apa Family assigned · medium auto-curated
H37Rv Rv1860 · MTBC0 - ·
325 aa · 2107736–2108713 (+) ·
RefSeq YP_177849.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains FAP (PF07174.18) domain(s); putative function inferred from the domain architecture. |
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 |
P9WIR7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Alanine and proline-rich secreted protein Apa |
| Curated function | A potent antigen in animals immunized with live bacteria, it induces a strong delayed-type hypersensitivity (DTH) in immunized animals. Elicits a mostly Th1 type of T-cell response in healthy humans; induces IFN-gamma production from CD4(+) and CD8(+) cells. Functions as an adhesin, binds to mouse macrophages via mannose residues. Might interact via host CD209. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | apa |
| eggNOG description | PFAM Fibronectin-attachment |
| Orthologous group | 2FEYE |
| Gene Ontology (49) |
GO:0002682, GO:0002684, GO:0005575, GO:0005576, GO:0006950, GO:0007154, GO:0008150, GO:0009267, GO:0009605, GO:0009607, GO:0009987, GO:0009991 +37 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 | 0.369 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 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 |
|---|---|---|---|---|
FAP | PF07174.18 | 9.8e-88 | 112–296 | Fibronectin-attachment protein (FAP) domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: modC (molybdenum ABC transporter ATP-binding protein ModC), high confidence from genomic context alone (score 797 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1859 modC |
molybdenum ABC transporter ATP-binding protein ModC | 801 | 797 ctx | neighborhood:796 |
Rv1857 modA |
molybdate ABC transporter substrate-binding lipoprotein ModA | 682 | 652 ctx | neighborhood:652 |
Rv1858 modB |
molybdenum ABC transporter permease ModB | 628 | 620 ctx | neighborhood:620 |
Rv1861 |
transmembrane protein | 550 | 551 ctx | neighborhood:544 |
Rv1862 adhA |
alcohol dehydrogenase A | 544 | 544 ctx | neighborhood:544 |
Rv1856c |
oxidoreductase | 424 | 424 ctx | neighborhood:422 |
Rv0934 pstS1 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 539 | 89 | textmining:515 |
Rv3763 lpqH |
lipoprotein LpqH | 681 | 64 | textmining:674 |
Rv1886c fbpB |
diacylglycerol acyltransferase/mycolyltransferase Ag85B | 632 | 55 | textmining:627 |
Rv0309 hyp |
hypothetical protein | 518 | 55 | textmining:511 |
Rv1096 |
glycosyl hydrolase | 432 | 55 | textmining:424 |
Rv0350 dnaK |
chaperone protein DnaK | 519 | 54 | textmining:513 |
Rv3418c groES |
chaperonin GroES | 657 | 52 | textmining:654 |
Rv0440 groEL2 |
molecular chaperone GroEL | 441 | 51 | textmining:436 |
Rv1926c mpt63 |
immunogenic protein Mpt63 | 804 | 50 | textmining:803 |
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): hypothetical protein
- Pfam (hmmscan --cut_ga): FAP PF07174.18 (E=1e-87)
- (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_177849.1)
- Domains: Pfam-A via hmmscan --cut_ga — FAP (PF07174.18)
- 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
2FEYE - Curated reference: UniProt P9WIR7 (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 —
27 functional partner(s); context anchor
modC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1860|apa MHQVDPNLTRRKGRLAALAIAAMASASLVTVAVPATANADPEPAPPVPTTAASPPSTAAAPPAPATPVAPPPPAAANTPNAQPGDPNAAPPPADPNAPPPPVIAPNAPQPVRIDNPVGGFSFALPAGWVESDAAHFDYGSALLSKTTGDPPFPGQPPPVANDTRIVLGRLDQKLYASAEATDSKAAARLGSDMGEFYMPYPGTRINQETVSLDANGVSGSASYYEVKFSDPSKPNGQIWTGVIGSPAANAPDAGPPQRWFVVWLGTANNPVDKGAAKALAESIRPLVAPPPAPAPAPAEPAPAPAPAGEVAPTPTTPTPQRTLPA