Rv3055 Family assigned · medium auto-curated
H37Rv Rv3055 · MTBC0 mtbc0_003247 ·
204 aa · 3437377–3437991 (+) ·
RefSeq NP_217571.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | TetR family transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | helix-turn-helix domain-containing protein |
| Revised (this work) | Helix-turn-helix domain-containing protein. Pfam: TetR_N (PF00440.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95103
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible transcriptional regulatory 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 | 0.369 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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-14 | 32–74 | Bacterial regulatory proteins, tetR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: moaR1 (transcriptional regulator MoaR), high confidence from genomic context alone (score 883 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3124 moaR1 |
transcriptional regulator MoaR | 885 | 883 ctx | cooccurence:544 coexpression:754 |
Rv3056 dinP |
DNA polymerase IV 2 | 905 | 876 ctx | neighborhood:876 |
Rv1725c hyp |
hypothetical protein | 872 | 869 | coexpression:850 |
Rv0737 |
transcriptional regulator | 865 | 865 | coexpression:819 |
Rv1167c |
transcriptional regulator | 864 | 864 ctx | cooccurence:445 coexpression:765 |
Rv1267c embR |
transcriptional regulator EmbR | 860 | 857 | coexpression:804 |
Rv0117 oxyS |
oxidative stress response regulatory protein OxyS | 851 | 846 | coexpression:801 |
Rv3167c |
TetR family transcriptional regulator | 837 | 838 | coexpression:802 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 838 | 834 | coexpression:806 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 832 | 832 | coexpression:803 |
Rv3830c |
TetR family transcriptional regulator | 835 | 831 | coexpression:799 |
Rv3183 higA3 |
transcriptional regulator | 824 | 825 | coexpression:800 |
Rv3054c hyp |
hypothetical protein | 828 | 824 ctx | neighborhood:736 |
Rv1985c lysG |
HTH-type transcriptional regulator | 825 | 822 | coexpression:800 |
Rv3840 |
transcriptional regulator | 820 | 821 | coexpression:797 |
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: helix-turn-helix domain-containing protein
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=4e-14)
- (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_217571.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30)
- 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 P95103 (TrEMBL, unreviewed; Predicted)
- 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 —
64 functional partner(s); context anchor
moaR1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003247|Rv3055| MSGAERLGDLPVFARQEPVPERGDAARNRALLLEAARRLIARSGADAITMDDVAAAAGVGKGTLFRRFGSRAGLMMVLLDEDERASQQAFLFGPPPLGPDAPPLDRLIAFGRERMRFVHAHHQLLSEANRDPQTRHSAALSVLRTHLRVLLASAPTTGDLDAQTDALLALLDVDYVEHQLNAGGHTLQTLGDAWESLARKLCGR