Rv2506 Family assigned · medium auto-curated
H37Rv Rv2506 · MTBC0 mtbc0_002668 ·
215 aa · 2844602–2845249 (+) ·
RefSeq NP_217022.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | TetR family 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_24 (PF17932.7). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06169
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Transcriptional regulator |
| 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 | 0.189 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 | 3.5e-18 | 30–76 | Bacterial regulatory proteins, tetR family |
TetR_C_24 | PF17932.7 | 7.8e-08 | 100–180 | Tetracyclin repressor-like, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2499c (oxidase regulatory-like protein), high confidence from genomic context alone (score 829 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2499c |
oxidase regulatory-like protein | 870 | 829 ctx | neighborhood:714 cooccurence:413 |
Rv0339c iniR |
transcriptional regulator | 802 | 802 | coexpression:802 |
Rv3055 |
TetR family transcriptional regulator | 788 | 788 | coexpression:788 |
Rv2501c accA1 |
acetyl/propionyl-CoA carboxylase subuit alpha | 871 | 781 ctx | neighborhood:714 textmining:436 |
Rv2498c citE |
citrate (pro-3S)-lyase subunit beta | 918 | 776 ctx | neighborhood:714 textmining:651 |
Rv2502c accD1 |
acetyl-/propionyl-CoA carboxylase subunit beta | 884 | 761 ctx | neighborhood:714 textmining:536 |
Rv0067c |
transcriptional regulator | 761 | 761 | coexpression:761 |
Rv2500c fadE19 |
acyl-CoA dehydrogenase FadE19 | 795 | 753 ctx | neighborhood:714 |
Rv3060c |
GntR family transcriptional regulator | 744 | 737 | coexpression:736 |
Rv3840 |
transcriptional regulator | 734 | 734 | coexpression:734 |
Rv3855 ethR |
HTH-type transcriptional repressor EthR | 801 | 732 | coexpression:732 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 739 | 732 | coexpression:732 |
Rv0273c |
transcriptional regulator | 730 | 730 | coexpression:730 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 730 | 730 | coexpression:730 |
Rv3183 higA3 |
transcriptional regulator | 729 | 729 | coexpression:729 |
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: TetR family transcriptional regulator
- MTBC0 PGAP product: TetR/AcrR family transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=3e-18), TetR_C_24 PF17932.7 (E=8e-08)
- (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_217022.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_24 (PF17932.7)
- 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 O06169 (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 —
47 functional partner(s); context anchor
Rv2499c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002668|Rv2506| MTASAPDGRPGQPEATNRRSQLKSDRRFQLLAAAERLFAERGFLAVRLEDIGAAAGVSGPAIYRHFPNKESLLVELLVGVSARLLAGARDVTTRSANLAAALDGLIEFHLDFALGEADLIRIQDRDLAHLPAVAERQVRKAQRQYVEVWVGVLRELNPGLAEADARLMAHAVFGLLNSTPHSMKAADSKPARTVRARAVLRAMTVAALSAADRCL