GapMind for Amino acid biosynthesis

 

glycine biosynthesis

Analysis of pathway gly in 276 genomes

Genome Best path
Acidovorax caeni R-24608 glyA
Actinokineospora bangkokensis 44EHW glyA
Actinomyces timonensis 7400942 glyA
Algiphilus aromaticivorans DG1253 glyA
Algoriphagus aquaeductus T4 glyA
Algoriphagus machipongonensis PR1 glyA
Alicyclobacillus ferrooxydans TC-34 glyA
Alishewanella agri BL06 aceA, agx1
Alistipes indistinctus YIT 12060 glyA
Alistipes shahii WAL 8301 glyA
Alkalitalea saponilacus SC/BZ-SP2 glyA
Amantichitinum ursilacus IGB-41 glyA
Amphibacillus jilinensis Y1 glyXL, glyXS
Amphritea japonica JAMM 1866 glyA
Amycolatopsis halophila YIM 93223 glyA
Amycolatopsis xylanica CPCC 202699 aceA, agx1
Aquimarina agarilytica ZC1 glyA
Aquimarina longa SW024 glyA
Aquimarina macrocephali JAMB N27 glyA
Archaeoglobus sulfaticallidus PM70-1 glyA
Arcticibacter svalbardensis MN12-7 glyA
Ardenticatena maritima 110S aceA, agx1
Arenimonas metalli CF5-1 glyA
Arenitalea lutea P7-3-5 glyA
Azospirillum humicireducens SgZ-5 glyA
Azospirillum thiophilum BV-S glyA
Bacillus altitudinis 41KF2b glyA
Bacillus coahuilensis m4-4 glyA
Bacillus cytotoxicus NVH 391-98 glyA
Bacillus horneckiae 1P01SC glyA
Bacillus okhensis Kh10-101 glyA
Bacillus safensis FO-36b glyA
Bacillus velezensis CBMB205 glyA
Bacteroides clarus YIT 12056 glyA
Bacteroides faecis MAJ27 glyA
Bacteroides fluxus YIT 12057 glyA
Bacteroides oleiciplenus YIT 12058 glyA
Barnesiella intestinihominis YIT 11860 glyA
Belnapia rosea CPCC 100156 glyA
Bizionia argentinensis JUB59 glyA
Bradyrhizobium diazoefficiens USDA110 glyA
Brevibacterium jeotgali SJ5-8 glyA
Brucella inopinata BO1 glyA
Brucella microti CCM 4915 glyA
Bryobacter aggregatus MPL3 glyA
Caldicellulosiruptor hydrothermalis 108 glyXL, glyXS
Caldicellulosiruptor kronotskyensis 2002 glyXL, glyXS
Carboxydothermus pertinax Ug1 glyXL, glyXS
Catellicoccus marimammalium M35/04/3 glyA
Chromobacterium vaccinii MWU205 glyA
Chryseobacterium angstadtii KM glyA
Chryseobacterium arthrosphaerae CC-VM-7 glyA
Chryseobacterium viscerum 687B-08 glyA
Cloacibacillus porcorum CL-84 glyXL, glyXS
Cobetia crustatorum JO1 glyA
Collimonas arenae Ter10 glyA
Collimonas pratensis Ter91 glyA
Collinsella tanakaei YIT 12063 glyXL, glyXS
Coprobacter fastidiosus NSB1 glyA
Corynebacterium deserti GIMN1.010 glyA
Corynebacterium frankenforstense ST18 glyA
Corynebacterium lactis RW2-5 glyA
Croceitalea dokdonensis DOKDO 023 glyA
Cronobacter condimenti 1330 glyA
Cronobacter muytjensii ATCC 51329 glyA
Cronobacter universalis NCTC 9529 glyA
Desulfatitalea tepidiphila S28bF glyA
Desulfotomaculum hydrothermale Lam5 glyXL, glyXS
Dethiosulfovibrio salsuginis USBA 82 glyA
Devosia chinhatensis IPL18 glyA
Devriesea agamarum IMP2 glyA
Dialister succinatiphilus YIT 11850 glyXL, glyXS
Dietzia timorensis ID05-A0528 glyA
Dokdonella koreensis DS-123 aceA, agx1
Domibacillus robiginosus WS 4628 glyA
Duganella sacchari Sac-22 glyA
Dyadobacter tibetensis Y620-1 glyA
Dyella jiangningensis SBZ3-12 glyA
Endozoicomonas montiporae CL-33 glyA
Enterococcus termitis LMG 8895 glyXL, glyXS
Enterorhabdus caecimuris B7 glyA
Epibacterium ulvae U95 glyA
Erythrobacter gangjinensis K7-2 glyA
Erythrobacter marinus HWDM-33 glyA
Ethanoligenens harbinense YUAN-3 glyXL, glyXS
Fervidicella metallireducens AeB glyA
Fibrella aestuarina BUZ 2 glyA
Flammeovirga pacifica WPAGA1 glyA
Flaviramulus ichthyoenteri Th78 glyA
Flavobacterium beibuense F44-8 glyA
Flavobacterium glycines Gm-149 glyA
Flavobacterium sp. LM5 glyA
Flavobacterium ummariense DS-12 glyA
Frischella perrara PEB0191 glyXL, glyXS
Galbibacter marinus ck-I2-15 glyA
Gallaecimonas xiamenensis 3-C-1 aceA, agx1
Geobacter daltonii FRC-32 glyA
Gillisia marina CBA3202 glyA
Gracilibacillus halophilus YIM-C55.5 glyXL, glyXS
Granulicella mallensis MP5ACTX8 glyA
Granulicella tundricola MP5ACTX9 glyA
Hafnia paralvei ATCC 29927 glyA
Haladaptatus cibarius D43 glyA
Halioglobus japonicus S1-36 glyA
Halobacillus alkaliphilus FP5 glyA
Halococcus hamelinensis 100A6 glyA
Halomonas salina B6 glyA
Halomonas smyrnensis AAD6 glyA
Halomonas stevensii S18214 glyA
Halomonas titanicae BH1 glyA
Halomonas xinjiangensis TRM 0175 glyA
Halopiger salifodinae KCY07-B2 glyA
Halostagnicola larsenii XH-48 glyA
Haloterrigena daqingensis JX313 glyA
Herbaspirillum aquaticum IEH 4430 glyA
Hippea alviniae EP5-r glyA
Hippea jasoniae Mar08-272r glyA
Hoeflea phototrophica DFL-43 aceA, agx1
Hyphomicrobium nitrativorans NL23 glyA
Imtechella halotolerans K1 glyA
Indibacter alkaliphilus LW1 glyA
Jannaschia aquimarina GSW-M26 glyA
Jeotgalibacillus soli P9 glyA
Kangiella geojedonensis YCS-5 glyA
Knoellia flava TL1 glyA
Kocuria flava HO-9041 glyA
Kocuria turfanensis HO-9042 glyA
Laceyella sediminis RHA1 glyA
Lacinutrix algicola AKS293 glyA
Lacinutrix himadriensis E4-9a glyA
Lacinutrix mariniflava AKS432 glyA
Lactobacillus curieae CCTCC M 2011381 glyXL, glyXS
Lactobacillus delbrueckii ZN7a-9 glyXL, glyXS
Lactobacillus hokkaidonensis LOOC260 glyXL, glyXS
Lactobacillus oryzae SG293 glyA
Lactobacillus pobuzihii E100301 glyXL, glyXS
Lactobacillus shenzhenensis LY-73 glyXL, glyXS
Lactobacillus silagei IWT126 glyA
Leeuwenhoekiella blandensis MED217 glyA
Lentibacillus jeotgali Grbi glyA
Limnohabitans curvus MWH-C5 glyA
Limnohabitans parvus II-B4 glyA
Listeria fleischmannii LU2006-1 glyA
Luteimonas huabeiensis HB2 glyA
Luteipulveratus mongoliensis MN07-A0370 glyA
Lutibaculum baratangense AMV1 glyA
Lysobacter daejeonensis GH1-9 glyA
Magnetovibrio blakemorei MV-1 glyA
Marinicella litoralis KMM 3900 glyA
Mariniradius saccharolyticus AK6 glyA
Marinobacter algicola DG893 glyA
Marinobacter guineae M3B glyA
Marinobacter psychrophilus 20041 glyA
Marinomonas arctica 328 glyA
Marivita geojedonensis DPG-138 glyA
Martelella endophytica YC6887 glyA
Megamonas funiformis YIT 11815 glyA
Mesorhizobium ciceri WSM1271 aceA, agx1
Methanobacterium arcticum M2 glyA
Methanobacterium veterum MK4 glyA
Methanocella arvoryzae MRE50 glyXL, glyXS
Methanococcus aeolicus Nankai-3 glyXL, glyXS
Methanoculleus horonobensis T10 glyXL, glyXS
Methanolinea tarda NOBI-1 glyA
Methanosarcina soligelidi SMA-21 glyXL, glyXS
Methanospirillum lacunae Ki8-1 glyXL, glyXS
Methanospirillum stamsii Pt1 glyXL, glyXS
Methylibium petroleiphilum PM1 glyA
Methylobacterium gossipiicola Gh-105 glyA
Methylocapsa aurea KYG glyA
Methylotenera versatilis 301 glyA
Microbacterium profundi Shh49 glyA
Microvirga lotononidis WSM3557 glyA
Moritella dasanensis ArB 0140 glyA
Mucilaginibacter gossypii Gh-67 glyA
Mucilaginibacter gossypiicola Gh-48 glyA
Mucilaginibacter mallensis MP1X4 glyA
Nafulsella turpanensis ZLM-10 glyA
Natronomonas moolapensis 8.8.11 glyA
Nautilia profundicola AmH glyA
Neiella marina J221 glyA
Neptunomonas antarctica S3-22 glyA
Nocardioides daejeonensis MJ31 glyA
Nocardioides dokdonensis FR1436 glyA
Nocardiopsis baichengensis YIM 90130 glyA
Nocardiopsis gilva YIM 90087 glyA
Novosphingobium barchaimii LL02 glyA
Novosphingobium fuchskuhlense FNE08-7 glyA
Novosphingobium lindaniclasticum LE124 glyA
Oceanisphaera arctica V1-41 glyA
Ochrobactrum rhizosphaerae PR17 glyA
Ochrobactrum thiophenivorans DSM 7216 glyA
Oscillibacter ruminantium GH1 glyXL, glyXS
Paenisporosarcina indica PN2 glyA
Palaeococcus pacificus DY20341 glyA
Paludibacter propionicigenes WB4 glyA
Pandoraea thiooxydans ATSB16 glyA
Pantoea rwandensis LMG 26275 glyA
Pedobacter arcticus A12 glyA
Photobacterium gaetbulicola Gung47 glyA
Photobacterium jeanii R-40508 glyA
Phyllobacterium brassicacearum STM 196 aceA, agx1
Phyllobacterium endophyticum PEPV15 aceA, agx1
Phyllobacterium leguminum ORS 1419 glyA
Planktomarina temperata RCA23 glyA
Planococcus halocryophilus Or1 glyA
Pleomorphomonas diazotrophica R5-392 glyA
Polaribacter dokdonensis DSW-5 glyA
Pontibacillus litoralis JSM 072002 glyXL, glyXS
Pontibacter lucknowensis DM9 glyA
Pontibacter ramchanderi LP43 glyA
Pontimonas salivibrio CL-TW6 glyA
Porphyrobacter dokdonensis DSW-74 glyA
Pseudoalteromonas arctica A 37-1-2 glyA
Pseudomonas baetica a390 glyA
Pseudomonas litoralis 2SM5 glyA
Pseudomonas taeanensis MS-3 glyA
Pseudovibrio axinellae Ad2 glyA
Psychrobacter arcticus 273-4 glyA
Psychrobacter cryohalolentis K5 glyA
Psychromonas ingrahamii 37 glyA
Psychromonas ossibalaenae JAMM 0738 glyA
Rhizobium freirei PRF 81 glyA
Rhizobium grahamii CCGE 502 glyA
Rhizobium subbaraonis JC85 glyA
Rhodanobacter denitrificans 2APBS1 glyA
Rhodobacter johrii JA192 glyA
Rhodobacter maris JA276 glyA
Rhodobacter ovatus JA234 glyA
Rhodobacter viridis JA737 glyA
Rhodococcus qingshengii djl-6-2 glyA
Rhodopseudomonas pseudopalustris DSM 123 glyA
Roseateles aquatilis CCUG 48205 glyA
Roseivirga spongicola UST030701-084 glyA
Rubrivirga marina SAORIC-28 glyA
Ruegeria conchae TW15 glyA
Saccharomonospora marina XMU15 aceA, agx1
Salinicoccus carnicancri Crm glyA
Serinicoccus profundi MCCC 1A05965 glyA
Shewanella halifaxensis HAW-EB4 aceA, agx1
Skermanella stibiiresistens SB22 glyA
Snodgrassella alvi wkB2 glyXL, glyXS
Sphaerochaeta globosa Buddy glyA
Sphaerochaeta pleomorpha Grapes glyA
Sphingobium baderi LL03 glyA
Sphingobium czechense LL01 glyA
Sphingobium quisquiliarum P25 glyA
Sphingomonas histidinilytica UM2 glyA
Sphingomonas indica Dd16 glyA
Sphingomonas laterariae LNB2 glyA
Sphingopyxis indica DS15 glyA
Sphingopyxis terrae UI2 glyA
Sporolactobacillus vineae SL153 glyXL, glyXS
Streptacidiphilus oryzae TH49 glyA
Streptococcus anginosus CCUG 39159 glyXL, glyXS
Streptococcus massiliensis 4401825 glyXL, glyXS
Streptococcus oralis 7747 glyXL, glyXS
Streptococcus oralis AZ_3a glyXL, glyXS
Streptomyces kebangsaanensis SUK12 glyA
Succinatimonas hippei YIT 12066 glyA
Sulfurimonas gotlandica GD1 glyA
Tatumella morbirosei LMG 23360 glyA
Thauera humireducens SgZ-1 glyA
Thermoactinomyces daqus H-18 glyA
Thermobifida halotolerans YIM 90462 glyA
Thermodesulfovibrio aggregans TGE-P1 glyA
Thermophagus xiamenensis HS1 glyA
Thermovenabulum gondwanense R270 glyXL, glyXS
Thioclava dalianensis DLFJ1-1 glyA
Thiohalospira halophila HL 3 glyA
Tistlia consotensis USBA 355 glyA
Vagococcus penaei CD276 glyXL, glyXS
Verminephrobacter eiseniae EF01-2 glyA
Weissella oryzae SG25 glyA
Williamsia sterculiae CPCC 203464 glyA
Yersinia intermedia Y228 glyA

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

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

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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