GapMind for catabolism of small carbon sources

 

L-arginine catabolism

Analysis of pathway arginine in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 rocE, adiA, speB, patA, patD, gabT, gabD
Acidithiobacillus ferrooxidans ATCC 23270 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Acidovorax sp. GW101-3H11 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Algiphilus aromaticivorans DG1253 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Alicycliphilus denitrificans K601 artJ, artM, artP, artQ, rocF, ocd, put1, putA
Alkalihalobacterium alkalinitrilicum DSM 22532 bgtB, artP, rocF, rocD, PRO3, put1, putA
Allochromatium vinosum DSM 180 rocE, rocF, rocD, rocA
Ammonifex degensii KC4 rocE, adiA, speB, patA, patD, gabT, gabD
Anaerobutyricum hallii DSM 3353 rocE, arcA, arcB, arcC, rocD, rocA
Aquimarina longa SW024 rocE, rocF, rocD, PRO3, put1, putA
Archaeoglobus veneficus SNP6 rocE, adiA, speB, patA, patD, gabT, gabD
Arcobacter nitrofigilis DSM 7299 rocE, adiA, speB, patA, patD, gabT, gabD
Azoarcus olearius BH72 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Azohydromonas australica DSM 1124 rocE, rocF, ocd, put1, putA
Azorhizobium caulinodans ORS 571 braC, braD, braE, braF, braG, adiA, speB, patA, patD, gabT, gabD
Azospirillum brasilense Sp245 braC, braD, braE, braF, braG, arcA, arcB, arcC, rocD, PRO3, put1, putA
Azospirillum sp. B510 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Bacteroides thetaiotaomicron VPI-5482 rocE, rocF, rocD, rocA
Beijerinckia indica ATCC 9039 rocE, rocF, rocD, PRO3, put1, putA
Beijerinckia mobilis UQM 1969 rocE, rocF, rocD, PRO3, put1, putA
Billgrantia desiderata SP1 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Bradyrhizobium sp. BTAi1 braC, braD, braE, braF, braG, rocF, odc, patA, patD, gabT, gabD
Brevundimonas sp. GW460-12-10-14-LB2 rocE, astA, astB, astC, astD, astE
Burkholderia phytofirmans PsJN artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Burkholderia vietnamiensis G4 artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Calditerrivibrio nitroreducens DSM 19672 rocE, rocF, rocD, PRO3, put1, putA
Caminibacter mediatlanticus TB-2 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Carboxydothermus pertinax Ug1 rocE, adiA, speB, patA, patD, gabT, gabD
Caulobacter crescentus NA1000 rocE, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Cereibacter sphaeroides ATCC 17029 bgtB, artP, rocF, odc, puuA, puuB, puuC, puuD, gabT, gabD
Chlorobaculum parvum NCIB 8327 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Chlorobaculum tepidum TLS rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Chlorobium limicola DSM 245 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Chlorobium phaeobacteroides BS1 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Clostridium acetobutylicum ATCC 824 rocE, rocF, rocD, rocA
Clostridium kluyveri DSM 555 rocE, adiA, speB, patA, patD, gabT, gabD
Clostridium tyrobutyricum FAM22553 rocE, rocF, rocD, PRO3, prdF, prdA, prdB, prdC, davT, davD, gcdG, gcdH, ech, fadB, atoB
Crocosphaera subtropica ATCC 51142 rocE, rocF, rocD, rocA
Cupriavidus basilensis FW507-4G11 artJ, artM, artP, artQ, rocF, ocd, put1, putA
Dechloromonas agitata is5 rocE, rocF, rocD, PRO3, put1, putA
Dechlorosoma suillum PS rocE, rocF, rocD, rocA
Dehalococcoides mccartyi 195 rocE, rocF, rocD, rocA
Denitrovibrio acetiphilus DSM 12809 rocE, rocF, rocD, PRO3, put1, putA
Derxia gummosa DSM 723 rocE, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Desulfacinum hydrothermale DSM 13146 rocE, rocF, rocD, rocA
Desulfacinum infernum DSM 9756 rocE, rocF, rocD, rocA
Desulfarculus baarsii DSM 2075 rocE, adiA, speB, patA, patD, gabT, gabD
Desulfatibacillum aliphaticivorans DSM 15576 rocE, adiA, speB, patA, patD, gabT, gabD
Desulfatiglans anilini DSM 4660 rocE, rocF, rocD, rocA
Desulfitobacterium hafniense DCB-2 rocE, adiA, speB, patA, patD, gabT, gabD
Desulfobacca acetoxidans DSM 11109 rocE, rocF, rocD, rocA
Desulfobacter vibrioformis DSM 8776 rocE, rocF, rocD, rocA
Desulfogranum mediterraneum DSM 13871 braC, braD, braE, braF, braG, rocF, rocD, rocA
Desulforamulus ruminis DSM 2154 rocE, rocF, rocD, PRO3, put1, putA
Desulfoscipio geothermicus DSM 3669 rocE, adiA, speB, patA, patD, gabT, gabD
Desulfotalea psychrophila LSv54 rocE, rocF, rocD, PRO3, put1, putA
Desulfovibrio oxyclinae DSM 11498 braC, braD, braE, braF, braG, rocF, rocD, rocA
Desulfovibrio vulgaris Hildenborough JW710 rocE, rocF, rocD, PRO3, put1, putA
Desulfovibrio vulgaris Miyazaki F rocE, rocF, rocD, PRO3, put1, putA
Desulfurobacterium atlanticum DSM 15668 rocE, rocF, rocD, rocA
Desulfuromonas acetexigens rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Desulfuromusa kysingii DSM 7343 rocE, rocF, rocD, PRO3, put1, putA
Dinoroseobacter shibae DFL-12 artJ, artM, artP, artQ, arcA, arcB, arcC, ocd, put1, putA
Dyella japonica UNC79MFTsu3.2 rocE, rocF, rocD, PRO3, put1, putA
Echinicola vietnamensis KMM 6221, DSM 17526 rocE, rocF, rocD, PRO3, put1, putA
Escherichia coli BW25113 artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Ferroglobus placidus DSM 10642 rocE, rocF, ocd, put1, putA
Frankia alni ACN14a rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Geobacter metallireducens GS-15 rocE, arcA, arcB, arcC, rocD, rocA
Geotalea uraniireducens Rf4 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Halococcus hamelinensis 100A6 rocE, adiA, speB, patA, patD, gabT, gabD
Haloechinothrix alba DSM 45207 rocE, rocF, rocD, PRO3, put1, putA
Haloferax volcanii DS2 rocE, adiA, speB*, patA, patD, gabT, gabD
Haloglycomyces albus DSM 45210 rocE, arcA, arcB, arcC, ocd, put1, putA
Halorhodospira halophila SL1 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Heliomicrobium modesticaldum Ice1; ATCC 51547 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Herbaspirillum autotrophicum IAM 14942 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Herbaspirillum seropedicae SmR1 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Hippea alviniae EP5-r rocE, rocF, rocD, PRO3, put1, putA
Hydrogenophaga taeniospiralis NBRC 102512 artJ, artM, artP, artQ, rocF, ocd, put1, putA
Hydrogenovibrio halophilus DSM 15072 rocE, rocF, rocD, rocA
Hydrogenovibrio kuenenii DSM 12350 rocE, rocF, rocD, rocA
Hydrogenovibrio marinus DSM 11271 rocE, rocF, rocD, rocA
Hyphomicrobium sulfonivorans WDL6 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Klebsiella michiganensis M5al artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Klebsiella variicola At-22 artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Kyrpidia tusciae DSM 2912 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Leptospirillum ferrooxidans C2-3 rocE, rocF, rocD, rocA
Magnetospirillum magneticum AMB-1 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Malonomonas rubra DSM 5091 rocE, rocF, rocD, PRO3, put1, putA
Maridesulfovibrio bastinii DSM 16055 braC, braD, braE, braF, braG, arcA, arcB, arcC, rocD, rocA
Maridesulfovibrio zosterae DSM 11974 rocE, rocF, rocD, rocA
Marinobacter adhaerens HP15 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Mesorhizobium ciceri WSM1271 braC, braD, braE, braF, braG, aruH, aruI, kauB, gbuA, gabT, gabD
Methanobacterium lacus AL-21 rocE, adiA, speB, patA, patD, gabT, gabD
Methanococcus aeolicus Nankai-3 rocE, rocF, rocD, rocA
Methanococcus maripaludis C5 rocE, rocF, rocD, rocA
Methanosarcina acetivorans C2A rocE, adiA, speB, patA, patD, gabT, gabD
Methanosarcina mazei Go1 rocE, adiA, speB, patA, patD, gabT, gabD
Methanospirillum lacunae Ki8-1 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Methanothermobacter thermautotrophicus Delta H rocE, adiA, speB, patA, patD, gabT, gabD
Methylobacterium nodulans ORS 2060 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Methylobacterium sp. 4-46 Apr-46 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Methylocapsa acidiphila B2 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Methylocapsa aurea KYG braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Methylocella silvestris BL2 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Methylococcus capsulatus Bath rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Methylocystis bryophila S285 rocE, rocF, rocD, PRO3, put1, putA
Methyloferula stellata AR4T braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Methylohalobius crimeensis 10Ki rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Methylomonas methanica MC09 rocE, rocF, rocD, PRO3, put1, putA
Methylosarcina fibrata AML-C10 rocE, arcA, arcB, arcC, ocd, put1, putA
Methylotuvimicrobium alcaliphilum 20Z rocE, rocF, ocd, put1, putA
Methylovulum miyakonense HT12 bgtB, artP, rocF, rocD, rocA
Mycolicibacterium vanbaalenii PYR-1 bgtB, artP, arcA, arcB, arcC, rocD, PRO3, put1, putA
Nitratifractor salsuginis DSM 16511 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Nitratiruptor tergarcus DSM 16512 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Nitriliruptor alkaliphilus DSM 45188 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Nocardioides dokdonensis FR1436 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Nocardiopsis lucentensis DSM 44048 rocE, arg-monooxygenase, gbamidase, kauB, gbuA, gabT, gabD
Nostoc punctiforme ATCC 29133; PCC 73102 bgtB, artP, rocF, rocD, rocA
Novosphingobium aromaticivorans DSM 12444 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Oleispira antarctica rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Paraburkholderia atlantica CCGE1002 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Paraburkholderia bryophila 376MFSha3.1 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Paraburkholderia phymatum STM815 artJ, artM, artP, artQ, arcA, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Paucidesulfovibrio gracilis DSM 16080 braC, braD, braE, braF, braG, rocF, rocD, rocA
Pedobacter sp. GW460-11-11-14-LB5 rocE, rocF, rocD, PRO3, put1, putA
Pelobacter propionicus DSM 2379 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Persephonella marina EX-H1 rocE, rocF, rocD, rocA
Phaeacidiphilus oryzae TH49 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Phaeobacter inhibens BS107 artJ, artM, artP, artQ, rocF, ocd, put1, putA
Polaromonas naphthalenivorans CJ2 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Prosthecochloris aestuarii DSM 271 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Pseudarthrobacter sulfonivorans Ar51 rocE, arg-monooxygenase, gbamidase, kauB, gbuA, gabT, gabD
Pseudomonas benzenivorans DSM 8628 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Pseudomonas fluorescens FW300-N1B4 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Pseudomonas fluorescens FW300-N2C3 artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas fluorescens FW300-N2E2 artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas fluorescens FW300-N2E3 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Pseudomonas fluorescens GW456-L13 artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas putida KT2440 artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Pseudomonas simiae WCS417 artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas stutzeri RCH2 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Pyrolobus fumarii 1A rocE, adiA, speB, patA, patD, gabT, gabD
Rhizobium etli CFN 42 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Rhizobium johnstonii 3841 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Rhizobium leguminosarum WSM1325 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Rhizorhabdus wittichii RW1 rocE, rocF, ocd, put1, putA
Rhodanobacter denitrificans FW104-10B01 rocE, rocF, rocD, PRO3, put1, putA
Rhodomicrobium vannielii ATCC 17100 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Rhodopseudomonas palustris CGA009 braC, braD, braE, braF, braG, rocF, odc, puuA, puuB, puuC, puuD, gabT, gabD
Rhodospirillum centenum SW; ATCC 51521 braC, braD, braE, braF, braG, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Rhodospirillum rubrum ATCC 11170 artJ, artM, artP, artQ, rocF, rocD, PRO3, put1, putA
Roseburia faecis M72 rocE, arcA, arcB, arcC, rocD, PRO3, put1*, putA
Saccharomonospora cyanea NA-134 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Sedimenticola selenatireducens DSM 17993 artJ, artM, artP, artQ, rocF, ocd, put1, putA
Shewanella amazonensis SB2B rocE, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Shewanella loihica PV-4 rocE, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Shewanella oneidensis MR-1 rocE, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Shewanella sp. ANA-3 rocE, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Sinorhizobium fredii NGR234 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Sinorhizobium medicae WSM419 braC, braD, braE, braF, braG, arcA, arcB, arcC, ocd, put1, putA
Sinorhizobium meliloti 1021 braC, braD, braE, braF, braG, arcA, arcB, arcC, ocd, put1, putA
Sphingomonas koreensis DSMZ 15582 rocE, astA, astB, astC, astD, astE
Stenotrophomonas chelatiphaga DSM 21508 rocE, rocF, rocD, PRO3, put1, putA
Steroidobacter denitrificans DSM 18526 rocE, rocF, ocd, put1, putA
Stutzerimonas stutzeri A1501 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Sulfuricurvum kujiense DSM 16994 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Sulfurihydrogenibium azorense Az-Fu1 rocE, rocF, rocD, rocA
Sulfurihydrogenibium subterraneum DSM 15120 rocE, rocF, rocD, rocA
Sulfurimonas denitrificans DSM 1251 rocE, rocF, rocD, rocA
Sulfuritalea hydrogenivorans DSM 22779 rocE, rocF, rocD, rocA
Sulfurivirga caldicuralii DSM 17737 rocE, rocF, rocD, rocA
Synechococcus elongatus PCC 7942 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Teredinibacter turnerae T7901 rocE, astA, astB, astC, astD, astE
Thauera aminoaromatica S2 artJ, artM, artP, artQ, rocF, ocd, put1*, putA
Thermithiobacillus tepidarius DSM 3134 rocE, rocF, rocD, rocA
Thermocrinis albus DSM 14484 rocE, rocF, rocD, rocA
Thermodesulforhabdus norvegica DSM 9990 rocE, rocF, rocD, PRO3, put1, putA
Thermomonospora curvata DSM 43183 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Thermovibrio ammonificans HB-1 rocE, adiA, speB, patA, patD, gabT, gabD
Thermus aquaticus YT-1 rocE, rocF, rocD, PRO3, put1, putA
Thioalkalivibrio denitrificans ALJD rocE, rocF, orr, oraS, oraE, ord, ortA, ortB
Thioalkalivibrio halophilus HL17 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Thioalkalivibrio paradoxus ARh 1 rocE, rocF, rocD, PRO3, put1, putA
Thioalkalivibrio thiocyanodenitrificans ARhD 1 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Thiohalomonas denitrificans HLD2 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Thiohalospira halophila HL 3 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Thiomicrorhabdus arctica DSM 13458 rocE, rocF, odc, patA, patD, gabT, gabD
Thiomicrorhabdus chilensis DSM 12352 rocE, rocF, rocD, rocA
Thiomicrospira cyclica ALM1 rocE, rocF, rocD, rocA
Thiomicrospira microaerophila ASL8-2 rocE, rocF, rocD, rocA
Thiomicrospira pelophila DSM 1534 rocE, rocF, rocD, rocA
Thiothrix lacustris DSM 21227 artJ, artM, artP, artQ, adiA, aguA, aguB, patA, patD, gabT, gabD
Tistlia consotensis USBA 355 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Trichlorobacter lovleyi SZ rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome rocE, adiA, speB, patA, patD, gabT, gabD
Trichormus variabilis ATCC 29413 bgtB, artP, rocF, rocD, rocA
Xanthobacter autotrophicus Py2 braC, braD, braE, braF, braG, adiA, speB, patA, patD, gabT, gabD
Xenophilus azovorans DSM 13620 braC, braD, braE, braF, braG, rocF, ocd, put1, putA

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory