Rv2146c Family assigned · medium auto-curated
H37Rv Rv2146c · MTBC0 mtbc0_002282 ·
96 aa · 2433045–2433335 (-) ·
RefSeq NP_216662.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | YggT family protein |
| Revised (this work) | YggT family protein. Pfam: CCB3_YggT (PF02325.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06230
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | integral membrane protein |
| Orthologous group | COG0762 |
| KEGG orthology |
K02221
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 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 |
|---|---|---|---|---|
CCB3_YggT | PF02325.24 | 1.2e-12 | 1–92 | CCB3/YggT |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sepF (cell division protein SepF), high confidence from genomic context alone (score 946 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2147c sepF |
cell division protein SepF | 953 | 946 ctx | neighborhood:747 coexpression:795 |
Rv2145c wag31 |
cell wall synthesis protein Wag31 | 899 | 892 ctx | neighborhood:722 coexpression:434 |
Rv2150c ftsZ |
cell division protein FtsZ | 850 | 844 ctx | neighborhood:569 coexpression:652 |
Rv2148c hyp |
hypothetical protein | 812 | 782 ctx | neighborhood:571 coexpression:513 |
Rv2256c hyp |
hypothetical protein | 773 | 774 ctx | cooccurence:763 |
Rv2413c hyp |
hypothetical protein | 742 | 726 ctx | cooccurence:719 |
Rv2144c |
transmembrane protein | 682 | 682 ctx | neighborhood:672 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 663 | 663 ctx | cooccurence:658 |
Rv3009c gatB |
aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B | 660 | 660 | coexpression:649 |
Rv2680 hyp |
hypothetical protein | 641 | 641 ctx | cooccurence:637 |
Rv1002c pmt |
dolichyl-phosphate-mannose--protein mannosyltransferase | 638 | 638 ctx | cooccurence:637 |
Rv0807 hyp |
hypothetical protein | 630 | 630 ctx | cooccurence:629 |
Rv2169c |
transmembrane protein | 627 | 627 ctx | cooccurence:612 |
Rv2699c hyp |
hypothetical protein | 621 | 621 ctx | cooccurence:618 |
Rv2745c clgR |
transcriptional regulator ClgR | 599 | 599 ctx | cooccurence:595 |
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: transmembrane protein
- MTBC0 PGAP product: YggT family protein
- Pfam (hmmscan --cut_ga): CCB3_YggT PF02325.24 (E=1e-12)
- (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_216662.1)
- Domains: Pfam-A via hmmscan --cut_ga — CCB3_YggT (PF02325.24)
- 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
COG0762 - Curated reference: UniProt O06230 (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 —
73 functional partner(s); context anchor
sepF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002282|Rv2146c| MVVFFQILGFALFIFWLLLIARVVVEFIRSFSRDWRPTGVTVVILEIIMSITDPPVKVLRRLIPQLTIGAVRFDLSIMVLLLVAFIGMQLAFGAAA