoisomerase [EC:1.1.1.267]"
+902,"K03526  gcpE, ispG, (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase [EC:1.17.7.1 1.17.7.3]"
+903,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+904,"K14680  E6.5.1.3, RNA ligase [EC:6.5.1.3]"
+905,TSUP family transporter
+906,ribosome assembly cofactor RimP
+907,"K02600  nusA, transcription termination/antitermination protein NusA"
+908,"K02519  infB, MTIF2, translation initiation factor IF-2"
+909,"K02834  rbfA, ribosome-binding factor A"
+910,"K03177  truB, PUS4, TRUB1, tRNA pseudouridine55 synthase [EC:5.4.99.25]"
+911,"K00760  hprT, hpt, HPRT1, hypoxanthine phosphoribosyltransferase [EC:2.4.2.8]"
+912,"K00861  RFK, FMN1, riboflavin kinase [EC:2.7.1.26]"
+913,"K16168  bpsB, srsB, methyltransferase"
+914,"K00962  pnp, PNPT1, polyribonucleotide nucleotidyltransferase [EC:2.7.7.8]"
+915,"K00215  dapB, 4-hydroxy-tetrahydrodipicolinate reductase [EC:1.17.1.8]"
+916,"K01714  dapA, 4-hydroxy-tetrahydrodipicolinate synthase [EC:4.3.3.7]"
+917,DNA translocase FtsK
+918,"K00995  pgsA, PGS1, CDP-diacylglycerol---glycerol-3-phosphate 3-phosphatidyltransferase [EC:2.7.8.5]"
+919,"K01436  yhaA, amidohydrolase [EC:3.5.1.-]"
+920,"K03553  recA, recombination protein RecA"
+921,"K07734  paiB, transcriptional regulator"
+922,"K06168  miaB, tRNA-2-methylthio-N6-dimethylallyladenosine synthase [EC:2.8.4.3]"
+923,"K03798  ftsH, hflB, cell division protease FtsH [EC:3.4.24.-]"
+924,"K01778  dapF, diaminopimelate epimerase [EC:5.1.1.7]"
+925,"K16168  bpsB, srsB, methyltransferase"
+926,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+927,"K03665  hflX, GTPase"
+928,"K03726  helS, ATP-dependent DNA helicase [EC:5.6.2.4]"
+929,"K01356  lexA, repressor LexA [EC:3.4.21.88]"
+930,histidinol-phosphate transaminase
+931,"K01495  GCH1, folE, GTP cyclohydrolase IA [EC:3.5.4.16]"
+932,"K02501  hisH, imidazole glycerol-phosphate synthase subunit HisH [EC:4.3.2.10]"
+933,"K04066  priA, primosomal protein N' (replication factor Y) (superfamily II helicase) [EC:5.6.2.4]"
+934,"K03712  marR, MarR family transcriptional regulator, multiple antibiotic resistance protein MarR"
+935,"K00299  ssuE, msuE, FMN reductase [EC:1.5.1.38]"
+936,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+937,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+938,"K00796  folP, dihydropteroate synthase [EC:2.5.1.15]"
+939,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+940,"K03466  ftsK, spoIIIE, DNA segregation ATPase FtsK/SpoIIIE, S-DNA-T family"
+941,"K02283  cpaF, tadA, pilus assembly protein CpaF [EC:7.4.2.8]"
+942,"K02279  cpaB, rcpC, pilus assembly protein CpaB"
+943,"K02836  prfB, peptide chain release factor 2"
+944,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+945,"K00626  ACAT, atoB, acetyl-CoA C-acetyltransferase [EC:2.3.1.9]"
+946,"K00394  aprA, adenylylsulfate reductase, subunit A [EC:1.8.99.2]"
+947,"K03664  smpB, SsrA-binding protein"
+948,"K05602  hisN, histidinol-phosphatase [EC:3.1.3.15]"
+949,"K06949  rsgA, engC, ribosome biogenesis GTPase / thiamine phosphate phosphatase [EC:3.6.1.- 3.1.3.100]"
+950,"K00800  aroA, 3-phosphoshikimate 1-carboxyvinyltransferase [EC:2.5.1.19]"
+951,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+952,"K00088  IMPDH, guaB, IMP dehydrogenase [EC:1.1.1.205]"
+953,"K06075  slyA, MarR family transcriptional regulator, transcriptional regulator for hemolysin"
+954,"K06075  slyA, MarR family transcriptional regulator, transcriptional regulator for hemolysin"
+955,metal ABC transporter substrate-binding protein
+956,metal ABC transporter permease
+957,metal ABC transporter ATP-binding protein
+958,"K00566  mnmA, trmU, tRNA-uridine 2-sulfurtransferase [EC:2.8.1.13]"
+959,"K01233  csn, chitosanase [EC:3.2.1.132]"
+960,"K03578  hrpA, ATP-dependent helicase HrpA [EC:3.6.4.13]"
+961,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+962,"K01246  tag, DNA-3-methyladenine glycosylase I [EC:3.2.2.20]"
+963,"K20859  phnPP, phosphoribosyl 1,2-cyclic phosphate 1,2-diphosphodiesterase [EC:3.1.4.57]"
+964,ABC transporter ATP-binding protein
+965,"K03147  thiC, phosphomethylpyrimidine synthase [EC:4.1.99.17]"
+966,"K00941  thiD, hydroxymethylpyrimidine/phosphomethylpyrimidine kinase [EC:2.7.1.49 2.7.4.7]"
+967,"K00788  thiE, thiamine-phosphate pyrophosphorylase [EC:2.5.1.3]"
+968,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+969,"K03149  thiG, thiazole synthase [EC:2.8.1.10]"
+970,"K20859  phnPP, phosphoribosyl 1,2-cyclic phosphate 1,2-diphosphodiesterase [EC:3.1.4.57]"
+971,ThiF family adenylyltransferase
+972,"K01887  RARS, argS, arginyl-tRNA synthetase [EC:6.1.1.19]"
+973,"K01586  lysA, diaminopimelate decarboxylase [EC:4.1.1.20]"
+974,"K00003  hom, homoserine dehydrogenase [EC:1.1.1.3]"
+975,"K01733  thrC, threonine synthase [EC:4.2.3.1]"
+976,"K00872  thrB, homoserine kinase [EC:2.7.1.39]"
+977,"K03628  rho, transcription termination factor Rho"
+978,"K02835  prfA, MTRF1, MRF1, peptide chain release factor 1"
+979,"K07566  tsaC, rimN, SUA5, YRDC, L-threonylcarbamoyladenylate synthase [EC:2.7.7.87]"
+980,undecaprenyl/decaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphate transferase
+981,"K02108  ATPF0A, atpB, F-type H+-transporting ATPase subunit a"
+982,"K00395  aprB, adenylylsulfate reductase, subunit B [EC:1.8.99.2]"
+983,"K02111  ATPF1A, atpA, F-type H+/Na+-transporting ATPase subunit alpha [EC:7.1.2.2 7.2.2.1]"
+984,"K00305  soxG, sarcosine oxidase, subunit gamma [EC:1.5.3.24 1.5.3.1]"
+985,"K02112  ATPF1B, atpD, F-type H+/Na+-transporting ATPase subunit beta [EC:7.1.2.2 7.2.2.1]"
+986,low molecular weight phosphotyrosine protein phosphatase
+987,"K07503  nucS, endonuclease [EC:3.1.-.-]"
+988,AI-2E family transporter
+989,ABC transporter ATP-binding protein
+990,Tat (twin-arginine translocation) pathway signal sequence
+991,"K06877  , DEAD/DEAH box helicase domain-containing protein"
+992,cadmium-translocating P-type ATPase
+993,"K00763  pncB, NAPRT1, nicotinate phosphoribosyltransferase [EC:6.3.4.21]"
+994,"K06891  clpS, ATP-dependent Clp protease adaptor protein ClpS"
+995,"K01776  murI, glutamate racemase [EC:5.1.1.3]"
+996,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+997,"K00989  rph, ribonuclease PH [EC:2.7.7.56]"
+998,"K07462  recJ, single-stranded-DNA-specific exonuclease [EC:3.1.-.-]"
+999,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+1000,SMC family ATPase
+1001,efflux RND transporter permease subunit
+1002,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+1003,ABC transporter substrate-binding protein
+1004,"K03564  BCP, PRXQ, DOT5, thioredoxin-dependent peroxiredoxin [EC:1.11.1.24]"
+1005,"K01687  ilvD, dihydroxy-acid dehydratase [EC:4.2.1.9]"
+1006,glycerophosphodiester phosphodiesterase
+1007,"K15755  carBb, 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase, large subunit [EC:1.13.11.-]"
+1008,"K01653  E2.2.1.6S, ilvH, ilvN, acetolactate synthase I/III small subunit [EC:2.2.1.6]"
+1009,"K00053  ilvC, ketol-acid reductoisomerase [EC:1.1.1.86]"
+1010,"K00058  serA, PHGDH, D-3-phosphoglycerate dehydrogenase / 2-oxoglutarate reductase [EC:1.1.1.95 1.1.1.399]"
+1011,"K01874  MARS, metG, methionyl-tRNA synthetase [EC:6.1.1.10]"
+1012,"K00052  leuB, IMDH, 3-isopropylmalate dehydrogenase [EC:1.1.1.85]"
+1013,"K00826  E2.6.1.42, ilvE, branched-chain amino acid aminotransferase [EC:2.6.1.42]"
+1014,"K06200  cstA, carbon starvation protein"
+1015,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+1016,"K01885  EARS, gltX, glutamyl-tRNA synthetase [EC:6.1.1.17]"
+1017,"K03595  era, ERAL1, GTPase"
+1018,thiamine-phosphate kinase
+1019,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+1020,"K02624  pcaR, IclR family transcriptional regulator, pca regulon regulatory protein"
+1021,"K01703  leuC, IPMI-L, 3-isopropylmalate/(R)-2-methylmalate dehydratase large subunit [EC:4.2.1.33 4.2.1.35]"
+1022,"K01704  leuD, IPMI-S, 3-isopropylmalate/(R)-2-methylmalate dehydratase small subunit [EC:4.2.1.33 4.2.1.35]"
+1023,"K00655  plsC, 1-acyl-sn-glycerol-3-phosphate acyltransferase [EC:2.3.1.51]"
+1024,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+1025,"K01910  citC, [citrate (pro-3S)-lyase] ligase [EC:6.2.1.22]"
+1026,"K03655  recG, ATP-dependent DNA helicase RecG [EC:5.6.2.4]"
+1027,"K08316  rsmD, 16S rRNA (guanine966-N2)-methyltransferase [EC:2.1.1.171]"
+1028,"K00841  patA, aminotransferase [EC:2.6.1.-]"
+1029,"K00954  E2.7.7.3A, coaD, kdtB, pantetheine-phosphate adenylyltransferase [EC:2.7.7.3]"
+1030,"K00963  UGP2, galU, galF, UTP--glucose-1-phosphate uridylyltransferase [EC:2.7.7.9]"
+1031,"K03685  rnc, DROSHA, RNT1, ribonuclease III [EC:3.1.26.3]"
+1032,"K10563  mutM, fpg, formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18]"
+1033,"K01918  panC, pantoate--beta-alanine ligase [EC:6.3.2.1]"
+1034,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+1035,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+1036,"K02472  wecC, UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase [EC:1.1.1.336]"
+1037,"K01784  galE, GALE, UDP-glucose 4-epimerase [EC:5.1.3.2]"
+1038,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+1039,ABC transporter ATP-binding protein
+1040,"K01791  wecB, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) [EC:5.1.3.14]"
+1041,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+1042,"K03110  ftsY, fused signal recognition particle receptor"
+1043,"K03320  amt, AMT, MEP, ammonium transporter, Amt family"
+1044,"K03106  SRP54, ffh, signal recognition particle subunit SRP54 [EC:3.6.5.4]"
+1045,"K02860  rimM, 16S rRNA processing protein RimM"
+1046,"K00554  trmD, tRNA (guanine37-N1)-methyltransferase [EC:2.1.1.228]"
+1047,"K02884  RP-L19, MRPL19, rplS, large subunit ribosomal protein L19"
+1048,"K03100  lepB, signal peptidase I [EC:3.4.21.89]"
+1049,"K03100  lepB, signal peptidase I [EC:3.4.21.89]"
+1050,"K03470  rnhB, ribonuclease HII [EC:3.1.26.4]"
+1051,YifB family Mg chelatase-like AAA ATPase
+1052,DNA-protecting protein DprA
+1053,"K09458  fabF, OXSM, CEM1, 3-oxoacyl-[acyl-carrier-protein] synthase II [EC:2.3.1.179]"
+1054,ketoacyl-ACP synthase III
+1055,"K00645  fabD, MCAT, MCT1, [acyl-carrier-protein] S-malonyltransferase [EC:2.3.1.39]"
+1056,M13 family metallopeptidase
+1057,"K00163  aceE, pyruvate dehydrogenase E1 component [EC:1.2.4.1]"
+1058,AzlC family ABC transporter permease
+1059,"K22468  ppk2, polyphosphate kinase [EC:2.7.4.34]"
+1060,"K03712  marR, MarR family transcriptional regulator, multiple antibiotic resistance protein MarR"
+1061,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+1062,"K00640  cysE, serine O-acetyltransferase [EC:2.3.1.30]"
+1063,"K01738  cysK, cysteine synthase [EC:2.5.1.47]"
+1064,"K07304  msrA, peptide-methionine (S)-S-oxide reductase [EC:1.8.4.11]"
+1065,"K03111  ssb, single-strand DNA-binding protein"
+1066,reverse transcriptase-like protein
+1067,"K00131  gapN, glyceraldehyde-3-phosphate dehydrogenase (NADP+) [EC:1.2.1.9]"
+1068,"K02100  araE, MFS transporter, SP family, arabinose:H+ symporter"
+1069,"K01462  PDF, def, peptide deformylase [EC:3.5.1.88]"
+1070,"K07481  , transposase, IS5 family"
+1071,"K07481  , transposase, IS5 family"
+1072,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+1073,"K13288  orn, REX2, REXO2, oligoribonuclease [EC:3.1.-.-]"
+1074,"K14339  mptB, alpha-1,6-mannosyltransferase [EC:2.4.1.-]"
+1075,"K14339  mptB, alpha-1,6-mannosyltransferase [EC:2.4.1.-]"
+1076,"K15929  jadS, glycosyltransferase [EC:2.4.1.-]"
+1077,"K03111  ssb, single-strand DNA-binding protein"
+1078,"K06020  ettA, energy-dependent translational throttle protein EttA"
+1079,"K06886  glbN, hemoglobin"
+1080,"K04567  KARS, lysS, lysyl-tRNA synthetase, class II [EC:6.1.1.6]"
+1081,"K01256  pepN, aminopeptidase N [EC:3.4.11.2]"
+1082,"K10563  mutM, fpg, formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18]"
+1083,"K03545  tig, trigger factor"
+1084,"K01358  clpP, CLPP, ATP-dependent Clp protease, protease subunit [EC:3.4.21.92]"
+1085,"K01358  clpP, CLPP, ATP-dependent Clp protease, protease subunit [EC:3.4.21.92]"
+1086,"K03544  clpX, CLPX, ATP-dependent Clp protease ATP-binding subunit ClpX"
+1087,"K07058  , membrane protein"
+1088,"K01873  VARS, valS, valyl-tRNA synthetase [EC:6.1.1.9]"
+1089,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+1090,"K02190  cbiK, sirohydrochlorin cobaltochelatase [EC:4.99.1.3]"
+1091,"K00392  sir, sulfite reductase (ferredoxin) [EC:1.8.7.1]"
+1092,phosphoadenylyl-sulfate reductase
+1093,"K00957  cysD, sulfate adenylyltransferase subunit 2 [EC:2.7.7.4]"
+1094,"K03978  engB, GTP-binding protein"
+1095,ABC transporter ATP-binding protein
+1096,ABC transporter permease subunit
+1097,"K02303  cobA, uroporphyrin-III C-methyltransferase [EC:2.1.1.107]"
+1098,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+1099,TIGR03085 family metal-binding protein
+1100,"K01870  IARS, ileS, isoleucyl-tRNA synthetase [EC:6.1.1.5]"
+1101,"K01910  citC, [citrate (pro-3S)-lyase] ligase [EC:6.2.1.22]"
+1102,"K00940  ndk, NME, nucleoside-diphosphate kinase [EC:2.7.4.6]"
+1103,Rne/Rng family ribonuclease
+1104,"K01358  clpP, CLPP, ATP-dependent Clp protease, protease subunit [EC:3.4.21.92]"
+1105,"K03979  obgE, cgtA, MTG2, GTPase [EC:3.6.5.-]"
+1106,"K00931  proB, glutamate 5-kinase [EC:2.7.2.11]"
+1107,"K00147  proA, glutamate-5-semialdehyde dehydrogenase [EC:1.2.1.41]"
+1108,"K00969  nadD, nicotinate-nucleotide adenylyltransferase [EC:2.7.7.18]"
+1109,"K08296  sixA, phosphohistidine phosphatase [EC:3.1.3.-]"
+1110,"K16015  rifL, asm44, oxidoreductase [EC:1.1.1.-]"
+1111,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+1112,"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]"
+1113,"K02521  ilvY, LysR family transcriptional regulator, positive regulator for ilvC"
+1114,"K00619  argA, amino-acid N-acetyltransferase [EC:2.3.1.1]"
+1115,"K18566  thnF, cmmF, N-acetyltransferase [EC:2.3.1.-]"
+1116,"K00526  E1.17.4.1B, nrdB, nrdF, ribonucleoside-diphosphate reductase beta chain [EC:1.17.4.1]"
+1117,MetQ/NlpA family ABC transporter substrate-binding protein
+1118,methionine ABC transporter ATP-binding protein
+1119,"K21791  redJ, thioesterase"
+1120,"K01910  citC, [citrate (pro-3S)-lyase] ligase [EC:6.2.1.22]"
+1121,"K18569  thnH, hydrolase [EC:3.1.3.-]"
+1122,"K20571  kanC, dehydrogenase [EC:1.1.1.-]"
+1123,SOS response-associated peptidase
+1124,"K02337  dnaE, DNA polymerase III subunit alpha [EC:2.7.7.7]"
+1125,"K01868  TARS, thrS, threonyl-tRNA synthetase [EC:6.1.1.3]"
+1126,"K01233  csn, chitosanase [EC:3.2.1.132]"
+1127,"K07560  dtd, DTD, D-aminoacyl-tRNA deacylase [EC:3.1.1.96]"
+1128,"K02426  sufE, cysteine desulfuration protein SufE"
+1129,"K00566  mnmA, trmU, tRNA-uridine 2-sulfurtransferase [EC:2.8.1.13]"
+1130,"K06916  zapE, cell division protein ZapE"
+1131,"K04485  radA, sms, DNA repair protein RadA/Sms"
+1132,"K01462  PDF, def, peptide deformylase [EC:3.5.1.88]"
+1133,"K00604  MTFMT, fmt, methionyl-tRNA formyltransferase [EC:2.1.2.9]"
+1134,"K16168  bpsB, srsB, methyltransferase"
+1135,"K01783  rpe, RPE, ribulose-phosphate 3-epimerase [EC:5.1.3.1]"
+1136,"K03811  pnuC, nicotinamide mononucleotide transporter"
+1137,"K11752  ribD, diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase [EC:3.5.4.26 1.1.1.193]"
+1138,"K00793  ribE, RIB5, riboflavin synthase [EC:2.5.1.9]"
+1139,"K01497  ribA, RIB1, GTP cyclohydrolase II [EC:3.5.4.25]"
+1140,"K03892  arsR, ArsR family transcriptional regulator, arsenate/arsenite/antimonite-responsive transcriptional repressor"
+1141,"K02040  pstS, phosphate transport system substrate-binding protein"
+1142,"K03699  tlyC, magnesium and cobalt exporter, CNNM family"
+1143,"K06075  slyA, MarR family transcriptional regulator, transcriptional regulator for hemolysin"
+1144,"K00765  hisG, ATP phosphoribosyltransferase [EC:2.4.2.17]"
+1145,"K02500  hisF, imidazole glycerol-phosphate synthase subunit HisF [EC:4.3.2.10]"
+1146,"K01496  hisI, phosphoribosyl-AMP cyclohydrolase [EC:3.5.4.19]"
+1147,"K02037  pstC, phosphate transport system permease protein"
+1148,chorismate-binding protein
+1149,"K07058  , membrane protein"
+1150,"K01609  trpC, indole-3-glycerol phosphate synthase [EC:4.1.1.48]"
+1151,"K01696  trpB, tryptophan synthase beta chain [EC:4.2.1.20]"
+1152,"K01695  trpA, tryptophan synthase alpha chain [EC:4.2.1.20]"
+1153,"K13292  lgt, umpA, phosphatidylglycerol---prolipoprotein diacylglyceryl transferase [EC:2.5.1.145]"
+1154,"K00265  gltB, glutamate synthase (NADPH) large chain [EC:1.4.1.13]"
+1155,"K00284  GLU, gltS, glutamate synthase (ferredoxin) [EC:1.4.7.1]"
+1156,"K00873  PK, pyk, pyruvate kinase [EC:2.7.1.40]"

Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/comparative-genomics_20260523_124658/final_answer.txt

@@ -0,0 +1,31 @@
+I apologize for the oversight. Let me provide the final summary with the proper formatting.
+
+The task has been completed successfully. Here's a summary of what was accomplished:
+
+**Approach:**
+1. Extracted 2,200 CDS protein sequences from the reference genome (GCF_023573625.1 - Micrococcus yunnanensis TT9) using GFF annotations
+2. Predicted ORFs from 4 other Micrococcus genomes using `annotate_open_reading_frames`
+3. Performed reciprocal best-hit (RBH) BLASTP analysis to identify ortholog clusters across all 5 genomes
+4. Used the Actinobacteria.RData reference (KEGG-based RDP classifier) to map proteins to KEGG Orthology (KO) numbers
+5. Filtered for clusters present in all genomes with high-confidence annotations
+6. Generated 1,156 co-evolving gene clusters with consensus annotations
+
+**Output file**: `/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/comparative-genomics_20260523_124658/cluster_annotation_mapping.csv`
+
+The solution is ready.
+
+<solution>
+The final output file has been successfully generated at:
+/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100_rerun_sharded10_20260523_124655/comparative-genomics_20260523_124658/cluster_annotation_mapping.csv
+
+The CSV contains 1,156 entries with the format:
+- cluster_number (sequential integer)
+- consensus_annotation (KO number + description, e.g., "K02038  pstA, phosphate transport system permease protein")
+
+Key results:
+- 1,156 high-confidence co-evolving gene clusters identified across all 5 Micrococcus genomes
+- 934 clusters (80.8%) have KEGG Orthology (KO) annotations
+- 222 clusters have product-based annotations
+- 580 unique KO numbers represented
+- All clusters are present in all genomes (core genome)
+</solution>