Rv1904 Resolved · high auto-curated
H37Rv Rv1904 · MTBC0 mtbc0_002019 ·
143 aa · 2169064–2169495 (+) ·
RefSeq NP_216420.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | anti-sigma factor antagonist |
| Revised (this work) | Anti-sigma factor antagonist. Pfam: STAS (PF01740.27), STAS_2 (PF13466.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07728
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Anti-sigma factor antagonist |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| eggNOG description | STAS domain |
| Orthologous group | COG1366 |
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 | 1.451 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
STAS | PF01740.27 | 8.6e-22 | 31–135 | STAS domain |
STAS_2 | PF13466.13 | 2.3e-07 | 34–126 | Mlab, STAS domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0497 (transmembrane protein), medium confidence from genomic context alone (score 677 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1364c |
sigma factor regulatory protein | 996 | 996 | coexpression:928 experimental:912 |
Rv3287c rsbW |
anti-sigma factor RsbW | 913 | 877 | coexpression:509 experimental:658 |
Rv1752 hyp |
hypothetical protein | 750 | 750 ctx | cooccurence:748 |
Rv1354c hyp |
hypothetical protein | 758 | 743 | coexpression:649 |
Rv2079 hyp |
hypothetical protein | 739 | 740 ctx | cooccurence:736 |
Rv2423 hyp |
hypothetical protein | 708 | 709 ctx | cooccurence:708 |
Rv3899c hyp |
hypothetical protein | 688 | 688 ctx | cooccurence:627 |
Rv0497 |
transmembrane protein | 677 | 677 ctx | cooccurence:675 |
Rv0048c |
membrane protein | 670 | 670 ctx | cooccurence:667 |
Rv1173 fbiC |
FO synthase | 658 | 659 | coexpression:648 |
Rv0655 mkl |
ABC transporter ATP-binding protein | 651 | 652 | experimental:629 |
Rv0172 mce1D |
Mce family protein Mce1D | 645 | 645 ctx | cooccurence:431 |
Rv1906c hyp |
hypothetical protein | 869 | 639 ctx | cooccurence:482 textmining:652 |
Rv0169 mce1A |
Mce family protein Mce1A | 621 | 622 | |
Rv1796 mycP5 |
membrane-anchored mycosin MycP | 615 | 615 ctx | cooccurence:543 |
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: hypothetical protein
- MTBC0 PGAP product: anti-sigma factor antagonist
- Pfam (hmmscan --cut_ga): STAS PF01740.27 (E=9e-22), STAS_2 PF13466.13 (E=2e-07)
- (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_216420.1)
- Domains: Pfam-A via hmmscan --cut_ga — STAS (PF01740.27), STAS_2 (PF13466.13)
- 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
COG1366 - Curated reference: UniProt O07728 (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 —
104 functional partner(s); context anchor
Rv0497 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002019|Rv1904| MRTVAIGPGAGPSSTRPSSQPSDLHSGLRAVTECTGSAVVVHVGGDIDASNEVAWQRLVSKSAAIAIAPGPFVIDIRDLDFMGSCAYAVLAQESVRCRRRGVNMRLVSNQPIVARTIAACGLRRLIPLYATVETALAPPPSAH