Rv3312A Resolved · high auto-curated
H37Rv Rv3312A · MTBC0 - ·
103 aa · 3700705–3701016 (-) ·
RefSeq YP_177957.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | pilin |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Pilin. Pfam: Pilin_Mycobact (PF26380.2). |
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 |
P9WI87
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Pilin |
| Curated function | Structural subunit of M.tuberculosis pili (MTP), which are thin (2- to 3-nm wide), flexible, coiled-coil, aggregative fibers. Has a strong affinity for laminin but lacks significant binding affinity for fibronectin or type IV collagen. Mediates adhesion to the extracellular matrix, an event that would facilitate direct interaction with the host epithelium during infection in the lung or other tissues. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | mtp |
| eggNOG description | Structural subunit of M.tuberculosis pili (MTP), which are thin |
| Orthologous group | 2B1R9 |
| Gene Ontology (15) |
GO:0005575, GO:0005623, GO:0008150, GO:0009289, GO:0009297, GO:0009987, GO:0016043, GO:0022607, GO:0030030, GO:0030031, GO:0042995, GO:0043711 +3 more
|
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 | 0.326 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.14% of strains (207) · 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 |
|---|---|---|---|---|
Pilin_Mycobact | PF26380.2 | 1.8e-16 | 30–62 | Mycobacterial Pilin Family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: add (adenosine deaminase), medium confidence from genomic context alone (score 629 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3313c add |
adenosine deaminase | 628 | 629 ctx | neighborhood:624 |
Rv3314c deoA |
thymidine phosphorylase | 707 | 625 ctx | neighborhood:624 |
Rv3315c cdd |
cytidine deaminase | 643 | 601 ctx | neighborhood:597 |
Rv3312c hyp |
hypothetical protein | 549 | 394 | |
Rv0309 hyp |
hypothetical protein | 556 | 58 | textmining:549 |
Rv1824 hyp |
hypothetical protein | 805 | 54 | textmining:803 |
Rv3717 hyp |
hypothetical protein | 443 | 52 | textmining:437 |
Rv3441c mrsA |
phosphoglucosamine mutase | 442 | 47 | textmining:439 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 653 | 46 | textmining:652 |
Rv2296 dhmA1 |
haloalkane dehalogenase | 575 | 46 | textmining:573 |
Rv2338c moeW |
molybdopterin biosynthesis protein MoeW | 548 | 46 | textmining:546 |
Rv0021c hyp |
hypothetical protein | 630 | 41 | textmining:630 |
Rv3503c fdxD |
ferredoxin FdxD | 510 | 41 | textmining:510 |
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): pilin
- Pfam (hmmscan --cut_ga): Pilin_Mycobact PF26380.2 (E=2e-16)
- (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_177957.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pilin_Mycobact (PF26380.2)
- 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
2B1R9 - Curated reference: UniProt P9WI87 (SwissProt, reviewed; 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 —
13 functional partner(s); context anchor
add - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3312A| MYRFACRTLMLAACILATGVAGLGVGAQSAAQTAPVPDYYWCPGQPFDPAWGPNWDPYTCHDDFHRDSDGPDHSRDYPGPILEGPVLDDPGAAPPPPAAGGGA