Rv2425c Family assigned · medium auto-curated
H37Rv Rv2425c · MTBC0 mtbc0_002582 ·
480 aa · 2746134–2747576 (-) ·
RefSeq NP_216941.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | VWA domain-containing protein |
| Revised (this work) | VWA domain-containing protein. Pfam: VWA_CoxE (PF05762.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71923
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | VWA domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein containing von Willebrand factor type A (VWA) domain |
| Orthologous group | COG3552 |
| KEGG orthology |
K07161
|
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 | 0.953 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.24% of strains (343) · clonal |
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 |
|---|---|---|---|---|
VWA_CoxE | PF05762.21 | 5.3e-67 | 252–473 | VWA domain containing CoxE-like protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: proA (gamma-glutamyl phosphate reductase), high confidence from genomic context alone (score 822 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) |
|---|---|---|---|---|
Rv2426c hyp |
hypothetical protein | 976 | 976 ctx | neighborhood:882 cooccurence:771 |
Rv2427c proA |
gamma-glutamyl phosphate reductase | 822 | 822 ctx | neighborhood:817 |
Rv0370c |
oxidoreductase | 762 | 759 ctx | cooccurence:728 |
Rv2417c |
DegV domain-containing protein | 606 | 606 ctx | neighborhood:544 |
Rv0696 mftF |
mycofactocin biosynthesis glycosyltransferase MftF | 605 | 606 ctx | cooccurence:582 |
Rv2424c |
transposase | 566 | 566 ctx | neighborhood:561 |
Rv0693 mftC |
mycofactocin radical SAM maturase MftC | 553 | 554 ctx | cooccurence:536 |
Rv2418c octT hyp |
hypothetical protein | 546 | 547 ctx | neighborhood:544 |
Rv2420c rsfS hyp |
hypothetical protein | 544 | 544 ctx | neighborhood:544 |
Rv2421c nadD |
nicotinate-nucleotide adenylyltransferase | 544 | 544 ctx | neighborhood:544 |
Rv0368c hyp |
hypothetical protein | 520 | 521 ctx | cooccurence:518 |
Rv0692 mftB |
mycofactocin system protein MftB | 499 | 500 ctx | cooccurence:464 |
Rv2427A oxyR |
Rv2427A, Pseudogene oxyR', inactivated by multiple mutations; identical to sequence in u16243 (see Deretic et al., 1995). | 445 | 445 ctx | neighborhood:445 |
Rv0207c hyp |
hypothetical protein | 437 | 438 ctx | cooccurence:434 |
Rv2453c mobA |
molybdenum cofactor guanylyltransferase | 837 | 179 | textmining:810 |
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: VWA domain-containing protein
- Pfam (hmmscan --cut_ga): VWA_CoxE PF05762.21 (E=5e-67)
- (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_216941.1)
- Domains: Pfam-A via hmmscan --cut_ga — VWA_CoxE (PF05762.21)
- 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
COG3552 - Curated reference: UniProt P71923 (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 —
18 functional partner(s); context anchor
proA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002582|Rv2425c| MAARRIRAARPLAPHGLPGHLVGFVEALRGSGISVGPSETVDAGRVMATLGLGDREVLREGIACAVLRRPDHRDTYDAMFDLWFPAALGARAVITTEDESAGSGGLPPDDVEAMRQLLLDLLANNQDLAGKDERLVEMIARIVEAYGKYSSSRGPSFSSYQALKAMALDELEGKLLAGLLAPYGDEPTATQEQIAKALAAQKIAQLRRMVDAETKRRTAEQLGREHVQMYGIPQLSENVEFLRASGEQLRQMRRVVAPLARTLATRLAARRRRARAGSIDLRKTLRKSMSTGGVPIDLVLHKPRPARPELVVLCDVSGSVAGFSHFTLLLVHALRQQFSRVRVFAFIDSTDEVTHMFGPESDLAIAIQRITREAGVYARDGHSDYGNAFVSFMQGFPNVLSPRSSLLVLGDGRTNYRNPATDVLADMVTASRHAHWLNPEPKHLWGSGDSAVPRYQEVITMHECRSAKQLATVIDQLLPV