cysW Family assigned · medium auto-curated
H37Rv Rv2398c · MTBC0 mtbc0_002553 ·
272 aa · 2719228–2720046 (-) ·
RefSeq NP_216914.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sulfate ABC transporter permease CysW |
|---|---|
| MTBC0 PGAP re-annotation | sulfate ABC transporter permease subunit CysW |
| Revised (this work) | Sulfate ABC transporter permease subunit CysW. Pfam: BPD_transp_1 (PF00528.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71746
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable sulfate-transport integral membrane protein ABC transporter CysW |
| Curated function | Part of the ABC transporter complex CysAWTP (TC 3.A.1.6.1) involved in sulfate/thiosulfate import. Probably responsible for the translocation of the substrate across the membrane. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | cysW |
| eggNOG description | sulfate ABC transporter |
| Orthologous group | COG4208 |
| KEGG orthology |
K02047
|
| KEGG pathways |
map00920, map02010
|
| KEGG modules |
M00185
|
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 | 0.38 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 3 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 |
|---|---|---|---|---|
BPD_transp_1 | PF00528.28 | 2.2e-13 | 73–265 | Binding-protein-dependent transport system inner membrane component |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: subI (sulfate ABC transporter substrate-binding lipoprotein SubI), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1286 cysC |
adenylyl-sulfate kinase | 999 | 1000 | coexpression:999 database:900 textmining:905 |
Rv2400c subI |
sulfate ABC transporter substrate-binding lipoprotein SubI | 999 | 1000 ctx | neighborhood:881 cooccurence:774 coexpression:965 database:900 textmining:865 |
Rv2397c cysA1 |
sulfate ABC transporter ATP-binding protein CysA | 999 | 1000 ctx | neighborhood:865 cooccurence:770 coexpression:960 database:900 textmining:914 |
Rv2399c cysT |
sulfate ABC transporter permease CysT | 999 | 1000 ctx | neighborhood:882 coexpression:976 database:900 |
Rv1285 cysD |
sulfate adenylyltransferase subunit 2 | 976 | 966 | coexpression:656 database:900 |
Rv1859 modC |
molybdenum ABC transporter ATP-binding protein ModC | 878 | 861 | coexpression:724 |
Rv2391 sirA |
sulfite reductase | 793 | 713 | coexpression:697 |
Rv2064 cobG |
precorrin-3B synthase | 744 | 711 | coexpression:694 |
Rv2392 cysH |
phosphoadenosine phosphosulfate reductase | 777 | 676 | coexpression:657 |
Rv1857 modA |
molybdate ABC transporter substrate-binding lipoprotein ModA | 769 | 627 ctx | cooccurence:617 textmining:408 |
Rv2401 hyp |
hypothetical protein | 584 | 583 ctx | neighborhood:578 |
Rv2334 cysK1 |
O-acetylserine sulfhydrylase | 500 | 453 | coexpression:435 |
Rv1336 cysM |
O-phosphoserine sulfhydrylase | 606 | 434 | coexpression:415 |
Rv0848 cysK2 |
cysteine synthase CysK | 748 | 431 | coexpression:412 textmining:576 |
Rv1077 cbs |
cystathionine beta-synthase | 501 | 429 | coexpression:410 |
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: sulfate ABC transporter permease CysW
- MTBC0 PGAP product: sulfate ABC transporter permease subunit CysW
- Pfam (hmmscan --cut_ga): BPD_transp_1 PF00528.28 (E=2e-13)
- (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_216914.1)
- Domains: Pfam-A via hmmscan --cut_ga — BPD_transp_1 (PF00528.28)
- 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
COG4208 - Curated reference: UniProt P71746 (TrEMBL, unreviewed; Predicted)
- 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 —
24 functional partner(s); context anchor
subI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002553|Rv2398c|cysW MTSLPAARYLVRSVALGYVFVLLIVPVALILWRTFEPGFGQFYAWISTPAAISALNLSLLVVAIVVPLNVIFGVTTALVLARNRFRGKGVLQAIIDLPFAVSPVIVGVSLILLWGSAGALGFVEQDLGFKIIFGLPGIVLASMFVTCPFVVREVEPVLHELGTDQEQAAATLGSGWWQTFWRITLPSIRWGLTYGIVLTVARTLGEYGAVIIVSSNLPGTSQTLTLLVSDRYHRGAEYGAYALSTLLMAVSVVVLIVQMVLDARRARAVSEG