GapMind for catabolism of small carbon sources

 

D-alanine catabolism

Analysis of pathway D-alanine in 276 genomes

Genome Best path
Acidovorax caeni R-24608 cycA, dadA
Actinokineospora bangkokensis 44EHW mctP, dadA
Actinomyces timonensis 7400942 cycA, dadA
Algiphilus aromaticivorans DG1253 cycA, dadA
Algoriphagus aquaeductus T4 cycA, dadA
Algoriphagus machipongonensis PR1 cycA, dadA
Alicyclobacillus ferrooxydans TC-34 cycA, dadA
Alishewanella agri BL06 cycA, dadA
Alistipes indistinctus YIT 12060 cycA, dadA
Alistipes shahii WAL 8301 cycA, dadA
Alkalitalea saponilacus SC/BZ-SP2 cycA, dadA
Amantichitinum ursilacus IGB-41 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Amphibacillus jilinensis Y1 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Amphritea japonica JAMM 1866 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Amycolatopsis halophila YIM 93223 cycA, dadA
Amycolatopsis xylanica CPCC 202699 mctP, dadA
Aquimarina agarilytica ZC1 cycA, dadA
Aquimarina longa SW024 cycA, dadA
Aquimarina macrocephali JAMB N27 cycA, dadA
Archaeoglobus sulfaticallidus PM70-1 cycA, dadA
Arcticibacter svalbardensis MN12-7 cycA, dadA
Ardenticatena maritima 110S cycA, dadA
Arenimonas metalli CF5-1 cycA, dadA
Arenitalea lutea P7-3-5 cycA, dadA
Azospirillum humicireducens SgZ-5 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Azospirillum thiophilum BV-S AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Bacillus altitudinis 41KF2b cycA, dadA
Bacillus coahuilensis m4-4 cycA, dadA
Bacillus cytotoxicus NVH 391-98 cycA, dadA
Bacillus horneckiae 1P01SC cycA, dadA
Bacillus okhensis Kh10-101 cycA, dadA
Bacillus safensis FO-36b cycA, dadA
Bacillus velezensis CBMB205 cycA, dadA
Bacteroides clarus YIT 12056 cycA, dadA
Bacteroides faecis MAJ27 cycA, dadA
Bacteroides fluxus YIT 12057 cycA, dadA
Bacteroides oleiciplenus YIT 12058 cycA, dadA
Barnesiella intestinihominis YIT 11860 cycA, dadA
Belnapia rosea CPCC 100156 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Bizionia argentinensis JUB59 cycA, dadA
Bradyrhizobium diazoefficiens USDA110 mctP, dadA
Brevibacterium jeotgali SJ5-8 cycA, dadA
Brucella inopinata BO1 cycA, dadA
Brucella microti CCM 4915 cycA, dadA
Bryobacter aggregatus MPL3 cycA, dadA
Caldicellulosiruptor hydrothermalis 108 cycA, dadA
Caldicellulosiruptor kronotskyensis 2002 cycA, dadA
Carboxydothermus pertinax Ug1 cycA, dadA
Catellicoccus marimammalium M35/04/3 cycA, dadA
Chromobacterium vaccinii MWU205 cycA, dadA
Chryseobacterium angstadtii KM cycA, dadA
Chryseobacterium arthrosphaerae CC-VM-7 cycA, dadA
Chryseobacterium viscerum 687B-08 cycA, dadA
Cloacibacillus porcorum CL-84 cycA, dadA
Cobetia crustatorum JO1 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Collimonas arenae Ter10 cycA, dadA
Collimonas pratensis Ter91 cycA, dadA
Collinsella tanakaei YIT 12063 cycA, dadA
Coprobacter fastidiosus NSB1 cycA, dadA
Corynebacterium deserti GIMN1.010 cycA, dadA
Corynebacterium frankenforstense ST18 cycA, dadA
Corynebacterium lactis RW2-5 cycA, dadA
Croceitalea dokdonensis DOKDO 023 cycA, dadA
Cronobacter condimenti 1330 cycA, dadA
Cronobacter muytjensii ATCC 51329 cycA, dadA
Cronobacter universalis NCTC 9529 cycA, dadA
Desulfatitalea tepidiphila S28bF Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Desulfotomaculum hydrothermale Lam5 cycA, dadA
Dethiosulfovibrio salsuginis USBA 82 cycA, dadA
Devosia chinhatensis IPL18 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Devriesea agamarum IMP2 cycA, dadA
Dialister succinatiphilus YIT 11850 cycA, dadA
Dietzia timorensis ID05-A0528 cycA, dadA
Dokdonella koreensis DS-123 cycA, dadA
Domibacillus robiginosus WS 4628 cycA, dadA
Duganella sacchari Sac-22 cycA, dadA
Dyadobacter tibetensis Y620-1 cycA, dadA
Dyella jiangningensis SBZ3-12 cycA, dadA
Endozoicomonas montiporae CL-33 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Enterococcus termitis LMG 8895 cycA, dadA
Enterorhabdus caecimuris B7 cycA, dadA
Epibacterium ulvae U95 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Erythrobacter gangjinensis K7-2 cycA, dadA
Erythrobacter marinus HWDM-33 cycA, dadA
Ethanoligenens harbinense YUAN-3 cycA, dadA
Fervidicella metallireducens AeB cycA, dadA
Fibrella aestuarina BUZ 2 cycA, dadA
Flammeovirga pacifica WPAGA1 cycA, dadA
Flaviramulus ichthyoenteri Th78 cycA, dadA
Flavobacterium beibuense F44-8 cycA, dadA
Flavobacterium glycines Gm-149 cycA, dadA
Flavobacterium sp. LM5 cycA, dadA
Flavobacterium ummariense DS-12 cycA, dadA
Frischella perrara PEB0191 cycA, dadA
Galbibacter marinus ck-I2-15 cycA, dadA
Gallaecimonas xiamenensis 3-C-1 cycA, dadA
Geobacter daltonii FRC-32 cycA, dadA
Gillisia marina CBA3202 cycA, dadA
Gracilibacillus halophilus YIM-C55.5 cycA, dadA
Granulicella mallensis MP5ACTX8 mctP, dadA
Granulicella tundricola MP5ACTX9 cycA, dadA
Hafnia paralvei ATCC 29927 cycA, dadA
Haladaptatus cibarius D43 cycA, dadA
Halioglobus japonicus S1-36 cycA, dadA
Halobacillus alkaliphilus FP5 cycA, dadA
Halococcus hamelinensis 100A6 cycA, dadA
Halomonas salina B6 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Halomonas smyrnensis AAD6 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Halomonas stevensii S18214 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Halomonas titanicae BH1 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Halomonas xinjiangensis TRM 0175 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Halopiger salifodinae KCY07-B2 cycA, dadA
Halostagnicola larsenii XH-48 cycA, dadA
Haloterrigena daqingensis JX313 cycA, dadA
Herbaspirillum aquaticum IEH 4430 mctP, dadA
Hippea alviniae EP5-r cycA, dadA
Hippea jasoniae Mar08-272r cycA, dadA
Hoeflea phototrophica DFL-43 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Hyphomicrobium nitrativorans NL23 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Imtechella halotolerans K1 cycA, dadA
Indibacter alkaliphilus LW1 cycA, dadA
Jannaschia aquimarina GSW-M26 cycA, dadA
Jeotgalibacillus soli P9 cycA, dadA
Kangiella geojedonensis YCS-5 cycA, dadA
Knoellia flava TL1 mctP, dadA
Kocuria flava HO-9041 cycA, dadA
Kocuria turfanensis HO-9042 cycA, dadA
Laceyella sediminis RHA1 cycA, dadA
Lacinutrix algicola AKS293 cycA, dadA
Lacinutrix himadriensis E4-9a cycA, dadA
Lacinutrix mariniflava AKS432 cycA, dadA
Lactobacillus curieae CCTCC M 2011381 cycA, dadA
Lactobacillus delbrueckii ZN7a-9 cycA, dadA
Lactobacillus hokkaidonensis LOOC260 cycA, dadA
Lactobacillus oryzae SG293 cycA, dadA
Lactobacillus pobuzihii E100301 cycA, dadA
Lactobacillus shenzhenensis LY-73 cycA, dadA
Lactobacillus silagei IWT126 cycA, dadA
Leeuwenhoekiella blandensis MED217 cycA, dadA
Lentibacillus jeotgali Grbi cycA, dadA
Limnohabitans curvus MWH-C5 cycA, dadA
Limnohabitans parvus II-B4 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Listeria fleischmannii LU2006-1 cycA, dadA
Luteimonas huabeiensis HB2 cycA, dadA
Luteipulveratus mongoliensis MN07-A0370 mctP, dadA
Lutibaculum baratangense AMV1 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Lysobacter daejeonensis GH1-9 cycA, dadA
Magnetovibrio blakemorei MV-1 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Marinicella litoralis KMM 3900 cycA, dadA
Mariniradius saccharolyticus AK6 cycA, dadA
Marinobacter algicola DG893 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Marinobacter guineae M3B Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Marinobacter psychrophilus 20041 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Marinomonas arctica 328 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Marivita geojedonensis DPG-138 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Martelella endophytica YC6887 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Megamonas funiformis YIT 11815 cycA, dadA
Mesorhizobium ciceri WSM1271 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Methanobacterium arcticum M2 cycA, dadA
Methanobacterium veterum MK4 cycA, dadA
Methanocella arvoryzae MRE50 cycA, dadA
Methanococcus aeolicus Nankai-3 cycA, dadA
Methanoculleus horonobensis T10 cycA, dadA
Methanolinea tarda NOBI-1 cycA, dadA
Methanosarcina soligelidi SMA-21 cycA, dadA
Methanospirillum lacunae Ki8-1 cycA, dadA
Methanospirillum stamsii Pt1 cycA, dadA
Methylibium petroleiphilum PM1 cycA, dadA
Methylobacterium gossipiicola Gh-105 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Methylocapsa aurea KYG mctP, dadA
Methylotenera versatilis 301 cycA, dadA
Microbacterium profundi Shh49 cycA, dadA
Microvirga lotononidis WSM3557 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Moritella dasanensis ArB 0140 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Mucilaginibacter gossypii Gh-67 cycA, dadA
Mucilaginibacter gossypiicola Gh-48 cycA, dadA
Mucilaginibacter mallensis MP1X4 cycA, dadA
Nafulsella turpanensis ZLM-10 cycA, dadA
Natronomonas moolapensis 8.8.11 cycA, dadA
Nautilia profundicola AmH cycA, dadA
Neiella marina J221 cycA, dadA
Neptunomonas antarctica S3-22 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Nocardioides daejeonensis MJ31 cycA, dadA
Nocardioides dokdonensis FR1436 cycA, dadA
Nocardiopsis baichengensis YIM 90130 cycA, dadA
Nocardiopsis gilva YIM 90087 cycA, dadA
Novosphingobium barchaimii LL02 cycA, dadA
Novosphingobium fuchskuhlense FNE08-7 cycA, dadA
Novosphingobium lindaniclasticum LE124 cycA, dadA
Oceanisphaera arctica V1-41 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Ochrobactrum rhizosphaerae PR17 cycA, dadA
Ochrobactrum thiophenivorans DSM 7216 cycA, dadA
Oscillibacter ruminantium GH1 cycA, dadA
Paenisporosarcina indica PN2 cycA, dadA
Palaeococcus pacificus DY20341 cycA, dadA
Paludibacter propionicigenes WB4 cycA, dadA
Pandoraea thiooxydans ATSB16 cycA, dadA
Pantoea rwandensis LMG 26275 cycA, dadA
Pedobacter arcticus A12 cycA, dadA
Photobacterium gaetbulicola Gung47 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Photobacterium jeanii R-40508 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Phyllobacterium brassicacearum STM 196 mctP, dadA
Phyllobacterium endophyticum PEPV15 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Phyllobacterium leguminum ORS 1419 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Planktomarina temperata RCA23 cycA, dadA
Planococcus halocryophilus Or1 cycA, dadA
Pleomorphomonas diazotrophica R5-392 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Polaribacter dokdonensis DSW-5 cycA, dadA
Pontibacillus litoralis JSM 072002 cycA, dadA
Pontibacter lucknowensis DM9 cycA, dadA
Pontibacter ramchanderi LP43 cycA, dadA
Pontimonas salivibrio CL-TW6 cycA, dadA
Porphyrobacter dokdonensis DSW-74 cycA, dadA
Pseudoalteromonas arctica A 37-1-2 cycA, dadA
Pseudomonas baetica a390 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Pseudomonas litoralis 2SM5 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Pseudomonas taeanensis MS-3 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Pseudovibrio axinellae Ad2 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Psychrobacter arcticus 273-4 cycA, dadA
Psychrobacter cryohalolentis K5 cycA, dadA
Psychromonas ingrahamii 37 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Psychromonas ossibalaenae JAMM 0738 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Rhizobium freirei PRF 81 cycA, dadA
Rhizobium grahamii CCGE 502 mctP, dadA
Rhizobium subbaraonis JC85 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Rhodanobacter denitrificans 2APBS1 cycA, dadA
Rhodobacter johrii JA192 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Rhodobacter maris JA276 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Rhodobacter ovatus JA234 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Rhodobacter viridis JA737 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Rhodococcus qingshengii djl-6-2 cycA, dadA
Rhodopseudomonas pseudopalustris DSM 123 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Roseateles aquatilis CCUG 48205 cycA, dadA
Roseivirga spongicola UST030701-084 cycA, dadA
Rubrivirga marina SAORIC-28 cycA, dadA
Ruegeria conchae TW15 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Saccharomonospora marina XMU15 mctP, dadA
Salinicoccus carnicancri Crm cycA, dadA
Serinicoccus profundi MCCC 1A05965 cycA, dadA
Shewanella halifaxensis HAW-EB4 cycA, dadA
Skermanella stibiiresistens SB22 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Snodgrassella alvi wkB2 cycA, dadA
Sphaerochaeta globosa Buddy cycA, dadA
Sphaerochaeta pleomorpha Grapes cycA, dadA
Sphingobium baderi LL03 cycA, dadA
Sphingobium czechense LL01 cycA, dadA
Sphingobium quisquiliarum P25 cycA, dadA
Sphingomonas histidinilytica UM2 cycA, dadA
Sphingomonas indica Dd16 cycA, dadA
Sphingomonas laterariae LNB2 cycA, dadA
Sphingopyxis indica DS15 cycA, dadA
Sphingopyxis terrae UI2 cycA, dadA
Sporolactobacillus vineae SL153 cycA, dadA
Streptacidiphilus oryzae TH49 mctP, dadA
Streptococcus anginosus CCUG 39159 cycA, dadA
Streptococcus massiliensis 4401825 cycA, dadA
Streptococcus oralis 7747 cycA, dadA
Streptococcus oralis AZ_3a cycA, dadA
Streptomyces kebangsaanensis SUK12 cycA, dadA
Succinatimonas hippei YIT 12066 cycA, dadA
Sulfurimonas gotlandica GD1 cycA, dadA
Tatumella morbirosei LMG 23360 cycA, dadA
Thauera humireducens SgZ-1 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Thermoactinomyces daqus H-18 cycA, dadA
Thermobifida halotolerans YIM 90462 cycA, dadA
Thermodesulfovibrio aggregans TGE-P1 cycA, dadA
Thermophagus xiamenensis HS1 cycA, dadA
Thermovenabulum gondwanense R270 cycA, dadA
Thioclava dalianensis DLFJ1-1 cycA, dadA
Thiohalospira halophila HL 3 cycA, dadA
Tistlia consotensis USBA 355 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Vagococcus penaei CD276 cycA, dadA
Verminephrobacter eiseniae EF01-2 cycA, dadA
Weissella oryzae SG25 cycA, dadA
Williamsia sterculiae CPCC 203464 cycA, dadA
Yersinia intermedia Y228 cycA, dadA

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