sugC Family assigned · medium auto-curated
H37Rv Rv1238 · MTBC0 mtbc0_001327 ·
393 aa · 1389128–1390309 (+) ·
RefSeq NP_215754.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sugar ABC transporter ATP-binding protein SugC |
|---|---|
| MTBC0 PGAP re-annotation | trehalose ABC transporter ATP-binding protein SugC |
| Revised (this work) | Trehalose ABC transporter ATP-binding protein SugC. Pfam: ABC_tran (PF00005.34), OB_MalK (PF17912.8). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQI3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Trehalose import ATP-binding protein SugC |
| EC (curated) |
EC 7.5.2.-
|
| 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
|
|---|---|
| Preferred name | sugC |
| eggNOG description | Belongs to the ABC transporter superfamily |
| Orthologous group | COG3842 |
| KEGG orthology |
K10112
|
| KEGG pathways |
map02010
|
| KEGG modules |
M00194, M00196, M00197, M00200, M00201, M00206, M00207, M00491, M00602, M00605, M00606
|
| Gene Ontology (17) |
GO:0006810, GO:0008150, GO:0008643, GO:0009405, GO:0015766, GO:0015771, GO:0015772, GO:0040007, GO:0044110, GO:0044116, GO:0044117, GO:0044403 +5 more
|
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 | 1.31 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 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 | 2.2e-32 | 21–162 | ABC transporter |
OB_MalK | PF17912.8 | 1.6e-11 | 236–287 | MalK OB fold domain |
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:881 cooccurence:771 coexpression:463 experimental:997 database:900 textmining:900 |
Rv1236 sugA |
sugar ABC transporter permease SugA | 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 | 995 ctx | neighborhood:881 cooccurence:477 coexpression:469 experimental:870 textmining:964 |
Rv2316 uspA |
sugar ABC transporter permease UspA | 949 | 932 ctx | cooccurence:767 coexpression:465 experimental:458 |
Rv2040c |
sugar ABC transporter permease | 940 | 932 ctx | cooccurence:771 coexpression:466 experimental:458 |
Rv2835c ugpA |
sn-glycerol-3-phosphate ABC transporter permease UgpA | 934 | 925 ctx | cooccurence:743 coexpression:463 experimental:458 |
Rv2039c |
sugar ABC transporter permease | 948 | 924 ctx | cooccurence:768 coexpression:439 experimental:441 |
Rv2317 uspB |
sugar ABC transporter permease UspB | 947 | 922 ctx | cooccurence:762 coexpression:439 experimental:441 |
Rv2834c ugpE |
sn-glycerol-3-phosphate ABC transporter permease UgpE | 937 | 920 ctx | cooccurence:759 coexpression:436 experimental:441 |
Rv2038c ugpC |
sugar ABC transporter ATP-binding protein | 906 | 905 | database:900 |
Rv1234 |
transmembrane protein | 846 | 846 ctx | neighborhood:845 |
Rv2041c |
sugar ABC transporter substrate-binding lipoprotein | 879 | 833 ctx | cooccurence:444 coexpression:466 experimental:444 |
Rv2833c ugpB |
sn-glycerol-3-phosphate ABC transporter substrate-binding lipoprotein UgpB | 843 | 758 | coexpression:466 experimental:469 |
Rv2318 uspC |
sugar ABC transporter substrate-binding lipoprotein UspC | 887 | 669 | coexpression:469 textmining:675 |
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 584 | 570 | database:540 |
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 SugC
- MTBC0 PGAP product: trehalose ABC transporter ATP-binding protein SugC
- Pfam (hmmscan --cut_ga): ABC_tran PF00005.34 (E=2e-32), OB_MalK PF17912.8 (E=2e-11)
- (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_215754.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC_tran (PF00005.34), OB_MalK (PF17912.8)
- 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 P9WQI3 (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 —
32 functional partner(s); context anchor
sugB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001327|Rv1238|sugC MAEIVLDHVNKSYPDGHTAVRDLNLTIADGEFLILVGPSGCGKTTTLNMIAGLEDISSGELRIAGERVNEKAPKDRDIAMVFQSYALYPHMTVRQNIAFPLTLAKMRKADIAQKVSETAKILDLTNLLDRKPSQLSGGQRQRVAMGRAIVRHPKAFLMDEPLSNLDAKLRVQMRGEIAQLQRRLGTTTVYVTHDQTEAMTLGDRVVVMYGGIAQQIGTPEELYERPANLFVAGFIGSPAMNFFPARLTAIGLTLPFGEVTLAPEVQGVIAAHPKPENVIVGVRPEHIQDAALIDAYQRIRALTFQVKVNLVESLGADKYLYFTTESPAVHSVQLDELAEVEGESALHENQFVARVPAESKVAIGQSVELAFDTARLAVFDADSGANLTIPHRA