Rv3008 Family assigned · low auto-curated
H37Rv Rv3008 · MTBC0 mtbc0_003197 ·
207 aa · 3387953–3388576 (+) ·
RefSeq NP_217524.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | MgtC/SapB family protein |
| Revised (this work) | MgtC/SapB 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 |
I6YEY1
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | MgtC/SapB family protein |
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.225 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 2 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: Rv3007c (oxidoreductase), medium confidence from genomic context alone (score 532 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) |
|---|---|---|---|---|
Rv1624c |
membrane protein | 687 | 657 | coexpression:646 |
Rv3007c |
oxidoreductase | 532 | 532 ctx | neighborhood:514 |
Rv0425c ctpH |
metal cation transporting ATPase H | 554 | 527 | coexpression:421 |
Rv1997 ctpF |
cation transporter ATPase F | 546 | 519 | coexpression:411 |
Rv0908 ctpE |
metal cation transporter ATPase E | 546 | 518 | coexpression:410 |
Rv0107c ctpI |
cation-transporter ATPase I | 543 | 515 | coexpression:407 |
Rv3432c gadB |
glutamate decarboxylase GadB | 436 | 413 | coexpression:413 |
Rv1901 cinA |
competence damage-inducible protein CinA | 400 | 187 | |
Rv3596c clpC1 |
ATP-dependent protease ATP-binding subunit ClpC | 482 | 115 | textmining:440 |
Rv3601c panD |
aspartate 1-decarboxylase | 525 | 69 | textmining:511 |
Rv1630 rpsA |
30S ribosomal protein S1 | 471 | 69 | textmining:456 |
Rv1667c |
Rv1667c, (MTV047.03c), len: 217 aa. Probable second part of macrolide-transport ATP-binding protein ABC transporter (see citation below), wi | 872 | 61 | textmining:870 |
Rv0191 |
MFS-type transporter | 871 | 54 | textmining:870 |
Rv3756c proZ |
glycine betaine/carnitine/choline/L-proline ABC transporter permease ProZ | 809 | 44 | textmining:809 |
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: MgtC/SapB 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_217524.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt I6YEY1 (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 —
14 functional partner(s); context anchor
Rv3007c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003197|Rv3008| MLTVVAVIGILECGLVLHMPDNDLWYCGPWTLWVMAGRGVASGAGVWRGDRVATPLAVAITAAGLVSGARIGPGAAAKRDPQLAQWNEIRSHYQEIAEWIDHDTATAHPAVAATQISAAGSFGRANMVDYLGLLDSRADETVRRDEFSRWLSAKPDYLVTTEQSVDAATIALPEFRHAYDRAATIGTLNVYRRNSPDGDEPLPADGN