gabP Resolved · high auto-curated
H37Rv Rv0522 · MTBC0 - ·
434 aa · 613038–614342 (+) ·
RefSeq YP_177734.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | GABA permease GabP |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | GABA permease GabP. Pfam: AA_permease (PF00324.28), AA_permease_2 (PF13520.13), Spore_permease (PF03845.20). |
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 |
L7N6B9
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable GABA permease GabP |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | gabP |
| eggNOG description | permease |
| Orthologous group | COG1113 |
| KEGG orthology |
K03293, K11735, K16237
|
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 | 1.621 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 9 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 |
|---|---|---|---|---|
AA_permease | PF00324.28 | 1.1e-113 | 1–406 | Amino acid permease |
AA_permease_2 | PF13520.13 | 1.1e-29 | 2–394 | Amino acid permease |
Spore_permease | PF03845.20 | 1.2e-05 | 5–237 | Spore germination protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0521 (Possible methyltransferase/methylase (fragment); Rv0521, (replaces MTCY20G10.11), len: 101 aa. Possible fragment of methyltransferase (possi), medium confidence from genomic context alone (score 522 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0521 |
Possible methyltransferase/methylase (fragment); Rv0521, (replaces MTCY20G10.11), len: 101 aa. Possible fragment of methyltransferase (possi | 523 | 522 ctx | neighborhood:521 |
Rv0520 |
Possible methyltransferase/methylase (fragment); Rv0520, (MTCY20G10.10), len: 116 aa. Possible fragment of methyltransferase (possibly first | 523 | 522 ctx | neighborhood:521 |
Rv1999c |
transporter | 670 | 324 | textmining:533 |
Rv2320c rocE |
cationic amino acid transporter permease RocE | 476 | 197 | |
Rv2531c |
amino acid decarboxylase | 603 | 187 | textmining:532 |
Rv1187 rocA |
pyrroline-5-carboxylate dehydrogenase RocA | 459 | 50 | textmining:454 |
Rv1001 arcA |
arginine deiminase | 440 | 44 | textmining:439 |
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): GABA permease GabP
- Pfam (hmmscan --cut_ga): AA_permease PF00324.28 (E=1e-113), AA_permease_2 PF13520.13 (E=1e-29), Spore_permease PF03845.20 (E=1e-05)
- (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_177734.1)
- Domains: Pfam-A via hmmscan --cut_ga — AA_permease (PF00324.28), AA_permease_2 (PF13520.13), Spore_permease (PF03845.20)
- 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
COG1113 - Curated reference: UniProt L7N6B9 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
7 functional partner(s); context anchor
Rv0521 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0522|gabP MIAIGGVIGAGLFVGSGVVIRATGPAAFLTYALCGALIVLVMRMLGEMAAANPSTGAFADYAAKALGGWAGFSVGWLYWYFWVIVVGFEAVAGGKVLTYWIDAPLWLASLCLMMMMTATNLVSVSSFGEFEFWFAGVKVATIVGFLVLGTAFAFGLLPGHGMDFSNLSAHGGFFPDGVGAVFAAIVVAIFSMTGTEVVTIAAAEAPDPQRAVQRAMSTVVARIVIFFVGSVFLLTVILPWNSLELGASPYVAALRHMGIGGADQIMNAVVLTAVLSCLNSGLYTASRMLFVLAARQEAPAQLVKVNRRGVPTFAIMGSSVVGFLCVIMAWVSPATVFVFLLNSSGAVILFVYLLIALSQIVLRRQTSGQNLGVRMWLFPGLSIVTVTGIVAVLARMAFDYAARSQLWLSLLSWAVVVGCYLVTTLVRRPLNRPW