Rv3525c Family assigned · low auto-curated
H37Rv Rv3525c · MTBC0 mtbc0_003741 ·
174 aa · 3985477–3986001 (-) ·
RefSeq NP_218042.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | siderophore-binding protein |
|---|---|
| MTBC0 PGAP re-annotation | gamma carbonic anhydrase family protein |
| Revised (this work) | Gamma carbonic anhydrase family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YCB9
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible siderophore-binding protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | gca |
| eggNOG description | Bacterial transferase hexapeptide (six repeats) |
| Orthologous group | COG0663 |
| Gene Ontology (17) |
GO:0003674, GO:0003824, GO:0004089, GO:0005488, GO:0008270, GO:0016829, GO:0016835, GO:0016836, GO:0043167, GO:0043168, GO:0043169, GO:0043199 +5 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 | 0.558 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: kshA (3-ketosteroid-9-alpha-monooxygenase oxygenase subunit), high confidence from genomic context alone (score 779 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3527 hyp |
hypothetical protein | 780 | 779 ctx | neighborhood:778 |
Rv3526 kshA |
3-ketosteroid-9-alpha-monooxygenase oxygenase subunit | 780 | 779 ctx | neighborhood:778 |
Rv3273 |
transmembrane carbonic anhydrase | 687 | 586 | experimental:570 |
Rv3588c canB |
carbonic anhydrase | 853 | 573 | experimental:570 textmining:670 |
Rv1284 canA |
beta-carbonic anhydrase | 629 | 573 | experimental:570 |
Rv1302 rfe |
decaprenyl-phosphate N-acetylglucosaminephosphotransferase | 495 | 477 | |
Rv1381 pyrC |
dihydroorotase | 492 | 473 | coexpression:430 |
Rv0106 hyp |
hypothetical protein | 488 | 459 | coexpression:415 |
Rv3667 acs |
acetyl-CoAsynthetase | 446 | 412 | |
Rv2156c murX |
phospho-N-acetylmuramoyl-pentappeptidetransferase | 426 | 405 | |
Rv2535c pepQ |
cytoplasmic peptidase PepQ | 483 | 109 | textmining:444 |
Rv0677c mmpS5 |
membrane protein MmpS5 | 512 | 44 | textmining:511 |
Rv0676c mmpL5 |
transmembrane transport protein MmpL5 | 443 | 44 | textmining:441 |
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: siderophore-binding protein
- MTBC0 PGAP product: gamma carbonic anhydrase family protein
- (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_218042.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG0663 - Curated reference: UniProt I6YCB9 (TrEMBL, unreviewed; 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 —
13 functional partner(s); context anchor
kshA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003741|Rv3525c| MPLFSFEGRSPRIDPTAFVAPTATLIGDVTIEAGASVWFNAVLRGDYAPVVVREGANVQDGAVLHAPPGIPVDIGPGATVAHLCVIHGVHVGSEALIANHATVLDGAVIGARCMIAAGALVVAGTQIPAGMLVTGAPAKVKGPIEGTGAEMWVNVNPQAYRDLAARHLAGLEPM