L-serine catabolism

GapMind for catabolism of small carbon sources

L-serine catabolism

Analysis of pathway serine in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	snatA, sdaB
Acidithiobacillus ferrooxidans ATCC 23270	snatA, sdaB
Alicycliphilus denitrificans K601	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Allochromatium vinosum DSM 180	serP, sdaB
Ammonifex degensii KC4	braC, braD *, braE, braF, braG, sdaB
Archaeoglobus veneficus SNP6	snatA, sdaB
Arcobacter nitrofigilis DSM 7299	snatA, sdaB
Azoarcus sp. BH72	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Azohydromonas australica DSM 1124	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Azorhizobium caulinodans ORS 571	braC, braD, braE, braF, braG, sdaB
Azospirillum lipoferum B510	sdaC, sdaB
Bacillus alkalinitrilicus DSM 22532	serP, sdaB
Beijerinckia indica ATCC 9039	snatA, sdaB
Beijerinckia mobilis UQM 1969	snatA, sdaB
Bradyrhizobium sp. BTAi1	braC, braD, braE, braF, braG, sdaB
Burkholderia vietnamiensis G4	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Calditerrivibrio nitroreducens DSM 19672	serP, sdaB
Caminibacter mediatlanticus TB-2	snatA, sdaB
Chlorobaculum parvum NCIB 8327	snatA, sdaB
Chlorobaculum tepidum TLS	snatA, sdaB
Chlorobium limicola DSM 245	serP, sdaB
Chlorobium phaeobacteroides BS1	snatA, sdaB
Clostridium acetobutylicum ATCC 824	serP, sdhA, sdhB
Clostridium kluyveri DSM 555	serP, sdhA, sdhB
Crocosphaera subtropica ATCC 51142	braC, braD, braE, braF, braG, sdaB
Dechloromonas agitata is5	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Dehalococcoides mccartyi 195	snatA, sdaB
Denitrovibrio acetiphilus DSM 12809	braC, braD, braE, braF, braG, sdaB
Derxia gummosa DSM 723	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Desulfacinum hydrothermale DSM 13146	braC, braD, braE, braF, braG, sdaB
Desulfacinum infernum DSM 9756	braC, braD, braE, braF, braG, sdaB
Desulfallas geothermicus DSM 3669	serP, sdaB
Desulfarculus baarsii DSM 2075	snatA, sdaB
Desulfatibacillum aliphaticivorans DSM 15576	braC, braD, braE, braF, braG, sdaB
Desulfatiglans anilini DSM 4660	braC, braD, braE, braF, braG, sdaB
Desulfitobacterium hafniense DCB-2	sstT, sdaB
Desulfobacca acetoxidans DSM 11109	braC, braD, braE, braF, braG, sdaB
Desulfobacter vibrioformis DSM 8776	serP, sdaB
Desulfobulbus mediterraneus DSM 13871	braC, braD, braE, braF, braG, sdaB
Desulfotalea psychrophila LSv54	sstT, sdaB
Desulfotomaculum ruminis DSM 2154	serP, sdaB
Desulfovibrio bastinii DSM 16055	sstT, sdaB
Desulfovibrio gracilis DSM 16080	braC, braD, braE, braF, braG, sdaB
Desulfovibrio oxyclinae DSM 11498	braC, braD, braE, braF, braG, sdaB
Desulfovibrio zosterae DSM 11974	sstT, sdaB
Desulfurobacterium atlanticum DSM 15668	braC, braD, braE, braF, braG, sdaB
Desulfuromonas acetexigens	snatA, sdaB
Desulfuromusa kysingii DSM 7343	braC, braD, braE, braF, braG, sdaB
Ferroglobus placidus DSM 10642	serP, sdaB
Frankia alni ACN14A	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Geobacter lovleyi SZ	serP, sdaB
Geobacter metallireducens GS-15	serP, sdaB
Geobacter uraniireducens Rf4	snatA, sdaB
Haloechinothrix alba DSM 45207	braC, braD, braE, braF, braG, sdaB
Haloglycomyces albus DSM 45210	serP, sdaB
Halomonas desiderata SP1	braC, braD, braE, braF, braG, sdaB
Halorhodospira halophila SL1	serP, sdaB
Heliobacterium modesticaldum Ice1; ATCC 51547	serP, sdaB
Herbaspirillum autotrophicum IAM 14942	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Hydrogenophaga taeniospiralis NBRC 102512	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Hydrogenovibrio halophilus DSM 15072	serP, sdaB
Hydrogenovibrio kuenenii DSM 12350	snatA, sdaB
Hydrogenovibrio marinus DSM 11271	snatA, sdaB
Hyphomicrobium sulfonivorans WDL6	braC, braD, braE, braF, braG, sdaB
Klebsiella variicola At-22	sdaC, sdaB
Kyrpidia tusciae DSM 2912	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Leptospirillum ferrooxidans C2-3	serP, sdaB
Malonomonas rubra DSM 5091	braC, braD, braE, braF, braG, sdaB
Mesorhizobium ciceri WSM1271	braC, braD, braE, braF, braG, sdaB
Methanobacterium lacus AL-21	serP, sdaB
Methanococcus aeolicus Nankai-3	snatA, sdaB
Methanococcus maripaludis C5	snatA, sdaB
Methanosarcina acetivorans C2A	snatA, sdaB
Methanosarcina barkeri Fusaro	snatA, sdaB
Methanosarcina mazei Go1	snatA, sdaB
Methanothermobacter thermautotrophicus Delta H	serP, sdaB
Methylobacterium nodulans ORS 2060	braC, braD, braE, braF, braG, sdaB
Methylobacterium sp. 4-46	braC, braD, braE, braF, braG, sdaB
Methylocapsa acidiphila B2	braC, braD, braE, braF, braG, sdaB
Methylocapsa aurea KYG T	braC, braD, braE, braF, braG, sdaB
Methylocella silvestris BL2	braC, braD, braE, braF, braG, sdaB
Methylococcus capsulatus Bath	snatA, sdaB
Methylocystis bryophila S285	serP, sdaB
Methyloferula stellata AR4T	braC, braD, braE, braF, braG, sdaB
Methylohalobius crimeensis 10Ki	snatA, sdaB
Methylomicrobium alcaliphilum 20Z	snatA, sdaB
Methylomonas methanica MC09	snatA, sdaB
Methylosarcina fibrata AML-C10	snatA, sdaB
Methylovulum miyakonense HT12	snatA, sdaB
Mycolicibacterium vanbaalenii PYR-1	braC, braD, braE, braF, braG, sdaB
Nitratifractor salsuginis DSM 16511	snatA, sdaB
Nitratiruptor tergarcus DSM 16512	snatA, sdaB
Nitriliruptor alkaliphilus DSM 45188	braC, braD, braE, braF, braG, sdaB
Nocardiopsis lucentensis DSM 44048	braC, braD, braE, braF, braG, sdaB
Nostoc punctiforme ATCC 29133; PCC 73102	braC, braD, braE, braF, braG, sdaB
Novosphingobium aromaticivorans DSM 12444	snatA, sdaB
Oleispira antarctica	serP, sdaB
Paraburkholderia phymatum STM815	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Paraburkholderia sp. CCGE1002	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Pelobacter propionicus DSM 2379	serP, sdaB
Persephonella marina EX-H1	serP, sdaB
Polaromonas naphthalenivorans CJ2	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Prosthecochloris aestuarii DSM 271	serP, sdaB
Pseudarthrobacter sulfonivorans Ar51	braC, braD, braE, braF, braG, sdaB
Pseudomonas benzenivorans DSM 8628	braC, braD, braE, braF, braG, sdaB
Pseudomonas stutzeri A1501	braC, braD, braE, braF, braG, sdaB
Pyrolobus fumarii 1A	snatA, sdaB
Rhizobium etli CFN 42	braC, braD, braE, braF, braG, sdaB
Rhizobium leguminosarum 3841	braC, braD, braE, braF, braG, sdaB
Rhizobium leguminosarum WSM1325	braC, braD, braE, braF, braG, sdaB
Rhodobacter sphaeroides ATCC 17029	snatA, sdaB
Rhodomicrobium vannielii ATCC 17100	snatA, sdaB
Rhodopseudomonas palustris CGA009	braC, braD, braE, braF, braG, sdaB
Rhodospirillum centenum SW; ATCC 51521	braC, braD, braE, braF, braG, sdaB
Rhodospirillum rubrum ATCC 11170	braC, braD, braE, braF, braG, sdaB
Saccharomonospora cyanea NA-134	serP, sdaB
Sedimenticola selenatireducens DSM 17993	braC, braD, braE, braF, braG, sdaB
Sinorhizobium fredii NGR234	braC, braD, braE, braF, braG, sdaB
Sinorhizobium medicae WSM419	braC, braD, braE, braF, braG, sdaB
Sphingomonas wittichii RW1	snatA, sdaB
Stenotrophomonas chelatiphaga DSM 21508	serP, sdaB
Steroidobacter denitrificans DSM 18526	snatA, sdaB
Sulfuricurvum kujiense DSM 16994	serP, sdaB
Sulfurihydrogenibium azorense Az-Fu1	snatA, sdaB
Sulfurihydrogenibium subterraneum DSM 15120	snatA, sdaB
Sulfurimonas denitrificans DSM 1251	serP, sdaB
Sulfuritalea hydrogenivorans DSM 22779	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Sulfurivirga caldicuralii DSM 17737	serP, sdaB
Teredinibacter turnerae T7901	snatA, sdaB
Thauera aminoaromatica S2	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Thermithiobacillus tepidarius DSM 3134	snatA, sdaB
Thermocrinis albus DSM 14484	serP, sdaB
Thermodesulforhabdus norvegica DSM 9990	snatA, sdaB
Thermomonospora curvata DSM 43183	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Thermovibrio ammonificans HB-1	serP, sdaB
Thioalkalivibrio denitrificans ALJD	snatA, sdaB
Thioalkalivibrio halophilus HL17	snatA, sdaB
Thioalkalivibrio paradoxus ARh 1	snatA, sdaB
Thioalkalivibrio thiocyanodenitrificans ARhD 1	snatA, sdaB
Thiohalomonas denitrificans HLD2	snatA, sdaB
Thiomicrorhabdus arctica DSM 13458	snatA, sdaB
Thiomicrorhabdus chilensis DSM 12352	snatA, sdaB
Thiomicrospira cyclica ALM1	serP, sdaB
Thiomicrospira microaerophila ASL8-2	serP, sdaB
Thiomicrospira pelophila DSM 1534	serP, sdaB
Thiothrix lacustris DSM 21227	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Trichodesmium erythraeum IMS101	serP, sdaB
Trichormus variabilis ATCC 29413	braC, braD, braE, braF, braG, sdaB
Xanthobacter autotrophicus Py2	braC, braD, braE, braF, braG, sdaB
Xenophilus azovorans DSM 13620	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB

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

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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:

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

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 catabolism of small carbon sources