sugA Family assigned · medium auto-curated
H37Rv Rv1236 · MTBC0 mtbc0_001325 ·
307 aa · 1387371–1388294 (+) ·
RefSeq NP_215752.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sugar ABC transporter permease SugA |
|---|---|
| MTBC0 PGAP re-annotation | trehalose ABC transporter permease SugA |
| Revised (this work) | Trehalose ABC transporter permease SugA. 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 |
P9WG03
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Trehalose transport system permease protein SugA |
| Curated function | Part of the ABC transporter complex LpqY-SugA-SugB-SugC, which is highly specific for uptake of trehalose. Involved in the recycling of extracellular trehalose released from trehalose-containing molecules synthesized by M.tuberculosis. Trehalose uptake is essential for virulence. Probably responsible for the translocation of the substrate across the membrane. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | sugA |
| eggNOG description | ABC transporter |
| Orthologous group | COG1175 |
| KEGG orthology |
K02025
|
| KEGG modules |
M00207
|
| Gene Ontology (8) |
GO:0008150, GO:0040007, GO:0044110, GO:0044116, GO:0044117, GO:0044403, GO:0044419, GO:0051704
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 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 | 3.9e-12 | 166–295 | Binding-protein-dependent transport system inner membrane component |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sugB (sugar ABC transporter permease SugB), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1237 sugB |
sugar ABC transporter permease SugB | 999 | 1000 ctx | neighborhood:882 cooccurence:774 coexpression:557 experimental:932 database:900 textmining:977 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 999 | 1000 ctx | neighborhood:881 cooccurence:769 coexpression:476 experimental:788 database:900 textmining:949 |
Rv1235 lpqY |
trehalose ABC transporter substrate-binding lipoprotein LpqY | 999 | 996 ctx | neighborhood:881 cooccurence:772 coexpression:453 experimental:788 textmining:936 |
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 985 | 968 ctx | cooccurence:719 coexpression:466 experimental:788 textmining:557 |
Rv2038c ugpC |
sugar ABC transporter ATP-binding protein | 981 | 967 ctx | cooccurence:710 coexpression:466 experimental:788 textmining:457 |
Rv2041c |
sugar ABC transporter substrate-binding lipoprotein | 948 | 930 ctx | cooccurence:431 coexpression:430 experimental:788 |
Rv2039c |
sugar ABC transporter permease | 956 | 926 ctx | cooccurence:765 coexpression:481 experimental:412 textmining:439 |
Rv2317 uspB |
sugar ABC transporter permease UspB | 957 | 925 ctx | cooccurence:760 coexpression:484 experimental:412 textmining:453 |
Rv2834c ugpE |
sn-glycerol-3-phosphate ABC transporter permease UgpE | 971 | 922 ctx | cooccurence:751 coexpression:481 experimental:412 textmining:651 |
Rv2833c ugpB |
sn-glycerol-3-phosphate ABC transporter substrate-binding lipoprotein UgpB | 934 | 907 | coexpression:428 experimental:788 |
Rv1234 |
transmembrane protein | 850 | 849 ctx | neighborhood:847 |
Rv2318 uspC |
sugar ABC transporter substrate-binding lipoprotein UspC | 916 | 694 | coexpression:432 experimental:412 textmining:739 |
Rv2471 aglA |
alpha-glucosidase AglA | 581 | 536 | |
Rv0126 treS |
trehalose synthase/amylase TreS | 656 | 513 | |
Rv1233c hyp |
hypothetical protein | 510 | 511 ctx | neighborhood:502 |
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 SugA
- MTBC0 PGAP product: trehalose ABC transporter permease SugA
- Pfam (hmmscan --cut_ga): BPD_transp_1 PF00528.28 (E=4e-12)
- (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_215752.1)
- 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 P9WG03 (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 —
23 functional partner(s); context anchor
sugB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001325|Rv1236|sugA MTSVEQRTATAVFSRTGSRMAERRLAFMLVAPAAMLMVAVTAYPIGYALWLSLQRNNLATPNDTAFIGLGNYHTILIDRYWWTALAVTLAITAVSVTIEFVLGLALALVMHRTLIGKGLVRTAVLIPYGIVTVVASYSWYYAWTPGTGYLANLLPYDSAPLTQQIPSLGIVVIAEVWKTTPFMSLLLLAGLALVPEDLLRAAQVDGASAWRRLTKVILPMIKPAIVVALLFRTLDAFRIFDNIYVLTGGSNNTGSVSILGYDNLFKGFNVGLGSAISVLIFGCVAVIAFIFIKLFGAAAPGGEPSGR