Rv0078 Family assigned · medium auto-curated
H37Rv Rv0078 · MTBC0 mtbc0_000086 ·
201 aa · 86691–87296 (+) ·
RefSeq NP_214592.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 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_41 (PF21351.3). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53623
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 | 0.236 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 | 6.5e-15 | 19–64 | Bacterial regulatory proteins, tetR family |
TetR_C_41 | PF21351.3 | 4.8e-33 | 91–198 | Tetracyclin repressor-like, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0077c (oxidoreductase), high confidence from genomic context alone (score 905 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0077c |
oxidoreductase | 987 | 905 ctx | neighborhood:749 cooccurence:632 textmining:870 |
Rv1963c mce3R |
transcriptional repressor Mce3R | 769 | 769 | coexpression:732 |
Rv3830c |
TetR family transcriptional regulator | 555 | 542 ctx | cooccurence:418 |
Rv0076c |
membrane protein | 924 | 445 ctx | neighborhood:437 textmining:870 |
Rv0144 |
transcriptional regulator | 439 | 440 ctx | cooccurence:436 |
Rv2912c |
TetR family HTH-type transcriptional regulator | 424 | 424 | |
Rv1353c |
HTH-type transcriptional regulator | 413 | 408 ctx | cooccurence:402 |
Rv1014c pth |
peptidyl-tRNA hydrolase | 403 | 403 | coexpression:401 |
Rv1267c embR |
transcriptional regulator EmbR | 409 | 396 | |
Rv1049 |
transcriptional repressor | 408 | 98 | |
Rv3177 |
peroxidase | 448 | 77 | textmining:427 |
Rv1557 mmpL6 |
transmembrane transport protein MmpL6 | 810 | 66 | textmining:805 |
Rv2215 dlaT |
pyruvate dehydrogenase E2 component dihydrolipoamide acyltransferase | 525 | 55 | textmining:519 |
Rv1254 |
acyltransferase | 521 | 54 | textmining:515 |
Rv3854c ethA |
monooxygenase EthA | 519 | 41 | textmining:519 |
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: transcriptional regulator
- MTBC0 PGAP product: TetR/AcrR family transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=6e-15), TetR_C_41 PF21351.3 (E=5e-33)
- (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_214592.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_41 (PF21351.3)
- 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 O53623 (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 —
15 functional partner(s); context anchor
Rv0077c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000086|Rv0078| MEIKRRTQEERSAATREALITGARKLWGLRGYAEVGTPEIATEAGVTRGAMYHQFADKAALFRDVVEVVEQDVMARMATLVAASGAATPADAIRAAVDAWLEVSGDPEVRQLILLDAPVVLGWAGFRDVAQRYSLGMTEQLITEAIRAGQLARQPVRPLAQVLIGALDEAAMFIATADDPKRARRETRQVLRRLIDGMLNG