L-cysteine biosynthesis

GapMind for Amino acid biosynthesis

L-cysteine biosynthesis

Analysis of pathway cys in 276 genomes

Genome	Best path
Acidovorax caeni R-24608	cysE, cysK
Actinokineospora bangkokensis 44EHW	serA, serC, cysO, moeZ, Mt_cysM, mec
Actinomyces timonensis 7400942	cysE, cysK
Algiphilus aromaticivorans DG1253	cysE, cysK
Algoriphagus aquaeductus T4	cysE, cysK
Algoriphagus machipongonensis PR1	cysE, cysK
Alicyclobacillus ferrooxydans TC-34	cysE, cysK
Alishewanella agri BL06	cysE, cysK
Alistipes indistinctus YIT 12060	serA, serC, PSSH
Alistipes shahii WAL 8301	serA, serC, PSSH
Alkalitalea saponilacus SC/BZ-SP2	cysE, cysK
Amantichitinum ursilacus IGB-41	cysE, cysK
Amphibacillus jilinensis Y1	cysE, cysK
Amphritea japonica JAMM 1866	cysE, cysK
Amycolatopsis halophila YIM 93223	serA, serC, cysO, moeZ, Mt_cysM, mec
Amycolatopsis xylanica CPCC 202699	serA, serC, cysO, moeZ, Mt_cysM, mec
Aquimarina agarilytica ZC1	serA, serC, PSSH
Aquimarina longa SW024	CBS, CGL
Aquimarina macrocephali JAMB N27	CBS, CGL
Archaeoglobus sulfaticallidus PM70-1	serA, serC, sepS, pscS
Arcticibacter svalbardensis MN12-7	cysE, cysK
Ardenticatena maritima 110S	CBS, CGL
Arenimonas metalli CF5-1	SST, cysK
Arenitalea lutea P7-3-5	serA, serC, PSSH
Azospirillum humicireducens SgZ-5	cysE, cysK
Azospirillum thiophilum BV-S	cysE, cysK
Bacillus altitudinis 41KF2b	cysE, cysK
Bacillus coahuilensis m4-4	cysE, cysK
Bacillus cytotoxicus NVH 391-98	cysE, cysK
Bacillus horneckiae 1P01SC	cysE, cysK
Bacillus okhensis Kh10-101	cysE, cysK
Bacillus safensis FO-36b	cysE, cysK
Bacillus velezensis CBMB205	cysE, cysK
Bacteroides clarus YIT 12056	cysE, cysK
Bacteroides faecis MAJ27	cysE, cysK
Bacteroides fluxus YIT 12057	cysE, cysK
Bacteroides oleiciplenus YIT 12058	cysE, cysK
Barnesiella intestinihominis YIT 11860	cysE, cysK
Belnapia rosea CPCC 100156	cysE, cysK
Bizionia argentinensis JUB59	serA, serC, PSSH
Bradyrhizobium diazoefficiens USDA110	cysE, cysK
Brevibacterium jeotgali SJ5-8	cysE, cysK
Brucella inopinata BO1	cysE, cysK
Brucella microti CCM 4915	cysE, cysK
Bryobacter aggregatus MPL3	cysE, cysK
Caldicellulosiruptor hydrothermalis 108	cysE, cysK
Caldicellulosiruptor kronotskyensis 2002	cysE, cysK
Carboxydothermus pertinax Ug1	cysE, cysK
Catellicoccus marimammalium M35/04/3	cysE, cysK
Chromobacterium vaccinii MWU205	cysE, cysK
Chryseobacterium angstadtii KM	serA, serC, PSSH
Chryseobacterium arthrosphaerae CC-VM-7	serA, serC, PSSH
Chryseobacterium viscerum 687B-08	serA, serC, PSSH
Cloacibacillus porcorum CL-84	cysE, cysK
Cobetia crustatorum JO1	cysE, cysK
Collimonas arenae Ter10	cysE, cysK
Collimonas pratensis Ter91	cysE, cysK
Collinsella tanakaei YIT 12063	cysE, cysK
Coprobacter fastidiosus NSB1	cysE, cysK
Corynebacterium deserti GIMN1.010	cysE, cysK
Corynebacterium frankenforstense ST18	cysE, cysK
Corynebacterium lactis RW2-5	cysE, cysK
Croceitalea dokdonensis DOKDO 023	serA, serC, PSSH
Cronobacter condimenti 1330	cysE, cysK
Cronobacter muytjensii ATCC 51329	cysE, cysK
Cronobacter universalis NCTC 9529	cysE, cysK
Desulfatitalea tepidiphila S28bF	serA, serC, PSSH
Desulfotomaculum hydrothermale Lam5	cysE, cysK
Dethiosulfovibrio salsuginis USBA 82	cysE, cysK
Devosia chinhatensis IPL18	cysE, cysK
Devriesea agamarum IMP2	cysE, cysK
Dialister succinatiphilus YIT 11850	serA, serC, PSSH
Dietzia timorensis ID05-A0528	cysE, cysK
Dokdonella koreensis DS-123	SST, cysK
Domibacillus robiginosus WS 4628	cysE, cysK
Duganella sacchari Sac-22	cysE, cysK
Dyadobacter tibetensis Y620-1	cysE, cysK
Dyella jiangningensis SBZ3-12	SST, cysK
Endozoicomonas montiporae CL-33	cysE, cysK
Enterococcus termitis LMG 8895	cysE, cysK
Enterorhabdus caecimuris B7	cysE, cysK
Epibacterium ulvae U95	cysE, cysK
Erythrobacter gangjinensis K7-2	cysE, cysK
Erythrobacter marinus HWDM-33	cysE, cysK
Ethanoligenens harbinense YUAN-3	cysE, cysK
Fervidicella metallireducens AeB	cysE, cysK
Fibrella aestuarina BUZ 2	cysE, cysK
Flammeovirga pacifica WPAGA1	cysE, cysK
Flaviramulus ichthyoenteri Th78	serA, serC, PSSH
Flavobacterium beibuense F44-8	serA, serC, PSSH
Flavobacterium glycines Gm-149	cysE, cysK
Flavobacterium sp. LM5	CBS, CGL
Flavobacterium ummariense DS-12	CBS, CGL
Frischella perrara PEB0191	cysE, cysK
Galbibacter marinus ck-I2-15	serA, serC, PSSH
Gallaecimonas xiamenensis 3-C-1	cysE, cysK
Geobacter daltonii FRC-32	cysE, cysK
Gillisia marina CBA3202	serA, serC, PSSH
Gracilibacillus halophilus YIM-C55.5	cysE, cysK
Granulicella mallensis MP5ACTX8	cysE, cysK
Granulicella tundricola MP5ACTX9	cysE, cysK
Hafnia paralvei ATCC 29927	cysE, cysK
Haladaptatus cibarius D43	cysE, cysK
Halioglobus japonicus S1-36	cysE, cysK
Halobacillus alkaliphilus FP5	cysE, cysK
Halococcus hamelinensis 100A6	cysE, cysK
Halomonas salina B6	cysE, cysK
Halomonas smyrnensis AAD6	cysE, cysK
Halomonas stevensii S18214	cysE, cysK
Halomonas titanicae BH1	cysE, cysK
Halomonas xinjiangensis TRM 0175	cysE, cysK
Halopiger salifodinae KCY07-B2	cysE, cysK
Halostagnicola larsenii XH-48	cysE, cysK
Haloterrigena daqingensis JX313	cysE, cysK
Herbaspirillum aquaticum IEH 4430	cysE, cysK
Hippea alviniae EP5-r	cysE, cysK
Hippea jasoniae Mar08-272r	cysE, cysK
Hoeflea phototrophica DFL-43	cysE, cysK
Hyphomicrobium nitrativorans NL23	cysE, cysK
Imtechella halotolerans K1	cysE, cysK
Indibacter alkaliphilus LW1	cysE, cysK
Jannaschia aquimarina GSW-M26	cysE, cysK
Jeotgalibacillus soli P9	cysE, cysK
Kangiella geojedonensis YCS-5	cysE, cysK
Knoellia flava TL1	cysE, cysK
Kocuria flava HO-9041	cysE, cysK
Kocuria turfanensis HO-9042	cysE, cysK
Laceyella sediminis RHA1	cysE, cysK
Lacinutrix algicola AKS293	serA, serC, PSSH
Lacinutrix himadriensis E4-9a	serA, serC, PSSH
Lacinutrix mariniflava AKS432	serA, serC, PSSH
Lactobacillus curieae CCTCC M 2011381	serA, serC, PSSH
Lactobacillus delbrueckii ZN7a-9	cysE, cysK
Lactobacillus hokkaidonensis LOOC260	cysE, cysK
Lactobacillus oryzae SG293	serA, serC, PSSH
Lactobacillus pobuzihii E100301	cysE, cysK
Lactobacillus shenzhenensis LY-73	cysE, cysK
Lactobacillus silagei IWT126	cysE, cysK
Leeuwenhoekiella blandensis MED217	serA, serC, PSSH
Lentibacillus jeotgali Grbi	cysE, cysK
Limnohabitans curvus MWH-C5	cysE, cysK
Limnohabitans parvus II-B4	cysE, cysK
Listeria fleischmannii LU2006-1	cysE, cysK
Luteimonas huabeiensis HB2	SST, cysK
Luteipulveratus mongoliensis MN07-A0370	cysE, cysK
Lutibaculum baratangense AMV1	cysE, cysK
Lysobacter daejeonensis GH1-9	SST, cysK
Magnetovibrio blakemorei MV-1	cysE, cysK
Marinicella litoralis KMM 3900	SST, cysK
Mariniradius saccharolyticus AK6	cysE, cysK
Marinobacter algicola DG893	cysE, cysK
Marinobacter guineae M3B	cysE, cysK
Marinobacter psychrophilus 20041	cysE, cysK
Marinomonas arctica 328	cysE, cysK
Marivita geojedonensis DPG-138	cysE, cysK
Martelella endophytica YC6887	cysE, cysK
Megamonas funiformis YIT 11815	cysE, cysK
Mesorhizobium ciceri WSM1271	cysE, cysK
Methanobacterium arcticum M2	serA, serC, sepS, pscS
Methanobacterium veterum MK4	serA, serC, sepS, pscS
Methanocella arvoryzae MRE50	serA, serC, sepS, pscS
Methanococcus aeolicus Nankai-3	serA, serC, sepS, pscS
Methanoculleus horonobensis T10	serA, serC, sepS, pscS
Methanolinea tarda NOBI-1	serA, serC, sepS, pscS
Methanosarcina soligelidi SMA-21	serA, serC, sepS, pscS
Methanospirillum lacunae Ki8-1	serA, serC, sepS, pscS
Methanospirillum stamsii Pt1	serA, serC, sepS, pscS
Methylibium petroleiphilum PM1	cysE, cysK
Methylobacterium gossipiicola Gh-105	cysE, cysK
Methylocapsa aurea KYG	cysE, cysK
Methylotenera versatilis 301	cysE, cysK
Microbacterium profundi Shh49	cysE, cysK
Microvirga lotononidis WSM3557	cysE, cysK
Moritella dasanensis ArB 0140	cysE, cysK
Mucilaginibacter gossypii Gh-67	cysE, cysK
Mucilaginibacter gossypiicola Gh-48	cysE, cysK
Mucilaginibacter mallensis MP1X4	serA, serC, PSSH
Nafulsella turpanensis ZLM-10	CBS, CGL
Natronomonas moolapensis 8.8.11	cysE, cysK
Nautilia profundicola AmH	cysE, cysK
Neiella marina J221	cysE, cysK
Neptunomonas antarctica S3-22	cysE, cysK
Nocardioides daejeonensis MJ31	serA, serC, cysO, moeZ, Mt_cysM, mec
Nocardioides dokdonensis FR1436	serA, serC, cysO, moeZ, Mt_cysM, mec
Nocardiopsis baichengensis YIM 90130	serA, serC, cysO, moeZ, Mt_cysM, mec
Nocardiopsis gilva YIM 90087	serA, serC, cysO, moeZ, Mt_cysM, mec
Novosphingobium barchaimii LL02	cysE, cysK
Novosphingobium fuchskuhlense FNE08-7	cysE, cysK
Novosphingobium lindaniclasticum LE124	cysE, cysK
Oceanisphaera arctica V1-41	cysE, cysK
Ochrobactrum rhizosphaerae PR17	cysE, cysK
Ochrobactrum thiophenivorans DSM 7216	cysE, cysK
Oscillibacter ruminantium GH1	cysE, cysK
Paenisporosarcina indica PN2	cysE, cysK
Palaeococcus pacificus DY20341	serK, PSSH
Paludibacter propionicigenes WB4	cysE, cysK
Pandoraea thiooxydans ATSB16	cysE, cysK
Pantoea rwandensis LMG 26275	cysE, cysK
Pedobacter arcticus A12	cysE, cysK
Photobacterium gaetbulicola Gung47	cysE, cysK
Photobacterium jeanii R-40508	cysE, cysK
Phyllobacterium brassicacearum STM 196	cysE, cysK
Phyllobacterium endophyticum PEPV15	cysE, cysK
Phyllobacterium leguminum ORS 1419	cysE, cysK
Planktomarina temperata RCA23	cysE, cysK
Planococcus halocryophilus Or1	cysE, cysK
Pleomorphomonas diazotrophica R5-392	cysE, cysK
Polaribacter dokdonensis DSW-5	serA, serC, PSSH
Pontibacillus litoralis JSM 072002	cysE, cysK
Pontibacter lucknowensis DM9	cysE, cysK
Pontibacter ramchanderi LP43	cysE, cysK
Pontimonas salivibrio CL-TW6	cysE, cysK
Porphyrobacter dokdonensis DSW-74	cysE, cysK
Pseudoalteromonas arctica A 37-1-2	cysE, cysK
Pseudomonas baetica a390	cysE, cysK
Pseudomonas litoralis 2SM5	cysE, cysK
Pseudomonas taeanensis MS-3	cysE, cysK
Pseudovibrio axinellae Ad2	cysE, cysK
Psychrobacter arcticus 273-4	cysE, cysK
Psychrobacter cryohalolentis K5	cysE, cysK
Psychromonas ingrahamii 37	cysE, cysK
Psychromonas ossibalaenae JAMM 0738	cysE, cysK
Rhizobium freirei PRF 81	cysE, cysK
Rhizobium grahamii CCGE 502	cysE, cysK
Rhizobium subbaraonis JC85	cysE, cysK
Rhodanobacter denitrificans 2APBS1	SST, cysK
Rhodobacter johrii JA192	cysE, cysK
Rhodobacter maris JA276	cysE, cysK
Rhodobacter ovatus JA234	cysE, cysK
Rhodobacter viridis JA737	cysE, cysK
Rhodococcus qingshengii djl-6-2	cysE, cysK
Rhodopseudomonas pseudopalustris DSM 123	cysE, cysK
Roseateles aquatilis CCUG 48205	cysE, cysK
Roseivirga spongicola UST030701-084	cysE, cysK
Rubrivirga marina SAORIC-28	cysE, cysK
Ruegeria conchae TW15	cysE, cysK
Saccharomonospora marina XMU15	serA, serC, cysO, moeZ, Mt_cysM, mec
Salinicoccus carnicancri Crm	cysE, cysK
Serinicoccus profundi MCCC 1A05965	cysE, cysK
Shewanella halifaxensis HAW-EB4	cysE, cysK
Skermanella stibiiresistens SB22	cysE, cysK
Snodgrassella alvi wkB2	cysE, cysK
Sphaerochaeta globosa Buddy	cysE, cysK
Sphaerochaeta pleomorpha Grapes	cysE, cysK
Sphingobium baderi LL03	cysE, cysK
Sphingobium czechense LL01	cysE, cysK
Sphingobium quisquiliarum P25	cysE, cysK
Sphingomonas histidinilytica UM2	cysE, cysK
Sphingomonas indica Dd16	cysE, cysK
Sphingomonas laterariae LNB2	cysE, cysK
Sphingopyxis indica DS15	cysE, cysK
Sphingopyxis terrae UI2	cysE, cysK
Sporolactobacillus vineae SL153	cysE, cysK
Streptacidiphilus oryzae TH49	serA, serC, cysO, moeZ, Mt_cysM, mec
Streptococcus anginosus CCUG 39159	cysE, cysK
Streptococcus massiliensis 4401825	cysE, cysK
Streptococcus oralis 7747	cysE, cysK
Streptococcus oralis AZ_3a	cysE, cysK
Streptomyces kebangsaanensis SUK12	serA, serC, cysO, moeZ, Mt_cysM, mec
Succinatimonas hippei YIT 12066	cysE, cysK
Sulfurimonas gotlandica GD1	cysE, cysK
Tatumella morbirosei LMG 23360	cysE, cysK
Thauera humireducens SgZ-1	cysE, cysK
Thermoactinomyces daqus H-18	cysE, cysK
Thermobifida halotolerans YIM 90462	serA, serC, cysO, moeZ, Mt_cysM, mec
Thermodesulfovibrio aggregans TGE-P1	serA, serC, PSSH
Thermophagus xiamenensis HS1	cysE, cysK
Thermovenabulum gondwanense R270	cysE, cysK
Thioclava dalianensis DLFJ1-1	cysE, cysK
Thiohalospira halophila HL 3	cysE, cysK
Tistlia consotensis USBA 355	cysE, cysK
Vagococcus penaei CD276	cysE, cysK
Verminephrobacter eiseniae EF01-2	cysE, cysK
Weissella oryzae SG25	cysE, cysK
Williamsia sterculiae CPCC 203464	serA, serC, cysO, moeZ, Mt_cysM, mec
Yersinia intermedia Y228	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.
In Aquimarina macrocephali JAMB N27, 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 macrocephali JAMB N27, 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.
In Ardenticatena maritima 110S, cys (using rule from-serine-homocysteine) is not allowed with met:transsulfuration.
- Cannot make cysteine from homocysteine and also make homocysteine from cysteine.
In Ardenticatena maritima 110S, 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.
In Flavobacterium sp. LM5, cys (using rule from-serine-homocysteine) is not allowed with met:transsulfuration.
- Cannot make cysteine from homocysteine and also make homocysteine from cysteine.
In Flavobacterium sp. LM5, 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.
In Flavobacterium ummariense DS-12, 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.
In Nafulsella turpanensis ZLM-10, 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 26 2024. The underlying query database was built on Jul 25 2024.

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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 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