glycine biosynthesis
Analysis of pathway gly in 150 genomes
| Genome | Best path |
|---|
| Acidimicrobium ferrooxidans DSM 10331 | glyA |
| Acidithiobacillus ferrooxidans ATCC 23270 | glyA |
| Alicycliphilus denitrificans K601 | glyA |
| Allochromatium vinosum DSM 180 | glyA |
| Ammonifex degensii KC4 | glyXL, glyXS |
| Archaeoglobus veneficus SNP6 | glyA |
| Arcobacter nitrofigilis DSM 7299 | glyA |
| Azoarcus sp. BH72 | glyA |
| Azohydromonas australica DSM 1124 | glyA |
| Azorhizobium caulinodans ORS 571 | glyA |
| Azospirillum lipoferum B510 | glyA |
| Bacillus alkalinitrilicus DSM 22532 | glyA |
| Beijerinckia indica ATCC 9039 | glyA |
| Beijerinckia mobilis UQM 1969 | glyA |
| Bradyrhizobium sp. BTAi1 | glyA |
| Burkholderia vietnamiensis G4 | glyA |
| Calditerrivibrio nitroreducens DSM 19672 | glyA |
| Caminibacter mediatlanticus TB-2 | 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 |
| Crocosphaera subtropica ATCC 51142 | glyA |
| Dechloromonas agitata is5 | 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 |
| Desulfallas geothermicus DSM 3669 | glyXL, glyXS |
| 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 |
| Desulfobulbus mediterraneus DSM 13871 | glyA |
| Desulfotalea psychrophila LSv54 | glyA |
| Desulfotomaculum ruminis DSM 2154 | glyXL, glyXS |
| Desulfovibrio bastinii DSM 16055 | glyA |
| Desulfovibrio gracilis DSM 16080 | glyA |
| Desulfovibrio oxyclinae DSM 11498 | glyA |
| Desulfovibrio zosterae DSM 11974 | glyA |
| Desulfurobacterium atlanticum DSM 15668 | glyA |
| Desulfuromonas acetexigens | glyA |
| Desulfuromusa kysingii DSM 7343 | glyA |
| Ferroglobus placidus DSM 10642 | glyA |
| Frankia alni ACN14A | glyA |
| Geobacter lovleyi SZ | glyA |
| Geobacter metallireducens GS-15 | glyA |
| Geobacter uraniireducens Rf4 | glyA |
| Haloechinothrix alba DSM 45207 | glyA |
| Haloglycomyces albus DSM 45210 | glyA |
| Halomonas desiderata SP1 | glyA |
| Halorhodospira halophila SL1 | glyA |
| Heliobacterium modesticaldum Ice1; ATCC 51547 | glyXL, glyXS |
| Herbaspirillum autotrophicum IAM 14942 | 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 variicola At-22 | glyA |
| Kyrpidia tusciae DSM 2912 | glyA |
| Leptospirillum ferrooxidans C2-3 | glyA |
| Malonomonas rubra DSM 5091 | 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 barkeri Fusaro | glyXL, glyXS |
| Methanosarcina mazei Go1 | glyXL, glyXS |
| Methanothermobacter thermautotrophicus Delta H | glyA |
| Methylobacterium nodulans ORS 2060 | glyA |
| Methylobacterium sp. 4-46 | glyA |
| Methylocapsa acidiphila B2 | glyA |
| Methylocapsa aurea KYG T | glyA |
| Methylocella silvestris BL2 | glyA |
| Methylococcus capsulatus Bath | glyA |
| Methylocystis bryophila S285 | glyA |
| Methyloferula stellata AR4T | glyA |
| Methylohalobius crimeensis 10Ki | glyA |
| Methylomicrobium alcaliphilum 20Z | glyA |
| Methylomonas methanica MC09 | glyA |
| Methylosarcina fibrata AML-C10 | 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 |
| Nocardiopsis lucentensis DSM 44048 | glyA |
| Nostoc punctiforme ATCC 29133; PCC 73102 | glyA |
| Novosphingobium aromaticivorans DSM 12444 | glyA |
| Oleispira antarctica | glyA |
| Paraburkholderia phymatum STM815 | glyA |
| Paraburkholderia sp. CCGE1002 | glyA |
| Pelobacter propionicus DSM 2379 | glyXL, glyXS |
| Persephonella marina EX-H1 | glyA |
| Polaromonas naphthalenivorans CJ2 | glyA |
| Prosthecochloris aestuarii DSM 271 | glyA |
| Pseudarthrobacter sulfonivorans Ar51 | glyA |
| Pseudomonas benzenivorans DSM 8628 | glyA |
| Pseudomonas stutzeri A1501 | glyA |
| Pyrolobus fumarii 1A | glyA |
| Rhizobium etli CFN 42 | glyA |
| Rhizobium leguminosarum 3841 | glyA |
| Rhizobium leguminosarum WSM1325 | glyA |
| Rhodobacter sphaeroides ATCC 17029 | glyA |
| Rhodomicrobium vannielii ATCC 17100 | glyA |
| Rhodopseudomonas palustris CGA009 | glyA |
| Rhodospirillum centenum SW; ATCC 51521 | glyA |
| Rhodospirillum rubrum ATCC 11170 | glyA |
| Saccharomonospora cyanea NA-134 | glyA |
| Sedimenticola selenatireducens DSM 17993 | glyA |
| Sinorhizobium fredii NGR234 | glyA |
| Sinorhizobium medicae WSM419 | glyA |
| Sphingomonas wittichii RW1 | glyA |
| Stenotrophomonas chelatiphaga DSM 21508 | glyA |
| Steroidobacter denitrificans DSM 18526 | 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 |
| 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 |
| Thioalkalivibrio denitrificans ALJD | glyA |
| Thioalkalivibrio halophilus HL17 | glyA |
| Thioalkalivibrio paradoxus ARh 1 | glyA |
| Thioalkalivibrio thiocyanodenitrificans ARhD 1 | glyA |
| Thiohalomonas denitrificans HLD2 | 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 |
| Trichodesmium erythraeum IMS101 | 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 10 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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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