cysA1 Family assigned · medium auto-curated
H37Rv Rv2397c · MTBC0 - ·
351 aa · 2693909–2694964 (-) ·
RefSeq YP_177879.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sulfate ABC transporter ATP-binding protein CysA |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Sulfate ABC transporter ATP-binding protein CysA. Pfam: ABC_tran (PF00005.34), TOBE_2 (PF08402.17), TOBE_3 (PF12857.14), TOBE (PF03459.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WQM1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Sulfate/thiosulfate import ATP-binding protein CysA |
| EC (curated) |
EC 7.3.2.3
|
| Curated function | Part of the ABC transporter complex CysAWTP involved in sulfate/thiosulfate import. Responsible for energy coupling to the transport system. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | cysA |
| eggNOG description | Part of the ABC transporter complex CysAWTP involved in sulfate thiosulfate import. Responsible for energy coupling to the transport system |
| Orthologous group | COG1118 |
| EC number |
EC 3.6.3.25
|
| KEGG orthology |
K02045
|
| KEGG pathways |
map00920, map02010
|
| KEGG modules |
M00185
|
| Gene Ontology (16) |
GO:0005575, GO:0005623, GO:0005886, GO:0006810, GO:0006811, GO:0006820, GO:0008150, GO:0008272, GO:0015698, GO:0016020, GO:0040007, GO:0044464 +4 more
|
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 | 0.062 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 1 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 |
|---|---|---|---|---|
ABC_tran | PF00005.34 | 2.0e-38 | 20–162 | ABC transporter |
TOBE_2 | PF08402.17 | 2.6e-05 | 246–325 | TOBE domain |
TOBE_3 | PF12857.14 | 2.9e-10 | 270–325 | TOBE-like domain |
TOBE | PF03459.24 | 1.0e-05 | 273–324 | TOBE domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cysW (sulfate ABC transporter permease CysW), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2398c cysW |
sulfate ABC transporter permease CysW | 999 | 1000 ctx | neighborhood:865 cooccurence:770 coexpression:960 database:900 textmining:914 |
Rv2399c cysT |
sulfate ABC transporter permease CysT | 999 | 1000 ctx | neighborhood:865 cooccurence:771 coexpression:952 database:900 textmining:885 |
Rv2400c subI |
sulfate ABC transporter substrate-binding lipoprotein SubI | 999 | 1000 ctx | neighborhood:865 cooccurence:771 coexpression:948 database:900 textmining:773 |
Rv1286 cysC |
adenylyl-sulfate kinase | 999 | 999 | coexpression:984 database:900 textmining:418 |
Rv1285 cysD |
sulfate adenylyltransferase subunit 2 | 970 | 950 | coexpression:506 database:900 textmining:432 |
Rv1858 modB |
molybdenum ABC transporter permease ModB | 937 | 929 ctx | fusion:503 cooccurence:563 coexpression:658 |
Rv1218c |
tetronasin ABC transporter ATP-binding protein | 900 | 900 ctx | fusion:900 |
Rv2391 sirA |
sulfite reductase | 758 | 683 | coexpression:672 |
Rv2064 cobG |
precorrin-3B synthase | 708 | 680 | coexpression:669 |
Rv2326c |
ABC transporter ATP-binding protein | 607 | 608 | |
Rv2401 hyp |
hypothetical protein | 557 | 557 ctx | neighborhood:552 |
Rv2392 cysH |
phosphoadenosine phosphosulfate reductase | 809 | 522 | coexpression:506 textmining:617 |
Rv2401A |
membrane protein | 480 | 481 ctx | neighborhood:478 |
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 462 | 462 | |
Rv2334 cysK1 |
O-acetylserine sulfhydrylase | 503 | 453 | coexpression:435 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): sulfate ABC transporter ATP-binding protein CysA
- Pfam (hmmscan --cut_ga): ABC_tran PF00005.34 (E=2e-38), TOBE_2 PF08402.17 (E=3e-05), TOBE_3 PF12857.14 (E=3e-10), TOBE PF03459.24 (E=1e-05)
- (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 YP_177879.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC_tran (PF00005.34), TOBE_2 (PF08402.17), TOBE_3 (PF12857.14), TOBE (PF03459.24)
- 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
COG1118 - Curated reference: UniProt P9WQM1 (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 —
31 functional partner(s); context anchor
cysW - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2397c|cysA1 MTYAIVVADATKRYGDFVALDHVDFVVPTGSLTALLGPSGSGKSTLLRTIAGLDQPDTGTITINGRDVTRVPPQRRGIGFVFQHYAAFKHLTVRDNVAFGLKIRKRPKAEIKAKVDNLLQVVGLSGFQSRYPNQLSGGQRQRMALARALAVDPEVLLLDEPFGALDAKVREELRAWLRRLHDEVHVTTVLVTHDQAEALDVADRIAVLHKGRIEQVGSPTDVYDAPANAFVMSFLGAVSTLNGSLVRPHDIRVGRTPNMAVAAADGTAGSTGVLRAVVDRVVVLGFEVRVELTSAATGGAFTAQITRGDAEALALREGDTVYVRATRVPPIAGGVSGVDDAGVERVKVTST