Rv3658c Family assigned · medium auto-curated
H37Rv Rv3658c · MTBC0 mtbc0_003876 ·
266 aa · 4119969–4120769 (-) ·
RefSeq NP_218175.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | type II secretion system F family protein |
| Revised (this work) | Type II secretion system F family 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.
Curated reference (UniProt)
| UniProt |
I6Y479
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| eggNOG description | Flp pilus assembly protein TadB |
| Orthologous group | COG4965 |
| 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 | 1.715 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 8 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 | 6.9e-09 | 97–220 | 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 948 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3659c |
conjugal transfer protein | 954 | 948 ctx | neighborhood:882 coexpression:579 |
Rv3657c |
membrane protein | 933 | 933 ctx | neighborhood:851 coexpression:415 |
Rv1364c |
sigma factor regulatory protein | 919 | 920 | coexpression:920 |
Rv3655c hyp |
hypothetical protein | 921 | 912 ctx | neighborhood:793 coexpression:593 |
Rv3660c ssd hyp |
hypothetical protein | 875 | 871 ctx | neighborhood:773 |
Rv3656c hyp |
hypothetical protein | 857 | 857 ctx | neighborhood:851 |
Rv3654c hyp |
hypothetical protein | 827 | 827 ctx | neighborhood:824 |
Rv0990c hyp |
hypothetical protein | 812 | 788 | coexpression:676 |
Rv3909 hyp |
hypothetical protein | 769 | 769 ctx | cooccurence:768 |
Rv2164c hyp |
hypothetical protein | 748 | 749 ctx | cooccurence:748 |
Rv1024 |
membrane protein | 747 | 748 ctx | cooccurence:746 |
Rv3835 hyp |
hypothetical protein | 725 | 725 ctx | cooccurence:722 |
Rv0007 |
membrane protein | 715 | 705 ctx | cooccurence:702 |
Rv1354c hyp |
hypothetical protein | 669 | 669 | coexpression:647 |
Rv1728c hyp |
hypothetical protein | 656 | 656 ctx | cooccurence:656 |
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: type II secretion system F family protein
- Pfam (hmmscan --cut_ga): T2SSF PF00482.29 (E=7e-09)
- (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_218175.1)
- 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
COG4965 - Curated reference: UniProt I6Y479 (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 —
43 functional partner(s); context anchor
Rv3659c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003876|Rv3658c| MSGIASAALILSLALVVLPGSPRCRLTPDDTGRRVLLVGARRVAWGVGCVAVGVAALLPLPTVVAVAVLGATLGLRYRRRRRYLRRSREGQALEAALELVVGELRAGAHPVRAFSIAADETGGPVAVALRAVAARARLGADVTAGLLAAARSSALPAYWERLAVCWQLGSDHGLAIASLMRAAQRDVAERQRFSARVSAGMAGARASAAILAILPLLGVLLGQLIGARPLSFLLTGRVGGWLLVVGLTLACAGLLWSDRITDRPVL