GapMind for catabolism of small carbon sources

 

L-proline catabolism

Analysis of pathway proline in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 natA, natB, natC*, natD, natE, put1, putA
Acidithiobacillus ferrooxidans ATCC 23270 proY, put1, putA
Acidovorax sp. GW101-3H11 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Algiphilus aromaticivorans DG1253 ectP, put1, putA
Alicycliphilus denitrificans K601 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Alkalihalobacterium alkalinitrilicum DSM 22532 putP, put1, putA
Allochromatium vinosum DSM 180 ectP, put1, putA
Ammonifex degensii KC4 natA, natB, natC, natD*, natE, put1, putA
Anaerobutyricum hallii DSM 3353 putP, put1, putA
Aquimarina longa SW024 proY, put1, putA
Archaeoglobus veneficus SNP6 putP, put1, putA
Arcobacter nitrofigilis DSM 7299 proV, proW, proX, put1, putA
Azoarcus olearius BH72 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Azohydromonas australica DSM 1124 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Azorhizobium caulinodans ORS 571 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Azospirillum brasilense Sp245 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Azospirillum sp. B510 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Bacteroides thetaiotaomicron VPI-5482 proY, put1, putA
Beijerinckia indica ATCC 9039 N515DRAFT_2924, put1, putA
Beijerinckia mobilis UQM 1969 N515DRAFT_2924, put1, putA
Billgrantia desiderata SP1 putP, put1, putA
Bradyrhizobium sp. BTAi1 aapJ, aapQ, aapM, aapP, put1, putA
Brevundimonas sp. GW460-12-10-14-LB2 betS, put1, putA
Burkholderia phytofirmans PsJN HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Burkholderia vietnamiensis G4 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Calditerrivibrio nitroreducens DSM 19672 proY, put1, putA
Caminibacter mediatlanticus TB-2 proY, put1, putA
Carboxydothermus pertinax Ug1 proY, put1, putA
Caulobacter crescentus NA1000 CCNA_00435, put1, putA
Cereibacter sphaeroides ATCC 17029 ectP, put1, putA
Chlorobaculum parvum NCIB 8327 proY, put1, putA
Chlorobaculum tepidum TLS CCNA_00435, put1, putA
Chlorobium limicola DSM 245 CCNA_00435, put1, putA
Chlorobium phaeobacteroides BS1 proY, put1, putA
Clostridium acetobutylicum ATCC 824 opuBA, opuBB, put1, putA
Clostridium kluyveri DSM 555 opuBA, opuBB, put1*, putA
Clostridium tyrobutyricum FAM22553 opuBA, opuBB, prdF, prdA, prdB, prdC, davT, davD, gcdG, gcdH, ech, fadB, atoB
Crocosphaera subtropica ATCC 51142 natA, natB, natC, natD, natE, put1, putA
Cupriavidus basilensis FW507-4G11 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Dechloromonas agitata is5 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Dechlorosoma suillum PS HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Dehalococcoides mccartyi 195 proY, put1, putA
Denitrovibrio acetiphilus DSM 12809 proV, proW, proX, put1, putA
Derxia gummosa DSM 723 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Desulfacinum hydrothermale DSM 13146 aapJ, aapQ, aapM, aapP, put1, putA
Desulfacinum infernum DSM 9756 aapJ, aapQ, aapM, aapP, put1, putA
Desulfarculus baarsii DSM 2075 proY, put1, putA
Desulfatibacillum aliphaticivorans DSM 15576 proV, proW, proX, put1, putA
Desulfatiglans anilini DSM 4660 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Desulfitobacterium hafniense DCB-2 putP, put1, putA
Desulfobacca acetoxidans DSM 11109 proY, put1, putA
Desulfobacter vibrioformis DSM 8776 proV, proW, proX, put1, putA
Desulfogranum mediterraneum DSM 13871 proV, proW, proX, put1, putA
Desulforamulus ruminis DSM 2154 proY, put1, putA
Desulfoscipio geothermicus DSM 3669 hutV, hutW, hutX, put1, putA
Desulfotalea psychrophila LSv54 proV, proW, proX, put1, putA
Desulfovibrio oxyclinae DSM 11498 proV, proW, proX, put1, putA
Desulfovibrio vulgaris Hildenborough JW710 proY, put1, putA
Desulfovibrio vulgaris Miyazaki F proY, put1, putA
Desulfurobacterium atlanticum DSM 15668 proY, put1, putA
Desulfuromonas acetexigens ectP, put1, putA
Desulfuromusa kysingii DSM 7343 proV, proW, proX, put1, putA
Dinoroseobacter shibae DFL-12 aapJ, aapQ, aapM, aapP, put1, putA
Dyella japonica UNC79MFTsu3.2 N515DRAFT_2924, put1, putA
Echinicola vietnamensis KMM 6221, DSM 17526 ectP, put1, putA
Escherichia coli BW25113 proV, proW, proX, put1, putA
Ferroglobus placidus DSM 10642 putP, put1, putA
Frankia alni ACN14a HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Geobacter metallireducens GS-15 proY, put1, putA
Geotalea uraniireducens Rf4 proY, put1, putA
Halococcus hamelinensis 100A6 ectP, put1, putA
Haloechinothrix alba DSM 45207 putP, put1, putA
Haloferax volcanii DS2 ectP, put1, putA
Haloglycomyces albus DSM 45210 putP, put1, putA
Halorhodospira halophila SL1 putP, put1, putA
Heliomicrobium modesticaldum Ice1; ATCC 51547 CCNA_00435, put1, putA
Herbaspirillum autotrophicum IAM 14942 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Herbaspirillum seropedicae SmR1 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Hippea alviniae EP5-r proY, put1, putA
Hydrogenophaga taeniospiralis NBRC 102512 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Hydrogenovibrio halophilus DSM 15072 ectP, put1, putA
Hydrogenovibrio kuenenii DSM 12350 ectP, put1, putA
Hydrogenovibrio marinus DSM 11271 proY, put1, putA
Hyphomicrobium sulfonivorans WDL6 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Klebsiella michiganensis M5al HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Klebsiella variicola At-22 proV, proW, proX, put1, putA
Kyrpidia tusciae DSM 2912 proY, put1, putA
Leptospirillum ferrooxidans C2-3 proY, put1, putA
Magnetospirillum magneticum AMB-1 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Malonomonas rubra DSM 5091 proV, proW, proX, put1, putA
Maridesulfovibrio bastinii DSM 16055 aapJ, aapQ, aapM, aapP, put1, putA
Maridesulfovibrio zosterae DSM 11974 putP, put1, putA
Marinobacter adhaerens HP15 putP, put1, putA
Mesorhizobium ciceri WSM1271 aapJ, aapQ, aapM, aapP, put1, putA
Methanobacterium lacus AL-21 putP, put1, putA
Methanococcus aeolicus Nankai-3 proY, put1, putA
Methanococcus maripaludis C5 putP, put1, putA
Methanosarcina acetivorans C2A putP, put1, putA
Methanosarcina mazei Go1 proY, put1, putA
Methanospirillum lacunae Ki8-1 putP, put1, putA
Methanothermobacter thermautotrophicus Delta H proY, put1, putA
Methylobacterium nodulans ORS 2060 proY, put1, putA
Methylobacterium sp. 4-46 Apr-46 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Methylocapsa acidiphila B2 N515DRAFT_2924, put1, putA
Methylocapsa aurea KYG N515DRAFT_2924, put1, putA
Methylocella silvestris BL2 N515DRAFT_2924, put1, putA
Methylococcus capsulatus Bath proP, put1, putA
Methylocystis bryophila S285 N515DRAFT_2924, put1, putA
Methyloferula stellata AR4T N515DRAFT_2924, put1, putA
Methylohalobius crimeensis 10Ki ectP, put1, putA
Methylomonas methanica MC09 proY, put1, putA
Methylosarcina fibrata AML-C10 proY, put1, putA
Methylotuvimicrobium alcaliphilum 20Z proY, put1, putA
Methylovulum miyakonense HT12 CCNA_00435, put1, putA
Mycolicibacterium vanbaalenii PYR-1 proP, put1, putA
Nitratifractor salsuginis DSM 16511 aapJ, aapQ, aapM, aapP, put1, putA
Nitratiruptor tergarcus DSM 16512 proY, put1, putA
Nitriliruptor alkaliphilus DSM 45188 putP, put1, putA
Nocardioides dokdonensis FR1436 natA, natB, natC, natD, natE, put1, putA
Nocardiopsis lucentensis DSM 44048 proY, put1, putA
Nostoc punctiforme ATCC 29133; PCC 73102 natA, natB, natC, natD, natE, put1, putA
Novosphingobium aromaticivorans DSM 12444 CCNA_00435, put1, putA
Oleispira antarctica proV, proW, proX, put1, putA
Paraburkholderia atlantica CCGE1002 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Paraburkholderia bryophila 376MFSha3.1 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Paraburkholderia phymatum STM815 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Paucidesulfovibrio gracilis DSM 16080 betS, put1, putA
Pedobacter sp. GW460-11-11-14-LB5 N515DRAFT_2924, put1, putA
Pelobacter propionicus DSM 2379 proY, put1, putA
Persephonella marina EX-H1 proP, put1, putA
Phaeacidiphilus oryzae TH49 proY, put1, putA
Phaeobacter inhibens BS107 ectP, put1, putA
Polaromonas naphthalenivorans CJ2 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Prosthecochloris aestuarii DSM 271 proY, put1, putA
Pseudarthrobacter sulfonivorans Ar51 proP, put1, putA
Pseudomonas benzenivorans DSM 8628 putP, put1, putA
Pseudomonas fluorescens FW300-N1B4 putP, put1, putA
Pseudomonas fluorescens FW300-N2C3 putP, put1, putA
Pseudomonas fluorescens FW300-N2E2 putP, put1, putA
Pseudomonas fluorescens FW300-N2E3 putP, put1, putA
Pseudomonas fluorescens GW456-L13 putP, put1, putA
Pseudomonas putida KT2440 putP, put1, putA
Pseudomonas simiae WCS417 putP, put1, putA
Pseudomonas stutzeri RCH2 putP, put1, putA
Pyrolobus fumarii 1A proY, put1, putA
Rhizobium etli CFN 42 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Rhizobium johnstonii 3841 aapJ, aapQ, aapM, aapP, put1, putA
Rhizobium leguminosarum WSM1325 aapJ, aapQ, aapM, aapP, put1, putA
Rhizorhabdus wittichii RW1 CCNA_00435, put1, putA
Rhodanobacter denitrificans FW104-10B01 CCNA_00435, put1, putA
Rhodomicrobium vannielii ATCC 17100 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Rhodopseudomonas palustris CGA009 N515DRAFT_2924, put1, putA
Rhodospirillum centenum SW; ATCC 51521 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Rhodospirillum rubrum ATCC 11170 proV, proW, proX, put1, putA
Roseburia faecis M72 putP, put1*, putA
Saccharomonospora cyanea NA-134 proY, put1, putA
Sedimenticola selenatireducens DSM 17993 proV, proW, proX, put1, putA
Shewanella amazonensis SB2B putP, put1, putA
Shewanella loihica PV-4 putP, put1, putA
Shewanella oneidensis MR-1 putP*, put1, putA
Shewanella sp. ANA-3 putP, put1, putA
Sinorhizobium fredii NGR234 aapJ, aapQ, aapM, aapP, put1, putA
Sinorhizobium medicae WSM419 aapJ, aapQ, aapM, aapP, put1, putA
Sinorhizobium meliloti 1021 aapJ, aapQ, aapM, aapP, put1, putA
Sphingomonas koreensis DSMZ 15582 CCNA_00435, put1, putA
Stenotrophomonas chelatiphaga DSM 21508 proP, put1, putA
Steroidobacter denitrificans DSM 18526 N515DRAFT_2924, put1, putA
Stutzerimonas stutzeri A1501 putP, put1, putA
Sulfuricurvum kujiense DSM 16994 proP, put1, putA
Sulfurihydrogenibium azorense Az-Fu1 N515DRAFT_2924, put1, putA
Sulfurihydrogenibium subterraneum DSM 15120 N515DRAFT_2924, put1, putA
Sulfurimonas denitrificans DSM 1251 putP, put1, putA
Sulfuritalea hydrogenivorans DSM 22779 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, prdF, prdA, prdB, prdC, davT, davD, gcdG, gcdH, ech, fadB, atoB
Sulfurivirga caldicuralii DSM 17737 proY, put1, putA
Synechococcus elongatus PCC 7942 natA, natB, natC, natD, natE, put1, putA
Teredinibacter turnerae T7901 putP, put1, putA
Thauera aminoaromatica S2 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1*, putA
Thermithiobacillus tepidarius DSM 3134 CCNA_00435, put1, putA
Thermocrinis albus DSM 14484 CCNA_00435, put1, putA
Thermodesulforhabdus norvegica DSM 9990 aapJ, aapQ, aapM, aapP, put1, putA
Thermomonospora curvata DSM 43183 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Thermovibrio ammonificans HB-1 proY, put1, putA
Thermus aquaticus YT-1 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Thioalkalivibrio denitrificans ALJD ectP, put1, putA
Thioalkalivibrio halophilus HL17 ectP, put1, putA
Thioalkalivibrio paradoxus ARh 1 ectP, put1, putA
Thioalkalivibrio thiocyanodenitrificans ARhD 1 ectP, put1, putA
Thiohalomonas denitrificans HLD2 ectP, put1, putA
Thiohalospira halophila HL 3 ectP, put1, putA
Thiomicrorhabdus arctica DSM 13458 proV, proW, proX, put1, putA
Thiomicrorhabdus chilensis DSM 12352 ectP, put1, putA
Thiomicrospira cyclica ALM1 ectP, put1, putA
Thiomicrospira microaerophila ASL8-2 proY, put1, putA
Thiomicrospira pelophila DSM 1534 ectP, put1, putA
Thiothrix lacustris DSM 21227 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Tistlia consotensis USBA 355 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Trichlorobacter lovleyi SZ proY, put1, putA
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome proV, proW, proX, put1, putA
Trichormus variabilis ATCC 29413 natA, natB, natC, natD, natE, put1, putA
Xanthobacter autotrophicus Py2 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Xenophilus azovorans DSM 13620 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, 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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About GapMind

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