Rv1685c Family assigned · medium auto-curated
H37Rv Rv1685c · MTBC0 mtbc0_001793 ·
207 aa · 1922791–1923414 (-) ·
RefSeq NP_216201.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | TetR family transcriptional regulator |
| Revised (this work) | TetR family transcriptional regulator. Pfam: TetR_N (PF00440.30), TetR_C_16 (PF17920.7). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33187
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH tetR-type domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | tetR family |
| Orthologous group | COG1309 |
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 | 0.118 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 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 |
|---|---|---|---|---|
TetR_N | PF00440.30 | 4.9e-16 | 24–70 | Bacterial regulatory proteins, tetR family |
TetR_C_16 | PF17920.7 | 6.7e-23 | 90–197 | Tetracyclin repressor-like, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1686c (ABC transporter permease), high confidence from genomic context alone (score 965 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) |
|---|---|---|---|---|
Rv1686c |
ABC transporter permease | 986 | 965 ctx | neighborhood:882 cooccurence:501 coexpression:449 textmining:638 |
Rv1687c |
ABC transporter ATP-binding protein | 979 | 811 ctx | neighborhood:651 textmining:897 |
Rv1688 mpg |
3-methyladenine DNA glycosylase | 724 | 724 ctx | neighborhood:722 |
Rv1689 tyrS |
tyrosine--tRNA ligase | 479 | 478 ctx | neighborhood:478 |
Rv1014c pth |
peptidyl-tRNA hydrolase | 402 | 403 | coexpression:400 |
Rv0685 tuf |
elongation factor Tu | 460 | 45 | textmining:458 |
Rv1545 hyp |
hypothetical protein | 803 | 44 | textmining:803 |
Rv1991c mazF6 |
mRNA interferase MazF6 | 538 | 44 | textmining:537 |
Rv0490 senX3 |
two component sensor histidine kinase SenX3 | 455 | 42 | textmining:455 |
Rv3907c pcnA |
poly(A) polymerase PcnA | 656 | 41 | textmining:656 |
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: TetR family transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=5e-16), TetR_C_16 PF17920.7 (E=7e-23)
- (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_216201.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_16 (PF17920.7)
- 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
COG1309 - Curated reference: UniProt O33187 (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 —
10 functional partner(s); context anchor
Rv1686c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001793|Rv1685c| MAAPDNSRRRPGRPAGSSDTRERILSSARELFAHNGIDRTSIRAVAAKAGVDAALVHHYFGTKQQLFAAAIHIPIDPMVIIGPIREAPVEELGYKLPSLLLPIWDSELGAGLIATLRSLISGSDVGLARSFLEEVVTVELGSRVDNPPGTGKIRTQFVASQLMGVVMARYIVRIEPFASLPAEQIVQTIAPNLQRYLTGELPDDLAP