Rv1556 Family assigned · medium auto-curated
H37Rv Rv1556 · MTBC0 mtbc0_001663 ·
202 aa · 1770808–1771416 (+) ·
RefSeq NP_216072.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | TetR/AcrR family transcriptional regulator |
| Revised (this work) | TetR/AcrR family transcriptional regulator. Pfam: TetR_N (PF00440.30), TetR_C_11 (PF16859.11). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMD1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv1556 |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv1556; the revised annotation above is ahead of the current UniProt record.
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 | 1.9e-15 | 25–71 | Bacterial regulatory proteins, tetR family |
TetR_C_11 | PF16859.11 | 1.1e-24 | 82–192 | Tetracyclin repressor-like, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3167c |
TetR family transcriptional regulator | 861 | 862 | coexpression:810 |
Rv3830c |
TetR family transcriptional regulator | 863 | 859 | coexpression:802 |
Rv0452 |
transcriptional regulator | 854 | 854 | coexpression:788 |
Rv1151c cobB |
NAD-dependent protein deacylase | 846 | 841 | coexpression:841 |
Rv1167c |
transcriptional regulator | 841 | 841 | coexpression:785 |
Rv1931c |
transcriptional regulator | 833 | 834 | coexpression:803 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 828 | 829 | coexpression:797 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 831 | 826 | coexpression:803 |
Rv1267c embR |
transcriptional regulator EmbR | 829 | 826 | coexpression:826 |
Rv2282c |
LysR family HTH-type transcriptional regulator | 830 | 825 | coexpression:803 |
Rv0117 oxyS |
oxidative stress response regulatory protein OxyS | 822 | 816 | coexpression:793 |
Rv1725c hyp |
hypothetical protein | 817 | 813 | coexpression:813 |
Rv3736 |
AraC/XylS family transcriptional regulator | 809 | 806 | coexpression:806 |
Rv0212c nadR |
transcriptional regulator NadR | 813 | 805 | coexpression:805 |
Rv1027c kdpE |
transcriptional regulator KdpE | 805 | 804 | coexpression:804 |
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
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=2e-15), TetR_C_11 PF16859.11 (E=1e-24)
- (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_216072.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_11 (PF16859.11)
- 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 P9WMD1 (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 — 68 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001663|Rv1556| MVGAVTQIADRPTDPSPWSPRETELLAVTLRLLQEHGYDRLTVDAVAASARASKATVYRRWPSKAELVLAAFIEGIRQVAVPPNTGNLRDDLLRLGELICREVGQHASTIRAVLVEVSRNPALNDVLQHQFVDHRKALIQYILQQAVDRGEISSAAISDELWDLLPGYLIFRSIIPNRPPTQDTVQALVDDVILPSLTRSTG