Rv2395 Family assigned · medium auto-curated
H37Rv Rv2395 · MTBC0 mtbc0_002548 ·
667 aa · 2714319–2716322 (+) ·
RefSeq NP_216911.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | oligopeptide transporter%2C OPT family |
| Revised (this work) | Oligopeptide transporter%2C OPT family. Pfam: OPT (PF03169.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71749
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | opt |
| eggNOG description | OPT oligopeptide transporter protein |
| Orthologous group | COG1297 |
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) pseudogene candidate
| pN/pS | 0.692 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 8 missense, 1 nonsense, 2 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 10.18% of strains (14778) · 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 |
|---|---|---|---|---|
OPT | PF03169.21 | 1.2e-119 | 10–605 | OPT oligopeptide transporter protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ggtB (gamma-glutamyltranspeptidase precursor GgtB), medium confidence from genomic context alone (score 577 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2394 ggtB |
gamma-glutamyltranspeptidase precursor GgtB | 577 | 577 ctx | neighborhood:552 |
Rv2395A aprA |
acid and phagosome regulated protein AprA | 599 | 476 ctx | neighborhood:476 |
Rv2393 che1 |
ferrochelatase | 460 | 460 ctx | neighborhood:443 |
Rv2392 cysH |
phosphoadenosine phosphosulfate reductase | 456 | 456 ctx | neighborhood:439 |
Rv2391 sirA |
sulfite reductase | 454 | 455 ctx | neighborhood:439 |
Rv1304 atpB |
ATP synthase subunit A | 450 | 451 | coexpression:451 |
Rv2881c cdsA |
phosphatidate cytidylyltransferase | 433 | 434 | coexpression:434 |
Rv2395B aprB |
acid and phagosome regulated protein AprB | 481 | 336 | |
Rv2396 PE_PGRS41 |
acid and phagosome regulated protein AprC | 850 | 265 | textmining:805 |
Rv2093c tatC |
Sec-independent protein translocase transmembrane protein TatC | 686 | 124 | textmining:657 |
Rv3661 hyp |
hypothetical protein | 514 | 50 | textmining:510 |
Rv2367c ybeY |
endoribonuclease | 446 | 47 | textmining:443 |
Rv2632c hyp |
hypothetical protein | 651 | 46 | textmining:650 |
Rv2633c hyp |
hypothetical protein | 654 | 44 | textmining:653 |
Rv2182c |
1-acylglycerol-3-phosphate O-acyltransferase | 509 | 42 | textmining:509 |
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: integral membrane protein
- MTBC0 PGAP product: oligopeptide transporter%2C OPT family
- Pfam (hmmscan --cut_ga): OPT PF03169.21 (E=1e-119)
- (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_216911.1)
- Domains: Pfam-A via hmmscan --cut_ga — OPT (PF03169.21)
- 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
COG1297 - Curated reference: UniProt P71749 (TrEMBL, unreviewed; 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 —
15 functional partner(s); context anchor
ggtB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002548|Rv2395| MSGATVGAREITIRGVVLGALITLVFTAANVYLGLRVGLTFATSIPAAVISMGVLRLFANHSVVENNIVQTIASAAGTLSSIIFVLPALLMIGWWSGFPYWTTAAVCALGGILGVMYSIPLRRALVTGSDLPYPEGVAGAEVLKIGDSAREMEHNRRGIGVIALGAAAAAGYALLASLRVINNSLSATFRVGSGATMIGASLSLALIGVGHLVGVTVGVAMIVGLAIAFGVMLPIRTAGQLPPDGDYAVAVARIFSTDVRFIGAGAIAVAAAWTFLKILGPILRGIADAAVSARTRRRGQAVGQTERDIPIHIVAMVVLLSLIPIGWLLADFTDGTPLDDRRPGAIAAGVLLVLVIGLMVAAVCGYMAGLIGSSNSPISGVGILVVVLAGLLIKTAYGPATGSQIPALVAYTVFTAALVFGVATISNDNLQDLKTGQLVGATPWKQQVALIIGVLVGSVVMAPILQLMQAGFGFQGAPGATANALAAPQAALMSALAKGVFGGSLNWSLVGVGALTGVIAVALDETLAKTTTNLRLPPLAVGMGMYLPAALTLMIPIGAFLGRIYDSWARWSGDDDERKKRLGVMLATGLIVGESLYGVLFAVIVATTGKEEPLAMVGDGFRFASQPLGAIVFAGLLAWLYQRTRVTASYRLAAPAGSSKPLPDLPG