Rv2061c Resolved · high auto-curated
H37Rv Rv2061c · MTBC0 mtbc0_002194 ·
134 aa · 2345294–2345698 (-) ·
RefSeq NP_216577.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | PPOX class F420-dependent oxidoreductase |
| Revised (this work) | PPOX class F420-dependent oxidoreductase. Pfam: PNPOx_N (PF01243.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O86340
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Pyridoxamine 5-phosphate |
| Orthologous group | COG3871 |
| KEGG orthology |
K07006
|
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 | 0.703 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
PNPOx_N | PF01243.28 | 7.0e-10 | 8–104 | Pyridoxamine 5'-phosphate oxidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cobN (cobalamin biosynthesis protein CobN), medium confidence from genomic context alone (score 612 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) |
|---|---|---|---|---|
Rv2062c cobN |
cobalamin biosynthesis protein CobN | 612 | 612 ctx | neighborhood:607 |
Rv1558 hyp |
hypothetical protein | 475 | 475 ctx | cooccurence:468 |
Rv0044c |
oxidoreductase | 474 | 474 ctx | cooccurence:471 |
Rv2066 cobIJ |
bifunctional S-adenosyl-L-methionine-precorrin-2 methyl transferase/precorrin-3 methylase | 451 | 451 ctx | neighborhood:446 |
Rv2064 cobG |
precorrin-3B synthase | 448 | 448 ctx | neighborhood:443 |
Rv2065 cobH |
precorrin-8X methylmutase | 463 | 441 ctx | neighborhood:438 |
Rv0407 fgd1 |
F420-dependent glucose-6-phosphate dehydrogenase | 438 | 438 ctx | cooccurence:422 |
Rv0868c moaD2 |
cyclic pyranopterin monophosphate synthase | 425 | 425 ctx | cooccurence:404 |
Rv2063 mazE7 |
antitoxin MazE7 | 409 | 409 ctx | neighborhood:407 |
Rv2063A mazF7 |
mRNA interferase MazF7 | 407 | 407 ctx | neighborhood:407 |
Rv3196 hyp |
hypothetical protein | 405 | 405 | |
Rv2609c |
membrane protein | 402 | 403 |
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: PPOX class F420-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): PNPOx_N PF01243.28 (E=7e-10)
- (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_216577.1)
- Domains: Pfam-A via hmmscan --cut_ga — PNPOx_N (PF01243.28)
- 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
COG3871 - Curated reference: UniProt O86340 (TrEMBL, unreviewed; 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 —
12 functional partner(s); context anchor
cobN - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002194|Rv2061c| MTPTFSDLAEAQYLLLTTFTKDGRPKPVPIWAALDTDRGDRLLVITEKKSWKVKRIRNTPRVTLATCTLRGRPTSEAVEATAAILDESQTGAVYDAIVKRYGIQGKLFTFVSKLRGGMRNNIGLELKVAESETG