Rv1534 Family assigned · medium auto-curated
H37Rv Rv1534 · MTBC0 mtbc0_001641 ·
225 aa · 1744543–1745220 (+) ·
RefSeq NP_216050.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | TetR family transcriptional regulator |
| Revised (this work) | TetR family transcriptional regulator. 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 |
O08377
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulator |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Bacterial regulatory proteins, 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 | 0.179 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 | 1.7e-19 | 24–70 | Bacterial regulatory proteins, tetR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1533 (monooxygenase), high confidence from genomic context alone (score 981 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1533 |
monooxygenase | 980 | 981 ctx | neighborhood:882 coexpression:843 |
Rv1532c hyp |
hypothetical protein | 825 | 826 ctx | neighborhood:787 |
Rv0302 |
transcriptional regulator | 565 | 565 ctx | cooccurence:559 |
Rv0238 |
transcriptional regulator | 551 | 552 ctx | cooccurence:545 |
Rv1014c pth |
peptidyl-tRNA hydrolase | 464 | 402 | |
Rv3239c |
transmembrane transport protein | 418 | 391 | |
Rv3728 |
membrane protein | 416 | 388 | |
Rv1395 |
HTH-type transcriptional regulator | 598 | 188 | textmining:526 |
Rv1536 ileS |
isoleucine--tRNA ligase | 458 | 70 | textmining:442 |
Rv3252c alkB |
transmembrane alkane 1-monooxygenase AlkB | 531 | 62 | textmining:521 |
Rv3312c hyp |
hypothetical protein | 785 | 60 | textmining:781 |
Rv1393c |
monoxygenase | 446 | 52 | textmining:440 |
Rv3460c rpsM |
30S ribosomal protein S13 | 520 | 47 | textmining:517 |
Rv1535 hyp |
hypothetical protein | 512 | 46 | textmining:510 |
Rv0071 |
maturase | 512 | 44 | textmining:511 |
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 family transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=2e-19)
- (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_216050.1)
- 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 O08377 (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
Rv1533 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001641|Rv1534| MSRASARRRRAVSDEDKSQRRDEILAAAKIVFAHKGFHATTVADIAKQAGLAYGLIYWYFDSKDDLFHALMAGEEEALRAHVAAELARVGGSTEAPLRALLQAAVQATFEFFETDKATVKLLFRDAYALGGRFEEHLGGIYERFIDDIEAVVVAAQRRGEVVEAPSRMAAYTLAALVGQLAHRRLNTDDNVTAAQVADFVVSLVLDGLRPRALAVGARGGRAART