Rv2598 Family assigned · low auto-curated
H37Rv Rv2598 · MTBC0 mtbc0_002765 ·
164 aa · 2950539–2951033 (+) ·
RefSeq NP_217114.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2617 family protein |
| Revised (this work) | DUF2617 family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL71
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv2598 |
UniProt still lists this protein as Uncharacterized protein Rv2598; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function DUF2617 |
| Orthologous group | 2E4HX |
| KEGG orthology |
K07483
|
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 | 0.38 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.10% of strains (146) · 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 |
|---|---|---|---|---|
DUF2617 | PF10936.16 | 1.8e-30 | 21–160 | Protein of unknown function DUF2617 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2597 (membrane protein), high confidence from genomic context alone (score 977 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) |
|---|---|---|---|---|
Rv2597 |
membrane protein | 976 | 977 ctx | neighborhood:874 cooccurence:773 |
Rv2600 |
integral membrane protein | 914 | 915 ctx | neighborhood:783 cooccurence:610 |
Rv2601 speE |
spermidine synthase | 912 | 912 ctx | neighborhood:638 cooccurence:757 |
Rv2599 |
membrane protein | 888 | 888 ctx | neighborhood:881 |
Rv1006 hyp |
hypothetical protein | 750 | 751 ctx | cooccurence:749 |
Rv1868 hyp |
hypothetical protein | 748 | 748 ctx | cooccurence:746 |
Rv1435c hyp |
hypothetical protein | 723 | 724 ctx | cooccurence:723 |
Rv0180c |
transmembrane protein | 694 | 695 ctx | cooccurence:690 |
Rv3033 hyp |
hypothetical protein | 688 | 688 ctx | cooccurence:685 |
Rv2047c hyp |
hypothetical protein | 651 | 651 ctx | cooccurence:651 |
Rv2596 vapC40 |
ribonuclease VapC40 | 587 | 587 ctx | neighborhood:584 |
Rv3099c hyp |
hypothetical protein | 584 | 585 ctx | cooccurence:582 |
Rv2595 vapB40 |
antitoxin VapB40 | 584 | 584 ctx | neighborhood:584 |
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 552 | 553 ctx | cooccurence:550 |
Rv1364c |
sigma factor regulatory protein | 541 | 541 ctx | cooccurence:539 |
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: DUF2617 family protein
- Pfam (hmmscan --cut_ga): DUF2617 PF10936.16 (E=2e-30)
- (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_217114.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2617 (PF10936.16)
- 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
2E4HX - Curated reference: UniProt P9WL71 (SwissProt, reviewed; Predicted)
- 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 —
24 functional partner(s); context anchor
Rv2597 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002765|Rv2598| MPLHQLAIAPVDVSGALLGLVLNAPAPRPLATHRLAHTDGSALQLGVLGASHVVTVEGRFCEEVSCVARSRGGDLPESTHAPGYHLQSHTETHDEAAFRRLARHLRERCTRATGWLGGVFPGDDAALTALAAEPDGTGWRWRTWHLYPSASGGTVVHTTSRWRP