Rv3659c Resolved · high auto-curated
H37Rv Rv3659c · MTBC0 - ·
352 aa · 4096936–4097994 (-) ·
RefSeq YP_178003.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | conjugal transfer protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conjugal transfer protein. Pfam: T2SSE (PF00437.27). |
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 |
P9WMT3
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | Putative conjugal transfer protein Rv3659c |
UniProt still lists this protein as Putative conjugal transfer protein Rv3659c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| Preferred name | cpaF |
| eggNOG description | secretion system protein |
| Orthologous group | COG4962 |
| KEGG orthology |
K02283
|
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 | 1.171 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 9 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 5.75% of strains (8345) · 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 |
|---|---|---|---|---|
T2SSE | PF00437.27 | 3.0e-52 | 19–302 | Type II/IV secretion system protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3657c (membrane protein), high confidence from genomic context alone (score 977 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3657c |
membrane protein | 997 | 977 ctx | neighborhood:851 coexpression:851 textmining:885 |
Rv3660c ssd hyp |
hypothetical protein | 977 | 954 ctx | neighborhood:773 coexpression:806 textmining:531 |
Rv3658c |
transmembrane protein | 954 | 948 ctx | neighborhood:882 coexpression:579 |
Rv3655c hyp |
hypothetical protein | 903 | 897 ctx | neighborhood:795 coexpression:516 |
Rv3656c hyp |
hypothetical protein | 982 | 859 ctx | neighborhood:851 textmining:881 |
Rv3654c hyp |
hypothetical protein | 964 | 827 ctx | neighborhood:824 textmining:803 |
Rv0990c hyp |
hypothetical protein | 576 | 508 | coexpression:468 |
Rv3454 |
Rv3454, (MTCY13E12.07), len: 422 aa. Probable conserved integral membrane protein, showing some similarity to various proteins (generally tr | 416 | 52 | textmining:410 |
Rv3236c |
integral membrane transport protein | 806 | 50 | textmining:805 |
Rv3453 |
Rv3453, (MTCY13E12.06), len: 110 aa. Possible conserved transmembrane protein, showing weak similarity with other proteins e.g. Q9F6C3 putat | 414 | 48 | textmining:410 |
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): conjugal transfer protein
- Pfam (hmmscan --cut_ga): T2SSE PF00437.27 (E=3e-52)
- (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_178003.1)
- Domains: Pfam-A via hmmscan --cut_ga — T2SSE (PF00437.27)
- 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
COG4962 - Curated reference: UniProt P9WMT3 (SwissProt, reviewed; Evidence at transcript 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 —
10 functional partner(s); context anchor
Rv3657c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3659c| MLGDTEVLANLRVLQTELTGAGILEPLLSADGTTDVLVTAPDSVWVDDGNGLRRSQIRFADESAVRRLAQRLALAAGRRLDDAQPWVDGQLTGIGVGGFAVRLHAVLPPVATQGTCLSLRVLRPATQDLAALAAAGAIDPAAAALVADIVTARLAFLVCGGTGAGKTTLLAAMLGAVSPDERIVCVEDAAELAPRHPHLVKLVARRANVEGIGEVTVRQLVRQALRMRPDRIVVGEVRGAEVVDLLAALNTGHEGGAGTVHANNPGEVPARMEALGALGGLDRAALHSQLAAAVQVLLHVARDRAGRRRLAEIAVLRQAEGRVQAVTVWHADRGMSDDAAALHDLLRSRASA