Rv2216 Family assigned · medium auto-curated
H37Rv Rv2216 · MTBC0 mtbc0_002352 ·
301 aa · 2509783–2510688 (+) ·
RefSeq NP_216732.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | epimerase family protein |
|---|---|
| MTBC0 PGAP re-annotation | TIGR01777 family oxidoreductase |
| Revised (this work) | TIGR01777 family oxidoreductase. Pfam: Epimerase (PF01370.28), DUF1731 (PF08338.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGP7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Epimerase family protein Rv2216 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | epimerase |
| Orthologous group | COG1090 |
| KEGG orthology |
K07071
|
| Gene Ontology (47) |
GO:0003674, GO:0003824, GO:0004497, GO:0005488, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006066, GO:0006629, GO:0006706, GO:0006707 +35 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 | 0.614 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
Epimerase | PF01370.28 | 1.5e-13 | 7–216 | NAD dependent epimerase/dehydratase family |
DUF1731 | PF08338.17 | 1.9e-14 | 250–293 | Domain of unknown function (DUF1731) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dlaT (pyruvate dehydrogenase E2 component dihydrolipoamide acyltransferase), high confidence from genomic context alone (score 923 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2215 dlaT |
pyruvate dehydrogenase E2 component dihydrolipoamide acyltransferase | 936 | 923 ctx | neighborhood:881 |
Rv2217 lipB |
octanoyltransferase | 871 | 817 ctx | neighborhood:808 |
Rv2218 lipA |
lipoyl synthase | 839 | 810 ctx | neighborhood:808 |
Rv2219 |
transmembrane protein | 786 | 787 ctx | neighborhood:780 |
Rv1001 arcA |
arginine deiminase | 659 | 660 | coexpression:660 |
Rv2214c ephD |
oxidoreductase EphD | 595 | 595 ctx | neighborhood:547 |
Rv1155 |
pyridoxine/pyridoxamine 5'-phosphate oxidase | 517 | 517 | coexpression:513 |
Rv2074 |
pyridoxamine 5'-phosphate oxidase | 515 | 516 | coexpression:512 |
Rv3369 hyp |
hypothetical protein | 515 | 516 | coexpression:512 |
Rv2991 hyp |
hypothetical protein | 511 | 511 | coexpression:507 |
Rv0318c |
integral membrane protein | 507 | 508 | coexpression:467 |
Rv1485 hemZ |
ferrochelatase | 464 | 464 | coexpression:420 |
Rv1932 tpx |
2-Cys peroxiredoxin | 443 | 444 | coexpression:444 |
Rv3066 |
DeoR family transcriptional regulator | 442 | 443 | coexpression:438 |
Rv0775 hyp |
hypothetical protein | 442 | 443 | coexpression:438 |
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: epimerase family protein
- MTBC0 PGAP product: TIGR01777 family oxidoreductase
- Pfam (hmmscan --cut_ga): Epimerase PF01370.28 (E=1e-13), DUF1731 PF08338.17 (E=2e-14)
- (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_216732.1)
- Domains: Pfam-A via hmmscan --cut_ga — Epimerase (PF01370.28), DUF1731 (PF08338.17)
- 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
COG1090 - Curated reference: UniProt P9WGP7 (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 —
53 functional partner(s); context anchor
dlaT - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002352|Rv2216| MANAVVAIAGSSGLIGSALTAALRAADHTVLRIVRRAPANSEELHWNPESGEFDPHALTDVDAVVNLCGVNIAQRRWSGAFKQSLRDSRITPTEVLSAAVADAGVATLINASAVGYYGNTKDRVVDENDSAGTGFLAQLCVDWETATRPAQQSGARVVLARTGVVLSPAGGMLRRMRPLFSVGLGARLGSGRQYMSWISLEDEVRALQFAIAQPNLSGPVNLTGPAPVTNAEFTTAFGRAVNRPTPLMLPSVAVRAAFGEFADEGLLIGQRAIPSALERAGFQFHHNTIGEALGYATTRPG