Rv1129c Family assigned · medium auto-curated
H37Rv Rv1129c · MTBC0 mtbc0_001212 ·
486 aa · 1261514–1262974 (-) ·
RefSeq NP_215645.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | short-chain fatty acyl-CoA regulator family protein |
| Revised (this work) | Short-chain fatty acyl-CoA regulator family protein. Pfam: HTH_31 (PF13560.13), HTH_3 (PF01381.29), Peptidase_M78 (PF06114.20), ScfRs (PF09856.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06581
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator PrpR |
| Curated function | Plays a key role in regulating expression of enzymes involved in the catabolism of short chain fatty acids (SCFA) via both the glyoxylate (acetyl degradation route) and the methylcitrate cycle (propionate degradation route). Required for intracellular growth in macrophages and for the assimilation of cholesterol-derived propionate. PrpR acts as a transcriptional activator of prpDC and icl genes when propionate is the main carbon source, and as a ramB repressor. During growth on propionate, PrpR also acts as a transcriptional repressor of dnaA, which encodes the DnaA initiator protein responsib. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | IrrE N-terminal-like domain |
| Orthologous group | COG1396 |
| KEGG orthology |
K07110, K21686
|
| Gene Ontology (56) |
GO:0001666, GO:0006082, GO:0006355, GO:0006629, GO:0006631, GO:0006950, GO:0008150, GO:0008152, GO:0009605, GO:0009607, GO:0009628, GO:0009889 +44 more
|
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 | 0.847 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 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 |
|---|---|---|---|---|
HTH_31 | PF13560.13 | 1.1e-10 | 19–72 | Helix-turn-helix domain |
HTH_3 | PF01381.29 | 1.3e-12 | 22–76 | Helix-turn-helix |
Peptidase_M78 | PF06114.20 | 7.9e-26 | 200–322 | IrrE N-terminal-like domain |
ScfRs | PF09856.15 | 7.4e-66 | 323–479 | Short-chain fatty acyl coenzyme A regulator, C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: prpD (2-methylcitrate dehydratase), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1130 prpD |
2-methylcitrate dehydratase | 991 | 884 ctx | neighborhood:621 cooccurence:519 coexpression:415 textmining:928 |
Rv1131 prpC |
methylcitrate synthase PrpC | 961 | 804 ctx | neighborhood:597 coexpression:533 textmining:810 |
Rv1132 hyp |
hypothetical protein | 606 | 606 ctx | neighborhood:553 |
Rv1128c hyp |
hypothetical protein | 549 | 546 ctx | neighborhood:534 |
Rv0332 hyp |
hypothetical protein | 506 | 479 | experimental:434 |
Rv0366c hyp |
hypothetical protein | 473 | 445 | experimental:434 |
Rv0467 icl1 |
isocitrate lyase | 755 | 394 | textmining:613 |
Rv1493 mutB |
methylmalonyl-CoA mutase large subunit | 413 | 242 | |
Rv3833 |
AraC family transcriptional regulator | 455 | 210 |
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: short-chain fatty acyl-CoA regulator family protein
- Pfam (hmmscan --cut_ga): HTH_31 PF13560.13 (E=1e-10), HTH_3 PF01381.29 (E=1e-12), Peptidase_M78 PF06114.20 (E=8e-26), ScfRs PF09856.15 (E=7e-66)
- (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_215645.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_31 (PF13560.13), HTH_3 (PF01381.29), Peptidase_M78 (PF06114.20), ScfRs (PF09856.15)
- 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
COG1396 - Curated reference: UniProt O06581 (SwissProt, reviewed; 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 —
9 functional partner(s); context anchor
prpD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001212|Rv1129c| MTRSNVLPVARTYSRTFSGARLRRLRQERGLTQVALAKALDLSTSYVNQLENDQRPITVPVLLLLTERFDLSAQYFSSDSDARLVADLSDVFTDIGVEHAVSGAQIEEFVARMPEVGHSLVAVHRRLRAATEELEGYRSRATAETELPPARPMPFEEVRDFFYDRNNYIHDLDMAAERMFTESGMRTGGLDIQLAELMRDRFGISVVIDDNLPDTAKRRYHPDTKVLRVAHWLMPGQRAFQIATQLALVGQSDLISSIVATDDQLSTEARGVARIGLANYFAGAFLLPYREFHRAAEQLRYDIDLLGRRFGVGFETVCHRLSTLQRPRQRGIPFIFVRTDKAGNISKRQSATAFHFSRVGGSCPLWVVHDAFAQPERIVRQVAQMPDGRSYFWVAKTTAADGLGYLGPHKNFAVGLGCDLAHAHKLVYSTGVVLDDPSTEVPIGAGCKICNRTSCAQRAFPYLGGRVAVDENAGSSLPYSSTEQSV