Rv0265c Family assigned · medium auto-curated
H37Rv Rv0265c · MTBC0 - ·
330 aa · 316511–317503 (-) ·
RefSeq YP_177705.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | iron ABC transporter substrate-binding lipoprotein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Iron ABC transporter substrate-binding lipoprotein. Pfam: Peripla_BP_2 (PF01497.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
L7N6B2
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable periplasmic iron-transport lipoprotein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | yhfQ |
| eggNOG description | Periplasmic binding protein |
| Orthologous group | COG0614 |
| KEGG orthology |
K02016
|
| KEGG pathways |
map02010
|
| KEGG modules |
M00240
|
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 | 0.584 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.37% of strains (543) · 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 |
|---|---|---|---|---|
Peripla_BP_2 | PF01497.24 | 1.1e-43 | 59–298 | Periplasmic binding protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: oplA (5-oxoprolinase OplA), high confidence from genomic context alone (score 855 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0266c oplA |
5-oxoprolinase OplA | 979 | 855 ctx | neighborhood:855 textmining:861 |
Rv0262c aac |
aminoglycoside 2'-N-acetyltransferase | 803 | 803 ctx | neighborhood:765 |
Rv3044 fecB |
FeIII-dicitrate-binding periplasmic lipoprotein | 849 | 787 ctx | cooccurence:626 |
Rv0264c hyp |
hypothetical protein | 954 | 778 ctx | neighborhood:776 textmining:803 |
Rv0263c hyp |
hypothetical protein | 768 | 768 ctx | neighborhood:766 |
Rv1289 hyp |
hypothetical protein | 732 | 732 | coexpression:732 |
Rv2895c viuB |
mycobactin utilization protein ViuB | 608 | 552 | |
Rv0269c hyp |
hypothetical protein | 546 | 546 ctx | neighborhood:544 |
Rv0267 narU |
nitrite extrusion protein NarU | 513 | 513 ctx | neighborhood:506 |
Rv0259c hyp |
hypothetical protein | 481 | 482 ctx | neighborhood:461 |
Rv2384 mbtA |
2,3-dihydroxybenzoate-AMP ligase | 487 | 456 | |
Rv3673c |
membrane-anchored thioredoxin-like protein | 420 | 421 ctx | cooccurence:407 |
Rv0260c |
transcriptional regulator | 416 | 378 | |
Rv2383c mbtB |
phenyloxazoline synthase | 404 | 374 | |
Rv0202c mmpL11 |
transmembrane transport protein MmpL11 | 494 | 314 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): iron ABC transporter substrate-binding lipoprotein
- Pfam (hmmscan --cut_ga): Peripla_BP_2 PF01497.24 (E=1e-43)
- (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 YP_177705.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peripla_BP_2 (PF01497.24)
- 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
COG0614 - Curated reference: UniProt L7N6B2 (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 —
28 functional partner(s); context anchor
oplA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0265c| MRQGCSRRGFLQVAEAAAATGLFAGCSSPKPPPGTPGGAAVTITHLFGQTVIKEPPKRVVSAGYTEQDDLLAVDVVPIAVTDWFGDQPFAVWPWAAPKLGGARPAVLNLDNGIQIDRIAALKPDLIVAINAGVDADTYQQLSAIAPTVAQSGGDAFFEPWKDQARSIGQAVFAADRMRSLIEAVDQKFAAVAQRHPRWRGKKALLLQGRLWQGNVVATLAGWRTDFLNDMGLVIADSIKPFAVDQRGVIPRDHIKAVLDAADVLIWMTESPEDEKALLADPEIAASQATAQRRHIFTSKEQAGAIAFSSVLSYPVVAEQLPPQISQILGA