Rv0340 Family assigned · medium auto-curated
H37Rv Rv0340 · MTBC0 mtbc0_000360 ·
179 aa · 411957–412496 (+) ·
RefSeq NP_214854.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | Rv0340 family IniB-related protein |
| Revised (this work) | Rv0340 family IniB-related protein. Pfam: IniB (PF27122.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33270
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2BXHV |
|---|
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 | 0.348 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
IniB | PF27122.1 | 2.0e-11 | 3–60 | Isoniazid-induced protein IniB |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: iniR (transcriptional regulator), high confidence from genomic context alone (score 766 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) |
|---|---|---|---|---|
Rv0339c iniR |
transcriptional regulator | 774 | 766 ctx | neighborhood:762 |
Rv0341 iniB |
isoniazid inducible protein IniB | 697 | 538 ctx | neighborhood:519 |
Rv0005 gyrB |
DNA gyrase subunit B | 546 | 499 | experimental:484 |
Rv0343 iniC |
iIsoniazid inductible protein IniC | 587 | 445 ctx | neighborhood:409 |
Rv0342 iniA |
isoniazid inductible protein IniA | 441 | 421 | |
Rv0899 arfA |
peptidoglycan-binding protein ArfA | 445 | 419 | |
Rv1288 hyp |
hypothetical protein | 448 | 415 | |
Rv1754c hyp |
hypothetical protein | 440 | 413 | |
Rv3668c |
protease | 440 | 405 | |
Rv2719c chiZ |
membrane protein | 438 | 403 | |
Rv0524 hemL |
glutamate-1-semialdehyde 2,1-aminomutase | 529 | 78 | textmining:511 |
Rv1592c hyp |
hypothetical protein | 527 | 68 | textmining:514 |
Rv0321 dcd |
deoxycytidine triphosphate deaminase | 448 | 65 | textmining:434 |
Rv2846c efpA |
MFS-type transporter EfpA | 704 | 56 | textmining:699 |
Rv3139 fadE24 |
acyl-CoA dehydrogenase | 577 | 52 | textmining:573 |
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: Rv0340 family IniB-related protein
- Pfam (hmmscan --cut_ga): IniB PF27122.1 (E=2e-11)
- (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_214854.1)
- Domains: Pfam-A via hmmscan --cut_ga — IniB (PF27122.1)
- 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
2BXHV - Curated reference: UniProt O33270 (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
iniR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000360|Rv0340| MANSLLDFVISLVRDPEAAARYAANPERSIAEAHLTDVTRADVNSLIPVVSDSLSMSEPIGAAGGAHAGDRGNVWASGAATAALDAFAPHADAGVVQQHGAVGSVLNQPTPPGPGVTPTDPRPFRAGPHETSALLTSAEIPDTTSEDGGLPTDHPAVWNHPVVDPHTVEPDHHGYDIHG