Rv2242 Family assigned · medium auto-curated
H37Rv Rv2242 · MTBC0 mtbc0_002384 ·
414 aa · 2541462–2542706 (+) ·
RefSeq NP_216758.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | PucR family transcriptional regulator |
| Revised (this work) | PucR family transcriptional regulator. Pfam: GGDEF_2 (PF17853.7), HTH_30 (PF13556.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPH5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2242 |
UniProt still lists this protein as Uncharacterized protein Rv2242; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K TranscriptionT Signal transduction mechanisms
|
|---|---|
| eggNOG description | Regulator of polyketide synthase expression |
| Orthologous group | COG3835 |
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.362 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 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 |
|---|---|---|---|---|
GGDEF_2 | PF17853.7 | 1.2e-16 | 180–295 | GGDEF-like domain |
HTH_30 | PF13556.13 | 1.1e-21 | 347–403 | PucR C-terminal helix-turn-helix domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fabD (malonyl CoA-acyl carrier protein transacylase), high confidence from genomic context alone (score 879 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2243 fabD |
malonyl CoA-acyl carrier protein transacylase | 915 | 879 ctx | neighborhood:727 cooccurence:574 |
Rv2241 aceE |
pyruvate dehydrogenase E1 component | 806 | 806 ctx | neighborhood:801 |
Rv2246 kasB |
3-oxoacyl-ACP synthase 2 | 698 | 676 ctx | neighborhood:613 |
Rv2247 accD6 |
acetyl-/propionyl-CoA carboxylase subunit beta | 707 | 647 ctx | neighborhood:645 |
Rv0635 hadA |
(3R)-hydroxyacyl-ACP dehydratase subunit HadA | 608 | 608 ctx | cooccurence:605 |
Rv0504c hyp |
hypothetical protein | 608 | 608 ctx | cooccurence:605 |
Rv0637 hadC |
(3R)-hydroxyacyl-ACP dehydratase subunit HadC | 600 | 600 ctx | cooccurence:599 |
Rv0636 hadB |
(3R)-hydroxyacyl-ACP dehydratase subunit HadB | 557 | 557 ctx | cooccurence:555 |
Rv2244 acpM |
meromycolate extension acyl carrier protein | 672 | 548 ctx | neighborhood:458 |
Rv2413c hyp |
hypothetical protein | 543 | 543 ctx | cooccurence:542 |
Rv2219A |
membrane protein | 528 | 528 ctx | cooccurence:526 |
Rv2245 kasA |
3-oxoacyl-ACP synthase 1 | 610 | 501 ctx | neighborhood:412 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 487 | 487 ctx | cooccurence:484 |
Rv0430 hyp |
hypothetical protein | 477 | 478 ctx | cooccurence:476 |
Rv2229c hyp |
hypothetical protein | 472 | 473 ctx | cooccurence:464 |
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: hypothetical protein
- MTBC0 PGAP product: PucR family transcriptional regulator
- Pfam (hmmscan --cut_ga): GGDEF_2 PF17853.7 (E=1e-16), HTH_30 PF13556.13 (E=1e-21)
- (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_216758.1)
- Domains: Pfam-A via hmmscan --cut_ga — GGDEF_2 (PF17853.7), HTH_30 (PF13556.13)
- 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
COG3835 - Curated reference: UniProt P9WPH5 (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 —
35 functional partner(s); context anchor
fabD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002384|Rv2242| MNDNQLAPVARPRSPLELLDTVPDSLLRRLKQYSGRLATEAVSAMQERLPFFADLEASQRASVALVVQTAVVNFVEWMHDPHSDVGYTAQAFELVPQDLTRRIALRQTVDMVRVTMEFFEEVVPLLARSEEQLTALTVGILKYSRDLAFTAATAYADAAEARGTWDSRMEASVVDAVVRGDTGPELLSRAAALNWDTTAPATVLVGTPAPGPNGSNSDGDSERASQDVRDTAARHGRAALTDVHGTWLVAIVSGQLSPTEKFLKDLLAAFADAPVVIGPTAPMLTAAHRSASEAISGMNAVAGWRGAPRPVLARELLPERALMGDASAIVALHTDVMRPLADAGPTLIETLDAYLDCGGAIEACARKLFVHPNTVRYRLKRITDFTGRDPTQPRDAYVLRVAATVGQLNYPTPH