Rv1979c Family assigned · medium auto-curated
H37Rv Rv1979c · MTBC0 mtbc0_002101 ·
481 aa · 2245332–2246777 (-) ·
RefSeq NP_216495.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | permease |
|---|---|
| MTBC0 PGAP re-annotation | APC family permease |
| Revised (this work) | APC family permease. Pfam: AA_permease_2 (PF13520.13), AA_permease (PF00324.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQM5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized transporter Rv1979c |
| Curated function | Probable amino-acid or metabolite transport protein. |
UniProt still lists this protein as Uncharacterized transporter Rv1979c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | Amino acid permease |
| Orthologous group | COG0531 |
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 | 1.799 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 10 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.14% of strains (200) · 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 |
|---|---|---|---|---|
AA_permease_2 | PF13520.13 | 9.4e-39 | 14–424 | Amino acid permease |
AA_permease | PF00324.28 | 3.3e-29 | 19–461 | Amino acid permease |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mpt64 (immunogenic protein Mpt64), medium confidence from genomic context alone (score 569 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2471 aglA |
alpha-glucosidase AglA | 777 | 766 | experimental:451 database:577 |
Rv0126 treS |
trehalose synthase/amylase TreS | 777 | 766 | experimental:451 database:577 |
Rv1327c glgE |
alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase | 775 | 764 | experimental:451 database:577 |
Rv1980c mpt64 |
immunogenic protein Mpt64 | 735 | 569 ctx | neighborhood:475 textmining:411 |
Rv0178 |
Mce associated membrane protein | 459 | 438 | |
Rv3492c |
Mce associated protein | 446 | 425 | |
Rv1334 mec |
[CysO | 418 | 419 | |
Rv1363c |
membrane protein | 438 | 417 | |
Rv0200 |
transmembrane protein | 436 | 414 | |
Rv1362c |
membrane protein | 436 | 414 | |
Rv1973 |
Mce associated membrane protein | 435 | 414 | |
Rv1972 |
Mce associated membrane protein | 435 | 414 | |
Rv2390c hyp |
hypothetical protein | 435 | 414 | |
Rv0199 |
membrane protein | 435 | 414 | |
Rv0177 |
Mce associated protein | 432 | 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: permease
- MTBC0 PGAP product: APC family permease
- Pfam (hmmscan --cut_ga): AA_permease_2 PF13520.13 (E=9e-39), AA_permease PF00324.28 (E=3e-29)
- (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_216495.2)
- Domains: Pfam-A via hmmscan --cut_ga — AA_permease_2 (PF13520.13), AA_permease (PF00324.28)
- 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
COG0531 - Curated reference: UniProt P9WQM5 (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 —
38 functional partner(s); context anchor
mpt64 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002101|Rv1979c| MVGPRTRGYAIHKLGFCSVVMLGINSIIGAGIFLTPGEVIGLAGPFAPMAYVLAGIFAGVVAIVFATAARYVRTNGASYAYTTAAFGRRIGIYVGVTHAITASIAWGVLASFFVSTLLRVAFPDKAWADAEQLFSVKTLTFLGFIGVLLAINLFGNRAIKWANGTSTVGKAFALSAFIVGGLWIITTQHVNNYATAWSAYSATPYSLLGVAEIGKGTFSSMALATIVALYAFTGFESIANAAEEMDAPDRNLPRAIPIAIFSVGAIYLLTLTVAMLLGSNKIAASGDTVKLAAAIGNATFRTIIVVGALISMFGINVAASFGAPRLWTALADSGVLPTRLSRKNQYDVPMVSFAITASLALAFPLALRFDNLHLTGLAVIARFVQFIIVPIALIALARSQAVEHAAVRRNAFTDKVLPLVAIVVSVGLAVSYDYRCIFLVRGGPNYFSIALIVITFIVVPAMAYLHYYRIIRRVGDRPSTR