GapMind for catabolism of small carbon sources

 

L-proline catabolism

Analysis of pathway proline in 276 genomes

Genome Best path
Acidovorax caeni R-24608 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Actinokineospora bangkokensis 44EHW HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Actinomyces timonensis 7400942 putP, put1, putA
Algiphilus aromaticivorans DG1253 ectP, put1, putA
Algoriphagus aquaeductus T4 proY, put1, putA
Algoriphagus machipongonensis PR1 ectP, put1, putA
Alicyclobacillus ferrooxydans TC-34 proY, put1, putA
Alishewanella agri BL06 putP, put1, putA
Alistipes indistinctus YIT 12060 proY, put1, putA
Alistipes shahii WAL 8301 proY, put1, putA
Alkalitalea saponilacus SC/BZ-SP2 ectP, put1, putA
Amantichitinum ursilacus IGB-41 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Amphibacillus jilinensis Y1 ectP, put1, putA
Amphritea japonica JAMM 1866 putP, put1, putA
Amycolatopsis halophila YIM 93223 putP, put1, putA
Amycolatopsis xylanica CPCC 202699 proY, put1, putA
Aquimarina agarilytica ZC1 proY, put1, putA
Aquimarina longa SW024 proY, put1, putA
Aquimarina macrocephali JAMB N27 proY, put1, putA
Archaeoglobus sulfaticallidus PM70-1 putP, put1, putA
Arcticibacter svalbardensis MN12-7 N515DRAFT_2924, put1, putA
Ardenticatena maritima 110S HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Arenimonas metalli CF5-1 N515DRAFT_2924, put1, putA
Arenitalea lutea P7-3-5 proY, put1, putA
Azospirillum humicireducens SgZ-5 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Azospirillum thiophilum BV-S AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Bacillus altitudinis 41KF2b opuBA, opuBB, put1, putA
Bacillus coahuilensis m4-4 putP, put1, putA
Bacillus cytotoxicus NVH 391-98 putP, put1, putA
Bacillus horneckiae 1P01SC opuBA, opuBB, put1, putA
Bacillus okhensis Kh10-101 putP, put1, putA
Bacillus safensis FO-36b opuBA, opuBB, put1, putA
Bacillus velezensis CBMB205 proY, put1, putA
Bacteroides clarus YIT 12056 proY, put1, putA
Bacteroides faecis MAJ27 proY, put1, putA
Bacteroides fluxus YIT 12057 N515DRAFT_2924, put1, putA
Bacteroides oleiciplenus YIT 12058 proY, put1, putA
Barnesiella intestinihominis YIT 11860 proY, put1, putA
Belnapia rosea CPCC 100156 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Bizionia argentinensis JUB59 betS, put1, putA
Bradyrhizobium diazoefficiens USDA110 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Brevibacterium jeotgali SJ5-8 proY, prdF, prdA, prdB, prdC, davT, davD, gcdG, gcdH, ech, fadB, atoB
Brucella inopinata BO1 aapJ, aapQ, aapM, aapP, put1, putA
Brucella microti CCM 4915 aapJ, aapQ, aapM, aapP, put1, putA
Bryobacter aggregatus MPL3 CCNA_00435, put1, putA
Caldicellulosiruptor hydrothermalis 108 proY, put1, putA
Caldicellulosiruptor kronotskyensis 2002 proY, put1, putA
Carboxydothermus pertinax Ug1 proY, put1, putA
Catellicoccus marimammalium M35/04/3 opuBA, opuBB, put1, putA
Chromobacterium vaccinii MWU205 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Chryseobacterium angstadtii KM proY, put1, putA
Chryseobacterium arthrosphaerae CC-VM-7 putP, put1, putA
Chryseobacterium viscerum 687B-08 N515DRAFT_2924, put1, putA
Cloacibacillus porcorum CL-84 putP, put1, putA
Cobetia crustatorum JO1 putP, put1, putA
Collimonas arenae Ter10 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Collimonas pratensis Ter91 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Collinsella tanakaei YIT 12063 proY, put1, putA
Coprobacter fastidiosus NSB1 proY, put1, putA
Corynebacterium deserti GIMN1.010 putP, put1, putA
Corynebacterium frankenforstense ST18 proY, put1, putA
Corynebacterium lactis RW2-5 proY, prdF, prdA, prdB, prdC, davT, davD, gcdG, gcdH, ech, fadB, atoB
Croceitalea dokdonensis DOKDO 023 proY, put1, putA
Cronobacter condimenti 1330 proV, proW, proX, put1, putA
Cronobacter muytjensii ATCC 51329 proV, proW, proX, put1, putA
Cronobacter universalis NCTC 9529 proV, proW, proX, put1, putA
Desulfatitalea tepidiphila S28bF proV, proW, proX, put1, putA
Desulfotomaculum hydrothermale Lam5 putP, put1*, putA
Dethiosulfovibrio salsuginis USBA 82 hutV, hutW, hutX, put1, putA
Devosia chinhatensis IPL18 betS, put1, putA
Devriesea agamarum IMP2 putP, put1, putA
Dialister succinatiphilus YIT 11850 putP, put1, putA
Dietzia timorensis ID05-A0528 ectP, put1, putA
Dokdonella koreensis DS-123 N515DRAFT_2924, put1, putA
Domibacillus robiginosus WS 4628 opuBA, opuBB, put1, putA
Duganella sacchari Sac-22 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Dyadobacter tibetensis Y620-1 N515DRAFT_2924, put1, putA
Dyella jiangningensis SBZ3-12 N515DRAFT_2924, put1, putA
Endozoicomonas montiporae CL-33 putP, put1, putA
Enterococcus termitis LMG 8895 opuBA, opuBB, prdF, prdA, prdB, prdC, davT, davD, glaH, lhgD
Enterorhabdus caecimuris B7 putP, put1, putA
Epibacterium ulvae U95 aapJ, aapQ, aapM, aapP, put1, putA
Erythrobacter gangjinensis K7-2 putP, put1, putA
Erythrobacter marinus HWDM-33 putP, put1, putA
Ethanoligenens harbinense YUAN-3 proY, put1, putA
Fervidicella metallireducens AeB proY, put1*, putA
Fibrella aestuarina BUZ 2 N515DRAFT_2924, put1, putA
Flammeovirga pacifica WPAGA1 ectP, put1, putA
Flaviramulus ichthyoenteri Th78 proY, put1, putA
Flavobacterium beibuense F44-8 betS, put1, putA
Flavobacterium glycines Gm-149 N515DRAFT_2924, put1, putA
Flavobacterium sp. LM5 betS, put1, putA
Flavobacterium ummariense DS-12 betS, put1, putA
Frischella perrara PEB0191 putP, put1, putA
Galbibacter marinus ck-I2-15 betS, put1, putA
Gallaecimonas xiamenensis 3-C-1 putP, put1, putA
Geobacter daltonii FRC-32 proY, put1, putA
Gillisia marina CBA3202 proY, put1, putA
Gracilibacillus halophilus YIM-C55.5 ectP, put1, putA
Granulicella mallensis MP5ACTX8 N515DRAFT_2924, put1, putA
Granulicella tundricola MP5ACTX9 N515DRAFT_2924, put1, putA
Hafnia paralvei ATCC 29927 proV, proW, proX, put1, putA
Haladaptatus cibarius D43 putP, put1, putA
Halioglobus japonicus S1-36 proY, put1, putA
Halobacillus alkaliphilus FP5 opuBA, opuBB, put1, putA
Halococcus hamelinensis 100A6 ectP, put1, putA
Halomonas salina B6 putP, put1, putA
Halomonas smyrnensis AAD6 proV, proW, proX, put1, putA
Halomonas stevensii S18214 putP, put1, putA
Halomonas titanicae BH1 putP, put1, putA
Halomonas xinjiangensis TRM 0175 putP, put1, putA
Halopiger salifodinae KCY07-B2 putP, put1, putA
Halostagnicola larsenii XH-48 ectP, put1, putA
Haloterrigena daqingensis JX313 proY, put1, putA
Herbaspirillum aquaticum IEH 4430 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Hippea alviniae EP5-r proY, put1, putA
Hippea jasoniae Mar08-272r HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Hoeflea phototrophica DFL-43 aapJ, aapQ, aapM, aapP, put1, putA
Hyphomicrobium nitrativorans NL23 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Imtechella halotolerans K1 proY, put1, putA
Indibacter alkaliphilus LW1 putP, put1, putA
Jannaschia aquimarina GSW-M26 ectP, put1, putA
Jeotgalibacillus soli P9 putP, put1, putA
Kangiella geojedonensis YCS-5 putP, put1, putA
Knoellia flava TL1 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Kocuria flava HO-9041 proY, put1, putA
Kocuria turfanensis HO-9042 putP, put1, putA
Laceyella sediminis RHA1 putP, put1, putA
Lacinutrix algicola AKS293 proY, put1, putA
Lacinutrix himadriensis E4-9a proY, put1, putA
Lacinutrix mariniflava AKS432 proY, put1, putA
Lactobacillus curieae CCTCC M 2011381 opuBA, opuBB, put1, putA
Lactobacillus delbrueckii ZN7a-9 opuBA, opuBB, put1, putA
Lactobacillus hokkaidonensis LOOC260 opuBA, opuBB, put1, putA
Lactobacillus oryzae SG293 opuBA, opuBB, put1, putA
Lactobacillus pobuzihii E100301 opuBA, opuBB, put1, putA
Lactobacillus shenzhenensis LY-73 opuBA, opuBB, put1, putA
Lactobacillus silagei IWT126 opuBA, opuBB, put1, putA
Leeuwenhoekiella blandensis MED217 ectP, put1, putA
Lentibacillus jeotgali Grbi opuBA, opuBB, put1, putA
Limnohabitans curvus MWH-C5 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Limnohabitans parvus II-B4 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Listeria fleischmannii LU2006-1 opuBA, opuBB, put1, putA
Luteimonas huabeiensis HB2 putP, put1, putA
Luteipulveratus mongoliensis MN07-A0370 proP, put1, putA
Lutibaculum baratangense AMV1 aapJ, aapQ, aapM, aapP, put1, putA
Lysobacter daejeonensis GH1-9 putP, put1, putA
Magnetovibrio blakemorei MV-1 proV, proW, proX, put1, putA
Marinicella litoralis KMM 3900 proY, put1, putA
Mariniradius saccharolyticus AK6 proY, put1, putA
Marinobacter algicola DG893 putP, put1, putA
Marinobacter guineae M3B putP, put1, putA
Marinobacter psychrophilus 20041 putP, put1, putA
Marinomonas arctica 328 putP, put1, putA
Marivita geojedonensis DPG-138 ectP, put1, putA
Martelella endophytica YC6887 aapJ, aapQ, aapM, aapP, put1, putA
Megamonas funiformis YIT 11815 putP, put1, putA
Mesorhizobium ciceri WSM1271 aapJ, aapQ, aapM, aapP, put1, putA
Methanobacterium arcticum M2 CCNA_00435, put1, putA
Methanobacterium veterum MK4 CCNA_00435, put1, putA
Methanocella arvoryzae MRE50 proY, put1, putA
Methanococcus aeolicus Nankai-3 proY, put1, putA
Methanoculleus horonobensis T10 ectP, put1, putA
Methanolinea tarda NOBI-1 proY, put1, putA
Methanosarcina soligelidi SMA-21 proY, put1, putA
Methanospirillum lacunae Ki8-1 putP, put1, putA
Methanospirillum stamsii Pt1 proY, put1, putA
Methylibium petroleiphilum PM1 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, prdF, prdA, prdB, prdC, davT, davD, gcdG, gcdH, ech, fadB, atoB
Methylobacterium gossipiicola Gh-105 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Methylocapsa aurea KYG N515DRAFT_2924, put1, putA
Methylotenera versatilis 301 CCNA_00435, put1, putA
Microbacterium profundi Shh49 putP, put1, putA
Microvirga lotononidis WSM3557 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Moritella dasanensis ArB 0140 ectP, put1, putA
Mucilaginibacter gossypii Gh-67 N515DRAFT_2924, put1, putA
Mucilaginibacter gossypiicola Gh-48 N515DRAFT_2924, put1, putA
Mucilaginibacter mallensis MP1X4 N515DRAFT_2924, put1, putA
Nafulsella turpanensis ZLM-10 proY, put1, putA
Natronomonas moolapensis 8.8.11 proY, put1, putA
Nautilia profundicola AmH proY, put1, putA
Neiella marina J221 putP, put1, putA
Neptunomonas antarctica S3-22 putP, put1, putA
Nocardioides daejeonensis MJ31 proP, put1, putA
Nocardioides dokdonensis FR1436 natA, natB, natC, natD, natE, put1, putA
Nocardiopsis baichengensis YIM 90130 proY, put1, putA
Nocardiopsis gilva YIM 90087 proY, put1, putA
Novosphingobium barchaimii LL02 proP, put1, putA
Novosphingobium fuchskuhlense FNE08-7 proY, put1, putA
Novosphingobium lindaniclasticum LE124 proY, put1, putA
Oceanisphaera arctica V1-41 putP, put1, putA
Ochrobactrum rhizosphaerae PR17 aapJ, aapQ, aapM, aapP, put1, putA
Ochrobactrum thiophenivorans DSM 7216 aapJ, aapQ, aapM, aapP, put1, putA
Oscillibacter ruminantium GH1 putP, put1, putA
Paenisporosarcina indica PN2 putP, put1, putA
Palaeococcus pacificus DY20341 putP, put1, putA
Paludibacter propionicigenes WB4 N515DRAFT_2924, put1, putA
Pandoraea thiooxydans ATSB16 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Pantoea rwandensis LMG 26275 proV, proW, proX, put1, putA
Pedobacter arcticus A12 N515DRAFT_2924, put1, putA
Photobacterium gaetbulicola Gung47 putP, put1, putA
Photobacterium jeanii R-40508 putP, put1, putA
Phyllobacterium brassicacearum STM 196 aapJ, aapQ, aapM, aapP, put1, putA
Phyllobacterium endophyticum PEPV15 aapJ, aapQ, aapM, aapP, put1, putA
Phyllobacterium leguminum ORS 1419 aapJ, aapQ, aapM, aapP, put1, putA
Planktomarina temperata RCA23 natA, natB, natC, natD, natE, put1, putA
Planococcus halocryophilus Or1 putP, put1, putA
Pleomorphomonas diazotrophica R5-392 aapJ, aapQ, aapM, aapP, put1, putA
Polaribacter dokdonensis DSW-5 proY, put1, putA
Pontibacillus litoralis JSM 072002 putP, put1, putA
Pontibacter lucknowensis DM9 ectP, put1, putA
Pontibacter ramchanderi LP43 proY, put1, putA
Pontimonas salivibrio CL-TW6 natA, natB, natC, natD, natE, put1, putA
Porphyrobacter dokdonensis DSW-74 putP, put1, putA
Pseudoalteromonas arctica A 37-1-2 putP, put1, putA
Pseudomonas baetica a390 putP, put1, putA
Pseudomonas litoralis 2SM5 putP, put1, putA
Pseudomonas taeanensis MS-3 proV, proW, proX, put1, putA
Pseudovibrio axinellae Ad2 ectP, put1, putA
Psychrobacter arcticus 273-4 putP, put1, putA
Psychrobacter cryohalolentis K5 putP, put1, putA
Psychromonas ingrahamii 37 proV, proW, proX, put1, putA
Psychromonas ossibalaenae JAMM 0738 putP, put1, putA
Rhizobium freirei PRF 81 aapJ, aapQ, aapM, aapP, put1, putA
Rhizobium grahamii CCGE 502 aapJ, aapQ, aapM, aapP, put1, putA
Rhizobium subbaraonis JC85 aapJ, aapQ, aapM, aapP, put1, putA
Rhodanobacter denitrificans 2APBS1 CCNA_00435, put1, putA
Rhodobacter johrii JA192 ectP, put1, putA
Rhodobacter maris JA276 natA, natB, natC, natD, natE, put1, putA
Rhodobacter ovatus JA234 proY, put1, putA
Rhodobacter viridis JA737 proV, proW, proX, put1, putA
Rhodococcus qingshengii djl-6-2 proY, put1, putA
Rhodopseudomonas pseudopalustris DSM 123 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Roseateles aquatilis CCUG 48205 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Roseivirga spongicola UST030701-084 proY, put1, putA
Rubrivirga marina SAORIC-28 CCNA_00435, put1, putA
Ruegeria conchae TW15 natA, natB, natC, natD, natE, put1, putA
Saccharomonospora marina XMU15 ectP, put1, putA
Salinicoccus carnicancri Crm opuBA, opuBB, put1, putA
Serinicoccus profundi MCCC 1A05965 ectP, put1, putA
Shewanella halifaxensis HAW-EB4 putP, put1, putA
Skermanella stibiiresistens SB22 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Snodgrassella alvi wkB2 putP, put1, putA
Sphaerochaeta globosa Buddy putP, put1*, putA
Sphaerochaeta pleomorpha Grapes putP, put1, putA
Sphingobium baderi LL03 proP, put1, putA
Sphingobium czechense LL01 proP, put1, putA
Sphingobium quisquiliarum P25 proP, put1, putA
Sphingomonas histidinilytica UM2 CCNA_00435, put1, putA
Sphingomonas indica Dd16 CCNA_00435, put1, putA
Sphingomonas laterariae LNB2 proP, put1, putA
Sphingopyxis indica DS15 putP, put1, putA
Sphingopyxis terrae UI2 proP, put1, putA
Sporolactobacillus vineae SL153 proY, put1, putA
Streptacidiphilus oryzae TH49 proY, put1, putA
Streptococcus anginosus CCUG 39159 opuBA, opuBB, put1, putA
Streptococcus massiliensis 4401825 opuBA, opuBB, put1, putA
Streptococcus oralis 7747 opuBA, opuBB, put1, putA
Streptococcus oralis AZ_3a opuBA, opuBB, put1, putA
Streptomyces kebangsaanensis SUK12 proY, put1, putA
Succinatimonas hippei YIT 12066 putP, put1, putA
Sulfurimonas gotlandica GD1 putP, put1, putA
Tatumella morbirosei LMG 23360 proV, proW, proX, put1, putA
Thauera humireducens SgZ-1 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Thermoactinomyces daqus H-18 opuBA, opuBB, put1, putA
Thermobifida halotolerans YIM 90462 putP, put1, putA
Thermodesulfovibrio aggregans TGE-P1 proY, put1, putA
Thermophagus xiamenensis HS1 proY, put1, putA
Thermovenabulum gondwanense R270 proY, prdF, prdA, prdB, prdC, davT, davD, gcdG, gcdH, ech, fadB, atoB
Thioclava dalianensis DLFJ1-1 putP, put1*, putA*
Thiohalospira halophila HL 3 ectP, put1, putA
Tistlia consotensis USBA 355 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Vagococcus penaei CD276 opuBA, opuBB, put1, putA
Verminephrobacter eiseniae EF01-2 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Weissella oryzae SG25 opuBA, opuBB, put1, putA
Williamsia sterculiae CPCC 203464 proY, put1, putA
Yersinia intermedia Y228 proV, proW, proX, 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 Sep 24 2021. 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