GapMind for Amino acid biosynthesis


glycine biosynthesis

Analysis of pathway gly in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 glyA
Acidithiobacillus ferrooxidans ATCC 23270 glyA
Acidovorax sp. GW101-3H11 glyA
Algiphilus aromaticivorans DG1253 glyA
Alicycliphilus denitrificans K601 glyA
Alkalihalobacterium alkalinitrilicum DSM 22532 glyA
Allochromatium vinosum DSM 180 glyA
Ammonifex degensii KC4 glyXL, glyXS
Anaerobutyricum hallii DSM 3353 glyXL, glyXS
Aquimarina longa SW024 glyA
Archaeoglobus veneficus SNP6 glyA
Arcobacter nitrofigilis DSM 7299 glyA
Azoarcus olearius BH72 glyA
Azohydromonas australica DSM 1124 glyA
Azorhizobium caulinodans ORS 571 glyA
Azospirillum brasilense Sp245 glyA
Azospirillum sp. B510 glyA
Bacteroides thetaiotaomicron VPI-5482 glyA
Beijerinckia indica ATCC 9039 glyA
Beijerinckia mobilis UQM 1969 glyA
Billgrantia desiderata SP1 glyA
Bradyrhizobium sp. BTAi1 glyA
Brevundimonas sp. GW460-12-10-14-LB2 glyA
Burkholderia phytofirmans PsJN glyA
Burkholderia vietnamiensis G4 glyA
Calditerrivibrio nitroreducens DSM 19672 glyA
Caminibacter mediatlanticus TB-2 glyA
Carboxydothermus pertinax Ug1 glyXL, glyXS
Caulobacter crescentus NA1000 glyA
Cereibacter sphaeroides ATCC 17029 glyA
Chlorobaculum parvum NCIB 8327 glyA
Chlorobaculum tepidum TLS glyA
Chlorobium limicola DSM 245 glyA
Chlorobium phaeobacteroides BS1 glyA
Clostridium acetobutylicum ATCC 824 glyXL, glyXS
Clostridium kluyveri DSM 555 glyXL, glyXS
Clostridium tyrobutyricum FAM22553 glyXL, glyXS
Crocosphaera subtropica ATCC 51142 glyA
Cupriavidus basilensis FW507-4G11 glyA
Dechloromonas agitata is5 glyA
Dechlorosoma suillum PS glyA
Dehalococcoides mccartyi 195 glyA
Denitrovibrio acetiphilus DSM 12809 glyA
Derxia gummosa DSM 723 glyA
Desulfacinum hydrothermale DSM 13146 glyA
Desulfacinum infernum DSM 9756 glyA
Desulfarculus baarsii DSM 2075 glyA
Desulfatibacillum aliphaticivorans DSM 15576 glyA
Desulfatiglans anilini DSM 4660 glyA
Desulfitobacterium hafniense DCB-2 glyXL, glyXS
Desulfobacca acetoxidans DSM 11109 glyA
Desulfobacter vibrioformis DSM 8776 glyA
Desulfogranum mediterraneum DSM 13871 glyA
Desulforamulus ruminis DSM 2154 glyXL, glyXS
Desulfoscipio geothermicus DSM 3669 glyXL, glyXS
Desulfotalea psychrophila LSv54 glyA
Desulfovibrio oxyclinae DSM 11498 glyA
Desulfovibrio vulgaris Hildenborough JW710 glyA
Desulfovibrio vulgaris Miyazaki F glyA
Desulfurobacterium atlanticum DSM 15668 glyA
Desulfuromonas acetexigens glyA
Desulfuromusa kysingii DSM 7343 glyA
Dinoroseobacter shibae DFL-12 glyA
Dyella japonica UNC79MFTsu3.2 glyA
Echinicola vietnamensis KMM 6221, DSM 17526 glyA
Escherichia coli BW25113 glyA
Ferroglobus placidus DSM 10642 glyA
Frankia alni ACN14a glyA
Geobacter metallireducens GS-15 glyA
Geotalea uraniireducens Rf4 glyA
Halococcus hamelinensis 100A6 glyA
Haloechinothrix alba DSM 45207 glyA
Haloferax volcanii DS2 glyA
Haloglycomyces albus DSM 45210 glyA
Halorhodospira halophila SL1 glyA
Heliomicrobium modesticaldum Ice1; ATCC 51547 glyXL, glyXS
Herbaspirillum autotrophicum IAM 14942 glyA
Herbaspirillum seropedicae SmR1 glyA
Hippea alviniae EP5-r glyA
Hydrogenophaga taeniospiralis NBRC 102512 glyA
Hydrogenovibrio halophilus DSM 15072 glyA
Hydrogenovibrio kuenenii DSM 12350 glyA
Hydrogenovibrio marinus DSM 11271 glyA
Hyphomicrobium sulfonivorans WDL6 glyA
Klebsiella michiganensis M5al glyA
Klebsiella variicola At-22 glyA
Kyrpidia tusciae DSM 2912 glyA
Leptospirillum ferrooxidans C2-3 glyA
Magnetospirillum magneticum AMB-1 glyA
Malonomonas rubra DSM 5091 glyA
Maridesulfovibrio bastinii DSM 16055 glyA
Maridesulfovibrio zosterae DSM 11974 glyA
Marinobacter adhaerens HP15 glyA
Mesorhizobium ciceri WSM1271 aceA, agx1
Methanobacterium lacus AL-21 glyA
Methanococcus aeolicus Nankai-3 glyXL, glyXS
Methanococcus maripaludis C5 glyXL, glyXS
Methanosarcina acetivorans C2A glyXL, glyXS
Methanosarcina mazei Go1 glyXL, glyXS
Methanospirillum lacunae Ki8-1 glyXL, glyXS
Methanothermobacter thermautotrophicus Delta H glyA
Methylobacterium nodulans ORS 2060 glyA
Methylobacterium sp. 4-46 Apr-46 glyA
Methylocapsa acidiphila B2 glyA
Methylocapsa aurea KYG glyA
Methylocella silvestris BL2 glyA
Methylococcus capsulatus Bath glyA
Methylocystis bryophila S285 glyA
Methyloferula stellata AR4T glyA
Methylohalobius crimeensis 10Ki glyA
Methylomonas methanica MC09 glyA
Methylosarcina fibrata AML-C10 glyA
Methylotuvimicrobium alcaliphilum 20Z glyA
Methylovulum miyakonense HT12 glyA
Mycolicibacterium vanbaalenii PYR-1 glyA
Nitratifractor salsuginis DSM 16511 glyA
Nitratiruptor tergarcus DSM 16512 glyA
Nitriliruptor alkaliphilus DSM 45188 glyA
Nocardioides dokdonensis FR1436 glyA
Nocardiopsis lucentensis DSM 44048 glyA
Nostoc punctiforme ATCC 29133; PCC 73102 glyA
Novosphingobium aromaticivorans DSM 12444 glyA
Oleispira antarctica glyA
Paraburkholderia atlantica CCGE1002 glyA
Paraburkholderia bryophila 376MFSha3.1 glyA
Paraburkholderia phymatum STM815 glyA
Paucidesulfovibrio gracilis DSM 16080 glyA
Pedobacter sp. GW460-11-11-14-LB5 glyA
Pelobacter propionicus DSM 2379 glyXL, glyXS
Persephonella marina EX-H1 glyA
Phaeacidiphilus oryzae TH49 glyA
Phaeobacter inhibens BS107 glyA
Polaromonas naphthalenivorans CJ2 glyA
Prosthecochloris aestuarii DSM 271 glyA
Pseudarthrobacter sulfonivorans Ar51 glyA
Pseudomonas benzenivorans DSM 8628 glyA
Pseudomonas fluorescens FW300-N1B4 glyA
Pseudomonas fluorescens FW300-N2C3 glyA
Pseudomonas fluorescens FW300-N2E2 glyA
Pseudomonas fluorescens FW300-N2E3 glyA
Pseudomonas fluorescens GW456-L13 glyA
Pseudomonas putida KT2440 glyA
Pseudomonas simiae WCS417 glyA
Pseudomonas stutzeri RCH2 glyA
Pyrolobus fumarii 1A glyA
Rhizobium etli CFN 42 glyA
Rhizobium johnstonii 3841 glyA
Rhizobium leguminosarum WSM1325 glyA
Rhizorhabdus wittichii RW1 glyA
Rhodanobacter denitrificans FW104-10B01 glyA
Rhodomicrobium vannielii ATCC 17100 glyA
Rhodopseudomonas palustris CGA009 glyA
Rhodospirillum centenum SW; ATCC 51521 glyA
Rhodospirillum rubrum ATCC 11170 glyA
Roseburia faecis M72 glyXL, glyXS
Saccharomonospora cyanea NA-134 glyA
Sedimenticola selenatireducens DSM 17993 glyA
Shewanella amazonensis SB2B aceA, agx1
Shewanella loihica PV-4 aceA, agx1
Shewanella oneidensis MR-1 aceA, agx1
Shewanella sp. ANA-3 aceA, agx1
Sinorhizobium fredii NGR234 glyA
Sinorhizobium medicae WSM419 glyA
Sinorhizobium meliloti 1021 aceA, agx1
Sphingomonas koreensis DSMZ 15582 glyA
Stenotrophomonas chelatiphaga DSM 21508 glyA
Steroidobacter denitrificans DSM 18526 glyA
Stutzerimonas stutzeri A1501 glyA
Sulfuricurvum kujiense DSM 16994 glyA
Sulfurihydrogenibium azorense Az-Fu1 glyA
Sulfurihydrogenibium subterraneum DSM 15120 glyA
Sulfurimonas denitrificans DSM 1251 glyA
Sulfuritalea hydrogenivorans DSM 22779 glyA
Sulfurivirga caldicuralii DSM 17737 glyA
Synechococcus elongatus PCC 7942 glyA
Teredinibacter turnerae T7901 glyA
Thauera aminoaromatica S2 glyA
Thermithiobacillus tepidarius DSM 3134 glyA
Thermocrinis albus DSM 14484 glyA
Thermodesulforhabdus norvegica DSM 9990 glyA
Thermomonospora curvata DSM 43183 glyA
Thermovibrio ammonificans HB-1 glyA
Thermus aquaticus YT-1 glyA
Thioalkalivibrio denitrificans ALJD glyA
Thioalkalivibrio halophilus HL17 glyA
Thioalkalivibrio paradoxus ARh 1 glyA
Thioalkalivibrio thiocyanodenitrificans ARhD 1 glyA
Thiohalomonas denitrificans HLD2 glyA
Thiohalospira halophila HL 3 glyA
Thiomicrorhabdus arctica DSM 13458 glyA
Thiomicrorhabdus chilensis DSM 12352 glyA
Thiomicrospira cyclica ALM1 glyA
Thiomicrospira microaerophila ASL8-2 glyA
Thiomicrospira pelophila DSM 1534 glyA
Thiothrix lacustris DSM 21227 glyA
Tistlia consotensis USBA 355 glyA
Trichlorobacter lovleyi SZ glyA
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome glyA
Trichormus variabilis ATCC 29413 glyA
Xanthobacter autotrophicus Py2 glyA
Xenophilus azovorans DSM 13620 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