uspA Family assigned · medium auto-curated
H37Rv Rv2316 · MTBC0 mtbc0_002464 ·
290 aa · 2613587–2614459 (+) ·
RefSeq NP_216832.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sugar ABC transporter permease UspA |
|---|---|
| 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 |
P71896
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable sugar-transport integral membrane protein ABC transporter UspA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | uspA |
| eggNOG description | ABC transporter |
| Orthologous group | COG1175 |
| KEGG orthology |
K02025
|
| KEGG modules |
M00207
|
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 | 0.64 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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 |
|---|---|---|---|---|
BPD_transp_1 | PF00528.28 | 1.4e-18 | 84–280 | Binding-protein-dependent transport system inner membrane component |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: uspB (sugar ABC transporter permease UspB), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2317 uspB |
sugar ABC transporter permease UspB | 999 | 999 ctx | neighborhood:882 cooccurence:774 coexpression:530 experimental:412 database:900 textmining:461 |
Rv2318 uspC |
sugar ABC transporter substrate-binding lipoprotein UspC | 998 | 982 ctx | neighborhood:882 cooccurence:589 coexpression:457 experimental:412 textmining:910 |
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 969 | 932 ctx | cooccurence:767 coexpression:468 experimental:458 textmining:573 |
Rv2038c ugpC |
sugar ABC transporter ATP-binding protein | 957 | 932 ctx | cooccurence:767 coexpression:466 experimental:458 textmining:404 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 949 | 932 ctx | cooccurence:767 coexpression:465 experimental:458 |
Rv2834c ugpE |
sn-glycerol-3-phosphate ABC transporter permease UgpE | 976 | 930 ctx | cooccurence:774 coexpression:482 experimental:412 textmining:673 |
Rv2039c |
sugar ABC transporter permease | 956 | 930 ctx | cooccurence:774 coexpression:480 experimental:412 textmining:403 |
Rv1237 sugB |
sugar ABC transporter permease SugB | 954 | 923 ctx | cooccurence:760 coexpression:480 experimental:412 textmining:438 |
Rv2041c |
sugar ABC transporter substrate-binding lipoprotein | 937 | 908 ctx | cooccurence:733 coexpression:428 experimental:412 |
Rv2833c ugpB |
sn-glycerol-3-phosphate ABC transporter substrate-binding lipoprotein UgpB | 907 | 851 ctx | cooccurence:558 coexpression:440 experimental:412 textmining:403 |
Rv2314c hyp |
hypothetical protein | 790 | 791 ctx | neighborhood:790 |
Rv2315c hyp |
hypothetical protein | 790 | 791 ctx | neighborhood:790 |
Rv2313c hyp |
hypothetical protein | 779 | 779 ctx | neighborhood:779 |
Rv1235 lpqY |
trehalose ABC transporter substrate-binding lipoprotein LpqY | 826 | 766 | coexpression:428 experimental:412 |
Rv2471 aglA |
alpha-glucosidase AglA | 441 | 410 |
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: sugar ABC transporter permease UspA
- MTBC0 PGAP product: sugar ABC transporter permease
- Pfam (hmmscan --cut_ga): BPD_transp_1 PF00528.28 (E=1e-18)
- (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_216832.1)
- 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 P71896 (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
uspB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002464|Rv2316|uspA MRDAPRRRTALAYALLAPSLVGVVAFLLLPILVVVWLSLHRWDLLGPLRYVGLTNWRSVLTDSGFADSLVVTAVFVAIVVPAQTVLGLLAASLLARRLPGTGLFRTLYVLPWICAPLAIAVMWRWILAPTDGAISTVLGHRIEWLTDPGLALPVVSAVVVWTNVGYVSLFFLAGLMAIPQDIHNAARTDGASAWQRFWRITLPMLRPTMFFVLVTGIISAAQVFDTVYALTGGGPQGSTDLVAHRIYAEAFGAAAIGRASVMAVVLFVILVGATVVQHLYFRRRISYELT