L-cysteine biosynthesis

GapMind for Amino acid biosynthesis

L-cysteine biosynthesis

Analysis of pathway cys in 150 genomes

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

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