ugpC Family assigned · medium auto-curated
H37Rv Rv2038c · MTBC0 mtbc0_002171 ·
357 aa · 2312336–2313409 (-) ·
RefSeq NP_216554.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sugar ABC transporter ATP-binding protein |
|---|---|
| MTBC0 PGAP re-annotation | sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC |
| Revised (this work) | Sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC. Pfam: ABC_tran (PF00005.34), OB_MalK (PF17912.8), TOBE_2 (PF08402.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53482
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Trehalose import ATP-binding protein SugC |
| 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. Responsible for energy coupling to the transport system. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | ABC transporter |
| Orthologous group | COG3842 |
| KEGG orthology |
K10112
|
| KEGG pathways |
map02010
|
| KEGG modules |
M00194, M00196, M00197, M00200, M00201, M00206, M00207, M00491, M00602, M00605, M00606
|
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 | 0.695 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 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 |
|---|---|---|---|---|
ABC_tran | PF00005.34 | 1.0e-30 | 21–163 | ABC transporter |
OB_MalK | PF17912.8 | 1.5e-07 | 237–282 | MalK OB fold domain |
TOBE_2 | PF08402.17 | 2.2e-07 | 275–348 | TOBE domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2039c (sugar ABC transporter permease), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2039c |
sugar ABC transporter permease | 999 | 1000 ctx | neighborhood:882 cooccurence:769 coexpression:890 experimental:441 database:900 textmining:829 |
Rv2040c |
sugar ABC transporter permease | 999 | 1000 ctx | neighborhood:801 cooccurence:772 coexpression:878 experimental:458 database:900 textmining:699 |
Rv2041c |
sugar ABC transporter substrate-binding lipoprotein | 998 | 992 ctx | neighborhood:800 cooccurence:570 coexpression:861 experimental:444 textmining:828 |
Rv1237 sugB |
sugar ABC transporter permease SugB | 981 | 979 ctx | cooccurence:739 coexpression:441 experimental:858 |
Rv1236 sugA |
sugar ABC transporter permease SugA | 981 | 967 ctx | cooccurence:710 coexpression:466 experimental:788 textmining:457 |
Rv2835c ugpA |
sn-glycerol-3-phosphate ABC transporter permease UgpA | 977 | 933 ctx | cooccurence:753 coexpression:479 experimental:458 textmining:679 |
Rv2316 uspA |
sugar ABC transporter permease UspA | 957 | 932 ctx | cooccurence:767 coexpression:466 experimental:458 textmining:404 |
Rv2834c ugpE |
sn-glycerol-3-phosphate ABC transporter permease UgpE | 954 | 929 ctx | cooccurence:762 coexpression:443 experimental:441 |
Rv2317 uspB |
sugar ABC transporter permease UspB | 967 | 925 ctx | cooccurence:764 coexpression:438 experimental:441 textmining:580 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 906 | 905 | database:900 |
Rv2037c |
transmembrane protein | 807 | 806 ctx | neighborhood:801 |
Rv2833c ugpB |
sn-glycerol-3-phosphate ABC transporter substrate-binding lipoprotein UgpB | 919 | 800 | coexpression:478 experimental:469 textmining:613 |
Rv1235 lpqY |
trehalose ABC transporter substrate-binding lipoprotein LpqY | 817 | 720 | coexpression:466 experimental:469 |
Rv2042c hyp |
hypothetical protein | 671 | 672 ctx | neighborhood:666 |
Rv2318 uspC |
sugar ABC transporter substrate-binding lipoprotein UspC | 879 | 670 | coexpression:471 textmining:650 |
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 ATP-binding protein
- MTBC0 PGAP product: sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
- Pfam (hmmscan --cut_ga): ABC_tran PF00005.34 (E=1e-30), OB_MalK PF17912.8 (E=1e-07), TOBE_2 PF08402.17 (E=2e-07)
- (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_216554.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC_tran (PF00005.34), OB_MalK (PF17912.8), TOBE_2 (PF08402.17)
- 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
COG3842 - Curated reference: UniProt O53482 (TrEMBL, unreviewed; Predicted)
- 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 —
29 functional partner(s); context anchor
Rv2039c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002171|Rv2038c|ugpC MASVSFEQATRRYPGTDRPALDRLDLIVGDGEFVVLVGPSGCGKTTSLRMVAGLETLDCGRIRIGERDVTEVDPKDRDVAMVFQNYALYPHMTVAQNMGFALKVAKIGKAEIRERVLAAAKLLDLQSYLDRKPKDLSGGQRQRVAMGRAIVRRPQVFLMDEPLSNLDAKLRGQTRNQIAALQRQLGTTTVYVTHDQVEAMTMGDRVAVLSDGVLQQCASPRELYRNPGNVFVAGFIGSPAMNLFRLSIADSTVSLGDWQILLPRAVVGTAAEVIIGVRPEHLELGGAGIEMDVDMVEELGADAYLYGRIVSGGCEMDQSIVARVDGRGPPERGSRVRLCPTPGHLHFFAVDGRRIPG