csd Resolved · high auto-curated
H37Rv Rv1464 · MTBC0 mtbc0_001566 ·
417 aa · 1661323–1662576 (+) ·
RefSeq NP_215980.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cysteine desulfurase |
|---|---|
| MTBC0 PGAP re-annotation | cysteine desulfurase |
| Revised (this work) | Cysteine desulfurase. Pfam: Aminotran_5 (PF00266.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ69
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable cysteine desulfurase |
| EC (curated) |
EC 2.8.1.7
|
| Curated function | Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L-selenocystine to produce L-alanine. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | sufS |
| eggNOG description | Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L- selenocystine to produce L-alanine |
| Orthologous group | COG0520 |
| EC number |
EC 2.8.1.7, EC 4.4.1.16
|
| KEGG orthology |
K11717
|
| KEGG pathways |
map00450, map01100
|
| Gene Ontology (8) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040007, GO:0044464, GO:0071944
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.72 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Aminotran_5 | PF00266.26 | 1.5e-141 | 32–403 | Aminotransferase class-V |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1465 (nitrogen fixation related protein), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1465 |
nitrogen fixation related protein | 999 | 1000 ctx | neighborhood:881 cooccurence:767 coexpression:955 experimental:785 textmining:824 |
Rv1463 sufC |
ABC transporter ATP-binding protein | 999 | 999 ctx | neighborhood:882 cooccurence:774 coexpression:955 textmining:692 |
Rv1462 sufD hyp |
hypothetical protein | 999 | 998 ctx | neighborhood:882 cooccurence:771 coexpression:941 textmining:817 |
Rv1461 sufB hyp |
hypothetical protein | 990 | 990 ctx | neighborhood:781 cooccurence:773 coexpression:782 |
Rv1466 hyp |
hypothetical protein | 988 | 987 ctx | neighborhood:881 cooccurence:635 coexpression:731 |
Rv3913 trxB2 |
thioredoxin reductase | 923 | 920 | database:900 |
Rv1471 trxB1 |
thioredoxin | 902 | 902 | database:900 |
Rv1079 metB |
cystathionine gamma-synthase | 909 | 901 | database:900 |
Rv1460 sufR |
transcriptional regulator | 886 | 886 ctx | neighborhood:882 |
Rv0888 spmT hyp |
hypothetical protein | 781 | 781 | experimental:780 |
Rv1459c mptB |
alpha-(1->6)-mannopyranosyltransferase | 777 | 774 ctx | neighborhood:772 |
Rv1457c |
antibiotic ABC transporter permease | 719 | 720 ctx | neighborhood:712 |
Rv1458c |
antibiotic ABC transporter ATP-binding protein | 715 | 715 ctx | neighborhood:712 |
Rv3284 hyp |
hypothetical protein | 701 | 670 | experimental:490 |
Rv1456c |
antibiotic ABC transporter permease | 587 | 587 ctx | neighborhood:586 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: cysteine desulfurase
- MTBC0 PGAP product: cysteine desulfurase
- Pfam (hmmscan --cut_ga): Aminotran_5 PF00266.26 (E=1e-141)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215980.1)
- Domains: Pfam-A via hmmscan --cut_ga — Aminotran_5 (PF00266.26)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG0520 - Curated reference: UniProt P9WQ69 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
23 functional partner(s); context anchor
Rv1465 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001566|Rv1464|csd MTASVNSLDLAAIRADFPILKRIMRGGNPLAYLDSGATSQRPLQVLDAEREFLTASNGAVHRGAHQLMEEATDAYEQGRADIALFVGADTDELVFTKNATEALNLVSYVLGDSRFERAVGPGDVIVTTELEHHANLIPWQELARRTGATLRWYGVTDDGRIDLDSLYLDDRVKVVAFTHHSNVTGVLTPVSELVSRAHQSGALTVLDACQSVPHQPVDLHELGVDFAAFSGHKMLGPNGIGVLYGRRELLAQMPPFLTGGSMIETVTMEGATYAPAPQRFEAGTPMTSQVVGLAAAARYLGAIGMAAVEAHERELVAAAIEGLSGIDGVRILGPTSMRDRGSPVAFVVEGVHAHDVGQVLDDGGVAVRVGHHCALPLHRRFGLAATARASFAVYNTADEVDRLVAGVRRSRHFFGRA