Rv2047c Family assigned · medium auto-curated
H37Rv Rv2047c · MTBC0 mtbc0_002180 ·
854 aa · 2320575–2323139 (-) ·
RefSeq NP_216563.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | sugar epimerase family protein |
| Revised (this work) | Sugar epimerase family protein. Pfam: Epimerase (PF01370.28), 3Beta_HSD (PF01073.26), NAD_binding_10 (PF13460.13), Rph_4th (PF27448.1), PEP-utilizers (PF00391.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIH5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2047c |
UniProt still lists this protein as Uncharacterized protein Rv2047c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolismM Cell wall / membrane / envelope biogenesisT Signal transduction mechanisms
|
|---|---|
| eggNOG description | PEP-utilising enzyme, mobile domain |
| Orthologous group | COG0451 |
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.33 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 8 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 |
|---|---|---|---|---|
Epimerase | PF01370.28 | 2.7e-15 | 3–105 | NAD dependent epimerase/dehydratase family |
3Beta_HSD | PF01073.26 | 2.1e-09 | 4–103 | 3-beta hydroxysteroid dehydrogenase/isomerase family |
NAD_binding_10 | PF13460.13 | 9.4e-13 | 7–104 | NAD(P)H-binding |
Rph_4th | PF27448.1 | 9.8e-12 | 521–657 | Rifampicin phosphotransferase fourth domain |
PEP-utilizers | PF00391.30 | 7.9e-22 | 762–832 | PEP-utilising enzyme, mobile domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pks12 (polyketide synthase), high confidence from genomic context alone (score 968 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) |
|---|---|---|---|---|
Rv2048c pks12 |
polyketide synthase | 990 | 968 ctx | neighborhood:811 coexpression:763 textmining:711 |
Rv0705 rpsS |
30S ribosomal protein S19 | 818 | 818 | experimental:463 database:574 |
Rv0682 rpsL |
30S ribosomal protein S12 | 814 | 806 | experimental:463 database:573 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 809 | 800 | experimental:463 database:578 |
Rv0707 rpsC |
30S ribosomal protein S3 | 805 | 797 | experimental:463 database:578 |
Rv2056c rpsN2 |
30S ribosomal protein S14 | 802 | 795 | experimental:436 database:548 |
Rv0717 rpsN1 |
30S ribosomal protein S14 | 801 | 794 | experimental:436 database:548 |
Rv0721 rpsE |
30S ribosomal protein S5 | 817 | 792 | experimental:463 database:575 |
Rv0053 rpsF |
30S ribosomal protein S6 | 790 | 790 | experimental:760 |
Rv0718 rpsH |
30S ribosomal protein S8 | 794 | 787 | experimental:463 database:578 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 789 | 785 | experimental:463 database:557 |
Rv2785c rpsO |
30S ribosomal protein S15 | 793 | 784 | experimental:463 database:573 |
Rv0702 rplD |
50S ribosomal protein L4 | 787 | 781 | experimental:463 database:575 |
Rv2890c rpsB |
30S ribosomal protein S2 | 787 | 778 | experimental:463 database:573 |
Rv1006 hyp |
hypothetical protein | 771 | 771 ctx | cooccurence:770 |
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: sugar epimerase family protein
- Pfam (hmmscan --cut_ga): Epimerase PF01370.28 (E=3e-15), 3Beta_HSD PF01073.26 (E=2e-09), NAD_binding_10 PF13460.13 (E=9e-13), Rph_4th PF27448.1 (E=1e-11), PEP-utilizers PF00391.30 (E=8e-22)
- (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_216563.1)
- Domains: Pfam-A via hmmscan --cut_ga — Epimerase (PF01370.28), 3Beta_HSD (PF01073.26), NAD_binding_10 (PF13460.13), Rph_4th (PF27448.1), PEP-utilizers (PF00391.30)
- 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
COG0451 - Curated reference: UniProt P9WIH5 (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 —
192 functional partner(s); context anchor
pks12 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002180|Rv2047c| MRIAVTGASGVLGRGLTARLLSQGHEVVGIARHRPDSWPSSADFIAADIRDATAVESAMTGADVVAHCAWVRGRNDHINIDGTANVLKAMAETGTGRIVFTSSGHQPRVEQMLADCGLEWVAVRCALIFGRNVDNWVQRLFALPVLPAGYADRVVQVVHSDDAQRLLVRALLDTVIDSGPVNLAAPGELTFRRIAAALGRPMVPIGSPVLRRVTSFAELELLHSAPLMDVTLLRDRWGFQPAWNAEECLEDFTLAVRGRIGLGKRTFSLPWRLANIQDLPAVDSPADDGVAPRLAGPEGANGEFDTPIDPRFPTYLATNLSEALPGPFSPSSASVTVRGLRAGGVGIAERLRPSGVIQREIAMRTVAVFAHRLYGAITSAHFMAATVPFAKPATIVSNSGFFGPSMASLPIFGAQRPPSESSRARRWLRTLRNIGVFGVNLVGLSAGSPRDTDAYVADVDRLERLAFDNLATHDDRRLLSLILLARDHVVHGWVLASGSFMLCAAFNVLLRGLCGRDTAPAAGPELVSARSVEAVQRLVAAARRDPVVIRLLAEPGERLDKLAVEAPEFHSAVLAELTLIGHRGPAEVEMAATSYADNPELLVRMVAKTLRAVPAPQPPTPVIPLRAKPVALLAARQLRDREVRRDRMVRAIWVLRALLREYGRRLTEAGVFDTPDDVFYLLVDEIDALPADVSGLVARRRAEQRRLAGIVPPTVFSGSWEPSPSSAAALAAGDTLRGVGVCGGRVRGRVRIVRPETIDDLQPGEILVAEVTDVGYTAAFCYAAAVVTELGGPMSHAAVVAREFGFPCVVDAQGATRFLPPGALVEVDGATGEIHVVELASEDGPALPGSDLSR