Rv2716 Family assigned · medium auto-curated
H37Rv Rv2716 · MTBC0 mtbc0_002890 ·
228 aa · 3051587–3052273 (+) ·
RefSeq NP_217232.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | PhzF family phenazine biosynthesis protein |
| Revised (this work) | PhzF family phenazine biosynthesis protein. Pfam: PhzC-PhzF (PF02567.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL43
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2716 |
UniProt still lists this protein as Uncharacterized protein Rv2716; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | phzF |
| eggNOG description | Phenazine biosynthesis protein, PhzF family |
| Orthologous group | COG0384 |
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) | 3 synonymous, 3 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 |
|---|---|---|---|---|
PhzC-PhzF | PF02567.22 | 4.1e-15 | 10–113 | Phenazine biosynthesis-like protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2715 (hydrolase), high confidence from genomic context alone (score 837 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) |
|---|---|---|---|---|
Rv2715 |
hydrolase | 836 | 837 ctx | neighborhood:813 |
Rv2714 hyp |
hypothetical protein | 754 | 754 ctx | neighborhood:753 |
Rv3338 |
Rv3338, (MTV016.38), len: 214 aa. Hypothetical protein, equivalent to C-termini of Q49926|ML0685 TPEA (putative hydrolase) from Mycobacteriu | 598 | 598 ctx | cooccurence:598 |
Rv0210 hyp |
hypothetical protein | 506 | 507 ctx | cooccurence:488 |
Rv1592c hyp |
hypothetical protein | 446 | 446 ctx | cooccurence:406 |
Rv0227c |
membrane protein | 442 | 443 ctx | cooccurence:440 |
Rv0479c |
membrane protein | 409 | 409 ctx | cooccurence:406 |
Rv2713 sthA |
pyridine nucleotide transhydrogenase | 420 | 390 | |
Rv1070c echA8 |
enoyl-CoA hydratase EchA8 | 667 | 156 | textmining:622 |
Rv2334 cysK1 |
O-acetylserine sulfhydrylase | 521 | 52 | textmining:516 |
Rv1074c fadA3 |
beta-ketoacyl CoA thiolase FadA | 550 | 49 | textmining:547 |
Rv2109c prcA |
proteasome subunit alpha | 441 | 47 | textmining: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: hypothetical protein
- MTBC0 PGAP product: PhzF family phenazine biosynthesis protein
- Pfam (hmmscan --cut_ga): PhzC-PhzF PF02567.22 (E=4e-15)
- (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_217232.1)
- Domains: Pfam-A via hmmscan --cut_ga — PhzC-PhzF (PF02567.22)
- 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
COG0384 - Curated reference: UniProt P9WL43 (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 —
12 functional partner(s); context anchor
Rv2715 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002890|Rv2716| MAIEVSVLRVFTDSDGNFGNPLGVINASKVEHRDRQQLAAQSGYSETIFVDLPSPGSTTAHATIHTPRTEIPFAGHPTVGASWWLRERGTPINTLQVPAGIVQVSYHGDLTAISARSEWAPEFAIHDLDSLDALAAADPADFPDDIAHYLWTWTDRSAGSLRARMFAANLGVTEDEATGAAAIRITDYLSRDLTITQGKGSLIHTTWSPEGWVRVAGRVVSDGVAQLD