Rv3657c Family assigned · medium auto-curated
H37Rv Rv3657c · MTBC0 - ·
191 aa · 4095540–4096115 (-) ·
RefSeq NP_218174.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Membrane protein. Pfam: T2SSF (PF00482.29). |
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 |
O69625
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible conserved alanine rich membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
N Cell motilityU Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| eggNOG description | type II secretion system protein |
| Orthologous group | COG2064 |
| KEGG orthology |
K12510
|
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, 3 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 |
|---|---|---|---|---|
T2SSF | PF00482.29 | 6.0e-14 | 46–173 | Type II secretion system (T2SS), protein F |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3659c (conjugal transfer protein), high confidence from genomic context alone (score 977 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3659c |
conjugal transfer protein | 997 | 977 ctx | neighborhood:851 coexpression:851 textmining:885 |
Rv3658c |
transmembrane protein | 933 | 933 ctx | neighborhood:851 coexpression:415 |
Rv1364c |
sigma factor regulatory protein | 930 | 931 | coexpression:920 |
Rv3660c ssd hyp |
hypothetical protein | 980 | 903 ctx | neighborhood:754 cooccurence:599 textmining:810 |
Rv3655c hyp |
hypothetical protein | 889 | 877 ctx | neighborhood:741 coexpression:545 |
Rv3656c hyp |
hypothetical protein | 983 | 874 ctx | neighborhood:835 textmining:870 |
Rv3654c hyp |
hypothetical protein | 962 | 824 ctx | neighborhood:813 textmining:796 |
Rv0990c hyp |
hypothetical protein | 844 | 824 ctx | cooccurence:450 coexpression:675 |
Rv3450c eccB4 |
ESX-4 secretion system protein EccB4 | 802 | 802 | coexpression:736 |
Rv3231c hyp |
hypothetical protein | 699 | 699 ctx | cooccurence:691 |
Rv2170 |
GCN5-like N-acetyltransferase | 676 | 676 ctx | cooccurence:675 |
Rv1354c hyp |
hypothetical protein | 672 | 672 | coexpression:650 |
Rv2219 |
transmembrane protein | 577 | 577 ctx | cooccurence:575 |
Rv2239c hyp |
hypothetical protein | 569 | 569 ctx | cooccurence:568 |
Rv3287c rsbW |
anti-sigma factor RsbW | 564 | 565 | coexpression:412 |
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): membrane protein
- Pfam (hmmscan --cut_ga): T2SSF PF00482.29 (E=6e-14)
- (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_218174.1)
- Domains: Pfam-A via hmmscan --cut_ga — T2SSF (PF00482.29)
- 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
COG2064 - Curated reference: UniProt O69625 (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 —
42 functional partner(s); context anchor
Rv3659c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3657c| MALWLGAGPSVVRARAGRPPRAHRPHQGLLLGRTDVADPLAVAASLDVLAVCLAAGMAVSTAAAATAAVAPPRLARVLRRAADLLALGADPNIAWSRPPDLPPGTHDAQTDAVLRLARRSAASGAALADGIVELAVQVRHDAAQAAAAAAERAGVLIAGPLGLCFLPAFLCVGIVPLVVGLAGDVLQFGLV