Rv3481c Family assigned · medium auto-curated
H37Rv Rv3481c · MTBC0 mtbc0_003696 ·
229 aa · 3925075–3925764 (-) ·
RefSeq NP_217998.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | GAP family protein |
| Revised (this work) | GAP family protein. Pfam: SfLAP (PF11139.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XHC3
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | Sap, sulfolipid-1-addressing protein |
| Orthologous group | COG1280 |
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 | 1.14 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
SfLAP | PF11139.15 | 3.3e-65 | 18–227 | Sap, sulfolipid-1-addressing protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0048c (membrane protein), high confidence from genomic context alone (score 708 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0048c |
membrane protein | 707 | 708 ctx | cooccurence:707 |
Rv1171 hyp |
hypothetical protein | 605 | 605 ctx | cooccurence:604 |
Rv3480c |
diacyglycerol O-acyltransferase | 591 | 591 ctx | neighborhood:591 |
Rv3773c hyp |
hypothetical protein | 570 | 571 ctx | cooccurence:568 |
Rv1635c |
mannosyltransferase | 545 | 545 ctx | cooccurence:545 |
Rv2558 hyp |
hypothetical protein | 525 | 525 ctx | cooccurence:525 |
Rv3482c |
membrane protein | 516 | 516 ctx | neighborhood:516 |
Rv2557 hyp |
hypothetical protein | 504 | 504 ctx | cooccurence:504 |
Rv0711 atsA |
arylsulfatase AtsA | 470 | 470 ctx | cooccurence:468 |
Rv1624c |
membrane protein | 459 | 460 ctx | cooccurence:458 |
Rv2525c hyp |
hypothetical protein | 450 | 450 ctx | cooccurence:446 |
Rv3483c hyp |
hypothetical protein | 431 | 431 ctx | neighborhood:428 |
Rv0188 |
transmembrane protein | 417 | 417 ctx | cooccurence:417 |
Rv2487c PE_PGRS42 |
PE-PGRS family protein PE_PGRS42 | 415 | 415 ctx | cooccurence:415 |
Rv3435c |
transmembrane protein | 414 | 414 ctx | cooccurence:411 |
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: integral membrane protein
- MTBC0 PGAP product: GAP family protein
- Pfam (hmmscan --cut_ga): SfLAP PF11139.15 (E=3e-65)
- (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_217998.1)
- Domains: Pfam-A via hmmscan --cut_ga — SfLAP (PF11139.15)
- 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
COG1280 - Curated reference: UniProt I6XHC3 (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 —
16 functional partner(s); context anchor
Rv0048c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003696|Rv3481c| MRGLLPVAGHWVSVLTGLVPLALVIALSPLSVIPAVLVVHSPQPRPSSLAFLGGWLLGLAVVTAVFVAASGALGGLSTTSPAWASWLRVVLGSALIVFGVLRWLTRHRHTEMPGWMRAFASFTPARAGLVGAVLVVVRPEVLIICAAAGLAIGSGGHGAAGSWIYTAFFAMLAASTVAIPILAYVAAGDRLDDSLERLKDWMEKNHAGMVAAILVVIGLLLLYNGVHAM