Rv1929c Family assigned · low auto-curated
H37Rv Rv1929c · MTBC0 mtbc0_002043 ·
214 aa · 2200378–2201022 (-) ·
RefSeq NP_216445.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | TIGR03085 family metal-binding protein |
| Revised (this work) | TIGR03085 family metal-binding 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 |
P95285
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | TIGR03085 family protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | molybdopterin cofactor binding |
| Orthologous group | COG0243 |
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 | 1.071 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.67% of strains (967) · clonal |
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: gltB (glutamate synthase large subunit), high confidence from genomic context alone (score 763 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) |
|---|---|---|---|---|
Rv0685 tuf |
elongation factor Tu | 784 | 770 | experimental:761 |
Rv1930c hyp |
hypothetical protein | 770 | 770 ctx | neighborhood:770 |
Rv3859c gltB |
glutamate synthase large subunit | 871 | 763 ctx | neighborhood:535 experimental:420 textmining:481 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 781 | 761 | experimental:690 |
Rv1931c |
transcriptional regulator | 757 | 757 ctx | neighborhood:755 |
Rv1928c |
short-chain type dehydrogenase/reductase | 658 | 656 ctx | neighborhood:645 |
Rv1932 tpx |
2-Cys peroxiredoxin | 513 | 513 ctx | neighborhood:511 |
Rv2239c hyp |
hypothetical protein | 505 | 505 ctx | cooccurence:502 |
Rv2375 hyp |
hypothetical protein | 499 | 499 ctx | cooccurence:499 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 539 | 496 | experimental:465 |
Rv2181 |
alpha-(1-2)-phosphatidylinositol mannoside mannosyltransferase | 475 | 476 ctx | cooccurence:473 |
Rv3015c hyp |
hypothetical protein | 447 | 448 ctx | cooccurence:443 |
Rv2694c hyp |
hypothetical protein | 471 | 446 ctx | cooccurence:440 |
Rv1162 narH |
nitrate reductase subunit beta | 489 | 441 | experimental:420 |
Rv1913 hyp |
hypothetical protein | 417 | 416 ctx | cooccurence:412 |
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: TIGR03085 family metal-binding 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_216445.1)
- 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
COG0243 - Curated reference: UniProt P95285 (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 —
23 functional partner(s); context anchor
gltB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002043|Rv1929c| MADVPLDAQERLELCDLLEELGPAVATLIEGWTAHDLAAHIVLRERDLVAGLCIVLPGPFQRFAERRRARLAQSKDFTWLVARIRSGPPMGFFRIGWVRTLANLNEFFVHHEDVRRASGRGPRSLTPEMDAALWRNVRRGSHFLSRRLHGCGLEIEWVGTGKRVRVRSGEPTARLTGPPGELLLYVFGRRAVARVEVSGPLEAIAAVHRTHFGM