Rv0144 Family assigned · medium auto-curated
H37Rv Rv0144 · MTBC0 - ·
280 aa · 170284–171126 (+) ·
RefSeq NP_214658.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transcriptional regulator. Pfam: TetR_N (PF00440.30), TetR_C_13 (PF16925.11). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P96821
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable 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) pseudogene candidate
| pN/pS | 1.236 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 missense, 1 nonsense, 2 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 6.38% of strains (9267) · clonal |
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 | 1.3e-15 | 93–139 | Bacterial regulatory proteins, tetR family |
TetR_C_13 | PF16925.11 | 3.2e-06 | 185–263 | Tetracyclin repressor-like, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0146 (S-adenosylmethionine-dependent methyltransferase), high confidence from genomic context alone (score 743 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0146 |
S-adenosylmethionine-dependent methyltransferase | 743 | 743 ctx | neighborhood:739 |
Rv0145 |
S-adenosylmethionine-dependent methyltransferase | 725 | 726 ctx | neighborhood:717 |
Rv0143c |
transmembrane protein | 560 | 559 ctx | neighborhood:555 |
Rv1123c bpoB |
peroxidase BpoB | 447 | 447 ctx | cooccurence:436 |
Rv0147 |
aldehyde dehydrogenase | 457 | 444 ctx | neighborhood:441 |
Rv0148 |
short-chain type dehydrogenase/reductase | 441 | 442 | |
Rv0078 |
transcriptional regulator | 439 | 440 ctx | cooccurence:436 |
Rv1014c pth |
peptidyl-tRNA hydrolase | 400 | 401 | |
Rv0334 rmlA |
glucose-1-phosphate thymidylyltransferase | 521 | 53 | textmining:515 |
Rv0373c |
carbon monoxyde dehydrogenase large subunit | 805 | 51 | textmining:803 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=1e-15), TetR_C_13 PF16925.11 (E=3e-06)
- (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_214658.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_13 (PF16925.11)
- 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 P96821 (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 —
10 functional partner(s); context anchor
Rv0146 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0144| MPHSWTPTSVMTPPLVVAAFRPVGHYRLATDRAGGPCSPPATGAKLTSSVASRPTVGTKPQWWHTLVMSMSLTAGRGPGRPPAAKADETRKRILHAARQVFSERGYDGATFQEIAVRADLTRPAINHYFANKRVLYQEVVEQTHELVIVAGIERARREPTLMGRLAVVVDFAMEADAQYPASTAFLATTVLESQRHPELSRTENDAVRATREFLVWAVNDAIERGELAADVDVSSLAETLLVVLCGVGFYIGFVGSYQRMATITDSFQQLLAGTLWRPPT