Rv0485 Family assigned · medium auto-curated
H37Rv Rv0485 · MTBC0 mtbc0_000510 ·
438 aa · 577349–578665 (+) ·
RefSeq NP_214999.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | transcriptional regulator |
| Revised (this work) | Transcriptional regulator. Pfam: ROK (PF00480.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKV1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcriptional regulator Rv0485 |
| Curated function | Positively regulates the expression of PE13 and PPE18. Can also regulate expression of some other genes. Plays a role in modulation of innate immune responses. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolismK Transcription
|
|---|---|
| eggNOG description | ROK family |
| Orthologous group | COG1940 |
| Gene Ontology (9) |
GO:0008150, GO:0009405, GO:0010468, GO:0019222, GO:0044419, GO:0050789, GO:0051704, GO:0060255, GO:0065007
|
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 | 0.264 · 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 |
|---|---|---|---|---|
ROK | PF00480.27 | 5.7e-18 | 110–377 | ROK family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0484c (short-chain type oxidoreductase), high confidence from genomic context alone (score 775 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0484c |
short-chain type oxidoreductase | 775 | 775 ctx | neighborhood:763 |
Rv0486 mshA |
D-inositol 3-phosphate glycosyltransferase | 728 | 718 ctx | neighborhood:718 |
Rv0487 hyp |
hypothetical protein | 700 | 699 ctx | neighborhood:695 |
Rv0489 gpm1 |
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | 672 | 647 ctx | neighborhood:639 |
Rv0490 senX3 |
two component sensor histidine kinase SenX3 | 637 | 620 ctx | neighborhood:614 |
Rv0491 regX3 |
two component sensory transduction protein RegX | 607 | 591 ctx | neighborhood:579 |
Rv1065 hyp |
hypothetical protein | 521 | 521 | |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 453 | 453 ctx | cooccurence:453 |
Rv0383c ttfA hyp |
hypothetical protein | 470 | 438 ctx | cooccurence:420 |
Rv1275 lprC |
lipoprotein LprC | 434 | 435 ctx | cooccurence:429 |
Rv0817c lmeA hyp |
hypothetical protein | 420 | 420 ctx | cooccurence:420 |
Rv1274 lprB |
lipoprotein LprB | 417 | 418 ctx | cooccurence:413 |
Rv2753c dapA |
4-hydroxy-tetrahydrodipicolinate synthase | 455 | 396 | |
Rv0815c cysA2 |
thiosulfate sulfurtransferase CysA | 486 | 342 | |
Rv2391 sirA |
sulfite reductase | 482 | 155 | textmining:413 |
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: transcriptional regulator
- Pfam (hmmscan --cut_ga): ROK PF00480.27 (E=6e-18)
- (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_214999.1)
- Domains: Pfam-A via hmmscan --cut_ga — ROK (PF00480.27)
- 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
COG1940 - Curated reference: UniProt P9WKV1 (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 —
18 functional partner(s); context anchor
Rv0484c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000510|Rv0485| MYSTNRTSQSLSRKPGRKHQLRSHRYVMPPSLHLSDSAAASVFRAVRLRGPVGRDVIAGSTSLSIATVNRQVIALLEAGLLRERADLAVSGAIGRPRVPVEVNHEPFVTLGIHIGARTTSIVATDLFGRTLDTVETPTPRNAAGAALTSLADSADRYLQRWRRRRALWVGVTLGGAVDSATGHVDHPRLGWRQAPVGPVLADALGLPVSVASHVDAMAGAELMLGMRRFAPSSSTSLYVYARETVGYALMIGGRVHCPASGPGTIAPLPVHSEMLGGTGQLESTVSDEAVLAAARRLRIIPGIASRTRTGGSATAITDLLRVARAGNQQAKELLAERARVLGGAVALLRDLLNPDEVVVGGQAFTEYPEAMEQVEAAFTAGSVLAPRDIRVTVFGNRVQEAGAGIVSLSGLYADPLGALRRSGALDARLQDTAPEALA