ugpA Family assigned · medium auto-curated
H37Rv Rv2835c · MTBC0 mtbc0_003014 ·
303 aa · 3161977–3162888 (-) ·
RefSeq NP_217351.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sn-glycerol-3-phosphate ABC transporter permease UgpA |
|---|---|
| MTBC0 PGAP re-annotation | sugar ABC transporter permease |
| Revised (this work) | Sugar ABC transporter permease. Pfam: BPD_transp_1 (PF00528.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XFF3
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable Sn-glycerol-3-phosphate transport integral membrane protein ABC transporter UgpA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | ugpA |
| eggNOG description | transport integral membrane protein ABC transporter |
| Orthologous group | COG1175 |
| KEGG orthology |
K05814
|
| KEGG pathways |
map02010
|
| KEGG modules |
M00198
|
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) pseudogene candidate
| pN/pS | 0.48 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 7.32% of strains (10623) · 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 |
|---|---|---|---|---|
BPD_transp_1 | PF00528.28 | 7.2e-21 | 95–302 | Binding-protein-dependent transport system inner membrane component |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ugpC (sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 999 | 999 ctx | neighborhood:882 cooccurence:761 coexpression:476 experimental:458 database:900 textmining:860 |
Rv2834c ugpE |
sn-glycerol-3-phosphate ABC transporter permease UgpE | 999 | 999 ctx | neighborhood:882 cooccurence:774 coexpression:602 experimental:412 database:900 textmining:930 |
Rv2833c ugpB |
sn-glycerol-3-phosphate ABC transporter substrate-binding lipoprotein UgpB | 999 | 998 ctx | neighborhood:882 cooccurence:769 coexpression:498 experimental:412 database:800 textmining:817 |
Rv2038c ugpC |
sugar ABC transporter ATP-binding protein | 977 | 933 ctx | cooccurence:753 coexpression:479 experimental:458 textmining:679 |
Rv2039c |
sugar ABC transporter permease | 979 | 932 ctx | cooccurence:774 coexpression:493 experimental:412 textmining:713 |
Rv2317 uspB |
sugar ABC transporter permease UspB | 980 | 931 ctx | cooccurence:774 coexpression:481 experimental:412 textmining:733 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 934 | 925 ctx | cooccurence:743 coexpression:463 experimental:458 |
Rv1237 sugB |
sugar ABC transporter permease SugB | 953 | 909 ctx | cooccurence:716 coexpression:480 experimental:412 textmining:517 |
Rv2041c |
sugar ABC transporter substrate-binding lipoprotein | 917 | 900 ctx | cooccurence:708 coexpression:432 experimental:412 |
Rv2837c nrnA |
bifunctional oligoribonuclease/PAP phosphatase NrnA | 784 | 785 ctx | neighborhood:782 |
Rv2838c rbfA |
ribosome-binding factor RbfA | 783 | 784 ctx | neighborhood:782 |
Rv2839c infB |
translation initiation factor IF-2 | 783 | 783 ctx | neighborhood:782 |
Rv2836c dinF |
DNA-damage-inducible protein DinF | 781 | 782 ctx | neighborhood:782 |
Rv2318 uspC |
sugar ABC transporter substrate-binding lipoprotein UspC | 914 | 752 | coexpression:430 experimental:412 textmining:670 |
Rv1235 lpqY |
trehalose ABC transporter substrate-binding lipoprotein LpqY | 749 | 729 | coexpression:426 experimental:412 |
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: sn-glycerol-3-phosphate ABC transporter permease UgpA
- MTBC0 PGAP product: sugar ABC transporter permease
- Pfam (hmmscan --cut_ga): BPD_transp_1 PF00528.28 (E=7e-21)
- (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_217351.1)
- Domains: Pfam-A via hmmscan --cut_ga — BPD_transp_1 (PF00528.28)
- 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
COG1175 - Curated reference: UniProt I6XFF3 (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 —
23 functional partner(s); context anchor
ugpC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003014|Rv2835c|ugpA MAAPQRARLRSSKERVRDYALFVVLVGPNVALLLLFVYRPLADNIRLSFFDWNVSDPSARFVGLSNYTEWFTRSDTRQIVFNTAVFTGAAVVGSMVLGLALAMLLDRPLRGRNLVRSTVFAPFVISGAAVGLAAQFVFDPHFGLIQDLLRRIGVGVPDFYQDARWALFMVTITYVWKNLGYTFVIYLAALQGVRRDLLEAAEIDGASRWAVFRRVLLPQLRPTTFFLSITVLINSLQVFDVINVMTRGGPEGTGTTTMVYQVYVETFRNFRAGYGATVATIMFLVLLAVTYYQVRVMDRGQRQ