Rv1353c Family assigned · medium auto-curated
H37Rv Rv1353c · MTBC0 mtbc0_001453 ·
261 aa · 1529902–1530687 (-) ·
RefSeq NP_215869.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | TetR/AcrR family transcriptional regulator C-terminal domain-containing protein |
| Revised (this work) | TetR/AcrR family transcriptional regulator C-terminal domain-containing protein. Pfam: TetR_N (PF00440.30), TetR_C_1 (PF02909.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMD3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional repressor Rv1353c |
| Curated function | Negatively regulates the expression of the efflux pump Rv0191 upon chloramphenicol exposure. Acts by binding to the Rv0191 promoter region. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Transcriptional regulator |
| Orthologous group | COG1309 |
| Gene Ontology (41) |
GO:0000976, GO:0001067, GO:0003674, GO:0003676, GO:0003677, GO:0003690, GO:0003700, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737 +29 more
|
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 | 0.337 · 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 |
|---|---|---|---|---|
TetR_N | PF00440.30 | 2.0e-11 | 21–67 | Bacterial regulatory proteins, tetR family |
TetR_C_1 | PF02909.23 | 2.5e-13 | 80–222 | Tetracyclin repressor-like, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: moeY (molybdopterin biosynthesis protein MoeY), high confidence from genomic context alone (score 953 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1354c hyp |
hypothetical protein | 981 | 970 ctx | neighborhood:793 coexpression:805 textmining:426 |
Rv1355c moeY |
molybdopterin biosynthesis protein MoeY | 982 | 953 ctx | neighborhood:723 coexpression:839 textmining:649 |
Rv1356c hyp |
hypothetical protein | 972 | 929 ctx | neighborhood:732 coexpression:746 textmining:628 |
Rv1358 |
transcriptional regulator | 785 | 775 | coexpression:774 |
Rv0895 |
diacyglycerol O-acyltransferase | 740 | 741 | coexpression:740 |
Rv0875c hyp |
hypothetical protein | 730 | 731 ctx | cooccurence:729 |
Rv0048c |
membrane protein | 680 | 680 ctx | cooccurence:680 |
Rv3779 |
transmembrane protein | 652 | 652 ctx | cooccurence:652 |
Rv1359 |
transcriptional regulator | 596 | 596 ctx | cooccurence:494 |
Rv1171 hyp |
hypothetical protein | 594 | 594 ctx | cooccurence:585 |
Rv2912c |
TetR family HTH-type transcriptional regulator | 585 | 586 ctx | cooccurence:567 |
Rv2079 hyp |
hypothetical protein | 564 | 565 ctx | cooccurence:541 |
Rv3202c adnA |
ATP-dependent DNA helicase | 554 | 554 ctx | cooccurence:551 |
Rv3829c |
dehydrogenase | 545 | 545 ctx | cooccurence:543 |
Rv2248 hyp |
hypothetical protein | 539 | 539 ctx | cooccurence:538 |
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: HTH-type transcriptional regulator
- MTBC0 PGAP product: TetR/AcrR family transcriptional regulator C-terminal domain-containing protein
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=2e-11), TetR_C_1 PF02909.23 (E=2e-13)
- (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_215869.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_1 (PF02909.23)
- 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 P9WMD3 (SwissProt, reviewed; 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 —
46 functional partner(s); context anchor
moeY - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001453|Rv1353c| MQTTPGKRQRRQRGSINPEDIISGAFELAQQVSIDNLSMPLLGKHLGVGVTSIYWYFRKKDDLLNAMTDRALSKYVFATPYIEAGDWRETLRNHARSMRKTFADNPVLCDLILIRAALSPKTARLGAQEMEKAIANLVTAGLSLEDAFDIYSAVSVHVRGSVVLDRLSRKSQSAGSGPSAIEHPVAIDPATTPLLAHATGRGHRIGAPDETNFEYGLECILDHAGRLIEQSSKAAGEVAVRRPTATADAPTPGARAKAVAR