L-cysteine biosynthesis

GapMind for Amino acid biosynthesis

L-cysteine biosynthesis

Analysis of pathway cys in 206 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	cysE, cysK
Acidithiobacillus ferrooxidans ATCC 23270	cysE, cysK
Acidovorax sp. GW101-3H11	cysE, cysK
Algiphilus aromaticivorans DG1253	cysE, cysK
Alicycliphilus denitrificans K601	cysE, cysK
Alkalihalobacterium alkalinitrilicum DSM 22532	cysE, cysK
Allochromatium vinosum DSM 180	cysE, cysK
Ammonifex degensii KC4	cysE, cysK
Anaerobutyricum hallii DSM 3353	cysE, cysK
Aquimarina longa SW024	CBS, CGL
Archaeoglobus veneficus SNP6	serA, serC, sepS, pscS
Arcobacter nitrofigilis DSM 7299	cysE, cysK
Azoarcus olearius BH72	cysE, cysK
Azohydromonas australica DSM 1124	cysE, cysK
Azorhizobium caulinodans ORS 571	cysE, cysK
Azospirillum brasilense Sp245	cysE, cysK
Azospirillum sp. B510	cysE, cysK
Bacteroides thetaiotaomicron VPI-5482	cysE, cysK
Beijerinckia indica subsp. indica ATCC 9039	cysE, cysK
Beijerinckia mobilis UQM 1969	cysE, cysK
Bradyrhizobium sp. BTAi1	cysE, cysK
Brevundimonas sp. GW460-12-10-14-LB2	cysE, cysK
Burkholderia phytofirmans PsJN	cysE, cysK
Burkholderia vietnamiensis G4	cysE, cysK
Calditerrivibrio nitroreducens DSM 19672	cysE, cysK
Caminibacter mediatlanticus TB-2	cysE, cysK
Carboxydothermus pertinax Ug1	cysE, cysK
Caulobacter crescentus NA1000	cysE, cysK
Cereibacter sphaeroides ATCC 17029	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
Clostridium tyrobutyricum FAM22553	cysE, cysK
Crocosphaera subtropica ATCC 51142	cysE, cysK
Cupriavidus basilensis FW507-4G11	cysE, cysK
Dechloromonas agitata is5	cysE, cysK
Dechlorosoma suillum PS	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
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
Desulfogranum mediterraneum DSM 13871	cysE, cysK
Desulforamulus ruminis DSM 2154	cysE, cysK
Desulfoscipio geothermicus DSM 3669	cysE, cysK
Desulfotalea psychrophila LSv54	cysE, cysK
Desulfovibrio oxyclinae DSM 11498	cysE, cysK
Desulfovibrio vulgaris Hildenborough JW710	cysE, cysK
Desulfovibrio vulgaris Miyazaki F	cysE, cysK
Desulfurobacterium atlanticum DSM 15668	cysE, cysK
Desulfuromonas acetexigens DSM 1397	cysE, cysK
Desulfuromusa kysingii DSM 7343	serA, serC, PSSH
Dinoroseobacter shibae DFL-12	cysE, cysK
Dyella japonica UNC79MFTsu3.2	SST, cysK
Echinicola vietnamensis KMM 6221, DSM 17526	cysE, cysK
Escherichia coli BW25113	cysE, cysK
Ferroglobus placidus DSM 10642	serA, serC, sepS, pscS
Frankia alni ACN14a	serA, serC, cysO, moeZ, Mt_cysM, mec
Geobacter metallireducens GS-15	cysE, cysK
Geotalea uraniireducens Rf4	cysE, cysK
Halococcus hamelinensis 100A6	cysE, cysK
Haloechinothrix alba DSM 45207	serA, serC, cysO, moeZ, Mt_cysM, mec
Haloferax volcanii DS2	cysE, cysK
Haloglycomyces albus DSM 45210	serA, serC, cysO, moeZ, Mt_cysM, mec
Halomonas desiderata SP1	serA, serC, PSSH
Halorhodospira halophila SL1	cysE, cysK
Heliomicrobium modesticaldum Ice1 Ice1; ATCC 51547	cysE, cysK
Herbaspirillum autotrophicum IAM 14942	cysE, cysK
Herbaspirillum seropedicae SmR1	cysE, cysK
Hippea alviniae EP5-r	cysE, cysK
Hydrogenophaga taeniospiralis CCUG 15921 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 michiganensis M5al	cysE, cysK
Klebsiella variicola At-22	cysE, cysK
Kyrpidia tusciae DSM 2912	cysE, cysK
Leptospirillum ferrooxidans C2-3	cysE, cysK
Lysobacter soli OAE881	SST, cysK
Magnetospirillum magneticum AMB-1	cysE, cysK
Malonomonas rubra DSM 5091	serA, serC, PSSH
Maridesulfovibrio bastinii DSM 16055	cysE, cysK
Maridesulfovibrio zosterae DSM 11974	cysE, cysK
Marinobacter adhaerens HP15	cysE, cysK
Mesorhizobium ciceri biovar biserrulae 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 mazei Go1	serA, serC, sepS, pscS
Methanospirillum lacunae Ki8-1	serA, serC, sepS, pscS
Methanothermobacter thermautotrophicus str. Delta H	serA, serC, sepS, pscS
Methylobacterium nodulans ORS 2060	cysE, cysK
Methylobacterium sp. 4-46 Apr-46	cysE, cysK
Methylocapsa acidiphila B2	cysE, cysK
Methylocapsa aurea KYG	cysE, cysK
Methylocella silvestris BL2	cysE, cysK
Methylococcus capsulatus str. Bath	cysE, cysK
Methylocystis bryophila S285	cysE, cysK
Methyloferula stellata AR4 AR4T	cysE, cysK
Methylohalobius crimeensis 10Ki	cysE, cysK
Methylomonas methanica MC09	cysE, cysK
Methylosarcina fibrata AML-C10	cysE, cysK
Methylotuvimicrobium alcaliphilum 20Z	cysE, cysK
Methylovulum miyakonense HT12	cysE, cysK
Mucilaginibacter yixingensis DSM 26809	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
Nitrosopumilus maritimus SCM1	serA, serC, PSSH
Nocardioides dokdonensis FR1436	serA, serC, cysO, moeZ, Mt_cysM, mec
Nocardiopsis lucentensis DSM 44048	serA, serC, cysO, moeZ, Mt_cysM, mec
Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102	cysE, cysK
Novosphingobium aromaticivorans DSM 12444	cysE, cysK
Oleispira antarctica RB-8	cysE, cysK
Paraburkholderia atlantica CCGE1002	cysE, cysK
Paraburkholderia bryophila 376MFSha3.1	cysE, cysK
Paraburkholderia phymatum STM815	cysE, cysK
Paucidesulfovibrio gracilis DSM 16080	cysE ?, cysK
Pedobacter sp. GW460-11-11-14-LB5	cysE, cysK
Pelobacter propionicus DSM 2379	serA, serC, PSSH
Persephonella marina EX-H1	serA, serC, PSSH
Phaeacidiphilus oryzae TH49	serA, serC, cysO, moeZ, Mt_cysM, mec
Phaeobacter inhibens BS107	cysE, cysK
Polaromonas naphthalenivorans CJ2	cysE, cysK
Prosthecochloris aestuarii DSM 271	cysE, cysK
Pseudarthrobacter sulfonivorans Ar51	cysE, cysK
Pseudomonas benzenivorans DSM 8628	cysE, cysK
Pseudomonas fluorescens FW300-N1B4	cysE, cysK
Pseudomonas fluorescens FW300-N2C3	cysE, cysK
Pseudomonas fluorescens FW300-N2E2	cysE, cysK
Pseudomonas fluorescens FW300-N2E3	cysE, cysK
Pseudomonas fluorescens GW456-L13	cysE, cysK
Pseudomonas putida KT2440	cysE, cysK
Pseudomonas simiae WCS417	cysE, cysK
Pseudomonas stutzeri RCH2	cysE, cysK
Pyrolobus fumarii 1A	serA, serC, PSSH
Rhizobium etli CFN 42	cysE, cysK
Rhizobium johnstonii 3841	cysE, cysK
Rhizobium leguminosarum bv. trifolii WSM1325	cysE, cysK
Rhizorhabdus wittichii RW1	cysE, cysK
Rhodanobacter denitrificans FW104-10B01	SST, cysK
Rhodomicrobium vannielii ATCC 17100	cysE, cysK
Rhodopseudomonas palustris CGA009	cysE, cysK
Rhodospirillum centenum SW SW; ATCC 51521	cysE, cysK
Rhodospirillum rubrum ATCC 11170	cysE, cysK
Roseburia faecis M72	cysE, cysK
Saccharomonospora cyanea NA-134	serA, serC, cysO, moeZ, Mt_cysM, mec
Sedimenticola selenatireducens DSM 17993	cysE, cysK
Shewanella amazonensis SB2B	cysE, cysK
Shewanella loihica PV-4	cysE, cysK
Shewanella oneidensis MR-1	cysE, cysK
Shewanella sp. ANA-3	cysE, cysK
Sinorhizobium fredii NGR234	cysE, cysK
Sinorhizobium medicae WSM419	cysE, cysK
Sinorhizobium meliloti 1021	cysE, cysK
Sphingomonas koreensis DSMZ 15582	cysE, cysK
Stenotrophomonas chelatiphaga DSM 21508	SST, cysK
Steroidobacter denitrificans DSM 18526	SST, cysK
Stutzerimonas stutzeri A1501	cysE, 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 sk43H DSM 22779	cysE, cysK
Sulfurivirga caldicuralii DSM 17737	cysE, cysK
Synechococcus elongatus PCC 7942	cysE, cysK
Teredinibacter turnerae T7901	cysE, cysK
Thauera aminoaromatica S2	cysE, cysK
Thermithiobacillus tepidarius DSM 3134	cysE, cysK
Thermoanaerobacter kivui LKT-1	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
Thermus aquaticus YT-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
Thiohalospira halophila DSM 15071 HL 3	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
Tistlia consotensis USBA 355	CBS, CGL
Trichlorobacter lovleyi SZ	cysE, cysK
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome	cysE, cysK
Trichormus variabilis ATCC 29413	cysE, cysK
Xanthobacter autotrophicus Py2	cysE, cysK
Xanthomonas campestris pv. campestris strain 8004	SST, 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

Dependencies

In Aquimarina longa SW024, cys (using rule from-serine-homocysteine) is not allowed with met:transsulfuration.
- Cannot make cysteine from homocysteine and also make homocysteine from cysteine.
In Aquimarina longa SW024, cys (using rule from-serine-homocysteine) also requires met:homocysteine, which is not high-confidence.
- Cysteine biosynthesis via the reverse transsulfuration pathway requires homocysteine, which is an intermediate in methionine biosynthesis. Homocysteine is also an intermediate in the S-adenosylmethionine cycle, so many organisms that cannot synthesize methionine can convert it to homocysteine.

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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