L-serine biosynthesis

GapMind for Amino acid biosynthesis

L-serine biosynthesis

Analysis of pathway ser in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	serA, serC, serB
Acidithiobacillus ferrooxidans ATCC 23270	serA, serC, serB
Alicycliphilus denitrificans K601	serA, serC, serB
Allochromatium vinosum DSM 180	serA, serC, serB
Ammonifex degensii KC4	serA, serC, serB
Archaeoglobus veneficus SNP6	serA, serC, serB
Arcobacter nitrofigilis DSM 7299	serA, serC ?, serB
Azoarcus sp. BH72	serA, serC, serB
Azohydromonas australica DSM 1124	serA, serC, serB
Azorhizobium caulinodans ORS 571	serA, serC, serB
Azospirillum lipoferum B510	serA, serC, serB
Bacillus alkalinitrilicus DSM 22532	serA, serC, serB
Beijerinckia indica ATCC 9039	serA, serC, serB
Beijerinckia mobilis UQM 1969	serA, serC, serB
Bradyrhizobium sp. BTAi1	serA, serC, serB
Burkholderia vietnamiensis G4	serA, serC, serB
Calditerrivibrio nitroreducens DSM 19672	serA, serC, serB ?
Caminibacter mediatlanticus TB-2	serA, serC ?, serB
Chlorobaculum parvum NCIB 8327	serA ?, serC, serB
Chlorobaculum tepidum TLS	serA ?, serC, serB
Chlorobium limicola DSM 245	serA, serC, serB
Chlorobium phaeobacteroides BS1	serA, serC, serB
Clostridium acetobutylicum ATCC 824	serA, serC, serB
Clostridium kluyveri DSM 555	serA, serC, serB
Crocosphaera subtropica ATCC 51142	serA, serC, serB
Dechloromonas agitata is5	serA, serC, serB
Dehalococcoides mccartyi 195	serA, serC, serB
Denitrovibrio acetiphilus DSM 12809	serA, serC, serB ?
Derxia gummosa DSM 723	serA, serC, serB
Desulfacinum hydrothermale DSM 13146	serA, serC, serB ?
Desulfacinum infernum DSM 9756	serA, serC, serB ?
Desulfallas geothermicus DSM 3669	serA, serC, serB
Desulfarculus baarsii DSM 2075	serA ?, serC, serB
Desulfatibacillum aliphaticivorans DSM 15576	serA, serC, serB
Desulfatiglans anilini DSM 4660	serA, serC, serB ?
Desulfitobacterium hafniense DCB-2	serA, serC, serB ?
Desulfobacca acetoxidans DSM 11109	serA, serC, serB ?
Desulfobacter vibrioformis DSM 8776	serA, serC, serB
Desulfobulbus mediterraneus DSM 13871	serA, serC, serB ?
Desulfotalea psychrophila LSv54	serA, serC, serB ?
Desulfotomaculum ruminis DSM 2154	serA, serC, serB ?
Desulfovibrio bastinii DSM 16055	serA ?, serC, serB
Desulfovibrio gracilis DSM 16080	serA ?, serC, serB
Desulfovibrio oxyclinae DSM 11498	serA ?, serC, serB
Desulfovibrio zosterae DSM 11974	serA ?, serC, serB
Desulfurobacterium atlanticum DSM 15668	serA, serC, serB
Desulfuromonas acetexigens	serA, serC, serB
Desulfuromusa kysingii DSM 7343	serA, serC, serB ?
Ferroglobus placidus DSM 10642	serA, serC, serB
Frankia alni ACN14A	serA, serC, serB
Geobacter lovleyi SZ	serA, serC, serB
Geobacter metallireducens GS-15	serA, serC, serB ?
Geobacter uraniireducens Rf4	serA, serC, serB ?
Haloechinothrix alba DSM 45207	serA, serC, serB
Haloglycomyces albus DSM 45210	serA, serC, serB
Halomonas desiderata SP1	serA, serC, serB
Halorhodospira halophila SL1	serA, serC, serB
Heliobacterium modesticaldum Ice1; ATCC 51547	serA, serC, serB
Herbaspirillum autotrophicum IAM 14942	serA, serC, serB
Hydrogenophaga taeniospiralis NBRC 102512	serA, serC, serB
Hydrogenovibrio halophilus DSM 15072	serA, serC, serB
Hydrogenovibrio kuenenii DSM 12350	serA, serC, serB
Hydrogenovibrio marinus DSM 11271	serA, serC, serB
Hyphomicrobium sulfonivorans WDL6	serA ?, serC, serB ?
Klebsiella variicola At-22	serA, serC, serB
Kyrpidia tusciae DSM 2912	serA, serC, serB
Leptospirillum ferrooxidans C2-3	serA, serC, serB ?
Malonomonas rubra DSM 5091	serA, serC, serB ?
Mesorhizobium ciceri WSM1271	serA, serC, serB
Methanobacterium lacus AL-21	serA, serC, serB
Methanococcus aeolicus Nankai-3	serA, serC, serB
Methanococcus maripaludis C5	serA, serC, serB
Methanosarcina acetivorans C2A	serA, serC, serB
Methanosarcina barkeri Fusaro	serA, serC, serB
Methanosarcina mazei Go1	serA, serC, serB
Methanothermobacter thermautotrophicus Delta H	serA, serC, serB
Methylobacterium nodulans ORS 2060	serA, serC, serB
Methylobacterium sp. 4-46	serA, serC, serB
Methylocapsa acidiphila B2	serA, serC, serB
Methylocapsa aurea KYG T	serA, serC, serB
Methylocella silvestris BL2	serA, serC, serB
Methylococcus capsulatus Bath	serA, serC, serB
Methylocystis bryophila S285	serA, serC, serB
Methyloferula stellata AR4T	serA ?, serC, serB
Methylohalobius crimeensis 10Ki	serA, serC, serB
Methylomicrobium alcaliphilum 20Z	serA, serC, serB
Methylomonas methanica MC09	serA, serC, serB
Methylosarcina fibrata AML-C10	serA, serC, serB
Methylovulum miyakonense HT12	serA, serC, serB
Mycolicibacterium vanbaalenii PYR-1	serA, serC, serB
Nitratifractor salsuginis DSM 16511	serA, serC ?, serB
Nitratiruptor tergarcus DSM 16512	serA, serC ?, serB
Nitriliruptor alkaliphilus DSM 45188	serA, serC, serB
Nocardiopsis lucentensis DSM 44048	serA, serC, serB
Nostoc punctiforme ATCC 29133; PCC 73102	serA, serC, serB
Novosphingobium aromaticivorans DSM 12444	serA, serC, serB
Oleispira antarctica	serA, serC, serB
Paraburkholderia phymatum STM815	serA, serC, serB
Paraburkholderia sp. CCGE1002	serA, serC, serB
Pelobacter propionicus DSM 2379	serA, serC, serB
Persephonella marina EX-H1	serA, serC, serB
Polaromonas naphthalenivorans CJ2	serA, serC, serB
Prosthecochloris aestuarii DSM 271	serA ?, serC ?, serB
Pseudarthrobacter sulfonivorans Ar51	serA, serC, serB
Pseudomonas benzenivorans DSM 8628	serA, serC, serB
Pseudomonas stutzeri A1501	serA, serC, serB
Pyrolobus fumarii 1A	serA, serC, serB ?
Rhizobium etli CFN 42	serA, serC, serB
Rhizobium leguminosarum 3841	serA, serC, serB
Rhizobium leguminosarum WSM1325	serA, serC, serB
Rhodobacter sphaeroides ATCC 17029	serA, serC, serB
Rhodomicrobium vannielii ATCC 17100	serA, serC, serB
Rhodopseudomonas palustris CGA009	serA, serC, serB
Rhodospirillum centenum SW; ATCC 51521	serA, serC, serB
Rhodospirillum rubrum ATCC 11170	serA, serC, serB
Saccharomonospora cyanea NA-134	serA, serC, serB
Sedimenticola selenatireducens DSM 17993	serA, serC, serB
Sinorhizobium fredii NGR234	serA, serC, serB
Sinorhizobium medicae WSM419	serA, serC, serB
Sphingomonas wittichii RW1	serA, serC, serB
Stenotrophomonas chelatiphaga DSM 21508	serA, serC, serB ?
Steroidobacter denitrificans DSM 18526	serA, serC, serB ?
Sulfuricurvum kujiense DSM 16994	serA, serC ?, serB
Sulfurihydrogenibium azorense Az-Fu1	serA, serC ?, serB
Sulfurihydrogenibium subterraneum DSM 15120	serA, serC ?, serB
Sulfurimonas denitrificans DSM 1251	serA, serC ?, serB
Sulfuritalea hydrogenivorans DSM 22779	serA, serC, serB
Sulfurivirga caldicuralii DSM 17737	serA, serC, serB
Teredinibacter turnerae T7901	serA, serC, serB
Thauera aminoaromatica S2	serA, serC, serB
Thermithiobacillus tepidarius DSM 3134	serA, serC, serB
Thermocrinis albus DSM 14484	serA, serC ?, serB
Thermodesulforhabdus norvegica DSM 9990	serA, serC, serB ?
Thermomonospora curvata DSM 43183	serA, serC, serB
Thermovibrio ammonificans HB-1	serA, serC ?, serB
Thioalkalivibrio denitrificans ALJD	serA, serC, serB ?
Thioalkalivibrio halophilus HL17	serA, serC, serB ?
Thioalkalivibrio paradoxus ARh 1	serA, serC, serB
Thioalkalivibrio thiocyanodenitrificans ARhD 1	serA, serC, serB ?
Thiohalomonas denitrificans HLD2	serA, serC, serB
Thiomicrorhabdus arctica DSM 13458	serA, serC, serB
Thiomicrorhabdus chilensis DSM 12352	serA, serC, serB
Thiomicrospira cyclica ALM1	serA, serC, serB
Thiomicrospira microaerophila ASL8-2	serA, serC, serB
Thiomicrospira pelophila DSM 1534	serA, serC, serB
Thiothrix lacustris DSM 21227	serA, serC, serB ?
Trichodesmium erythraeum IMS101	serA, serC, serB ?
Trichormus variabilis ATCC 29413	serA, serC, serB
Xanthobacter autotrophicus Py2	serA, serC, serB
Xenophilus azovorans DSM 13620	serA, serC, serB

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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis