uspC Family assigned · medium auto-curated
H37Rv Rv2318 · MTBC0 mtbc0_002466 ·
440 aa · 2615267–2616589 (+) ·
RefSeq NP_216834.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sugar ABC transporter substrate-binding lipoprotein UspC |
|---|---|
| MTBC0 PGAP re-annotation | sugar ABC transporter substrate-binding protein |
| Revised (this work) | Sugar ABC transporter substrate-binding protein. Pfam: SBP_bac_1 (PF01547.31), SBP_bac_8 (PF13416.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71894
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable periplasmic sugar-binding lipoprotein UspC |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | uspC |
| eggNOG description | Bacterial extracellular solute-binding protein |
| Orthologous group | COG1653 |
| KEGG orthology |
K02027
|
| 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 | 0.482 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 7 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 |
|---|---|---|---|---|
SBP_bac_1 | PF01547.31 | 3.3e-39 | 51–351 | Bacterial extracellular solute-binding protein |
SBP_bac_8 | PF13416.12 | 8.2e-23 | 58–368 | Bacterial extracellular solute-binding protein |
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 987 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2317 uspB |
sugar ABC transporter permease UspB | 997 | 987 ctx | neighborhood:882 cooccurence:615 coexpression:559 experimental:412 textmining:806 |
Rv2316 uspA |
sugar ABC transporter permease UspA | 998 | 982 ctx | neighborhood:882 cooccurence:589 coexpression:457 experimental:412 textmining:910 |
Rv2315c hyp |
hypothetical protein | 790 | 791 ctx | neighborhood:790 |
Rv2314c hyp |
hypothetical protein | 789 | 790 ctx | neighborhood:790 |
Rv2039c |
sugar ABC transporter permease | 924 | 786 | coexpression:449 experimental:412 textmining:664 |
Rv2040c |
sugar ABC transporter permease | 812 | 763 | coexpression:430 experimental:412 |
Rv2835c ugpA |
sn-glycerol-3-phosphate ABC transporter permease UgpA | 914 | 752 | coexpression:430 experimental:412 textmining:670 |
Rv2834c ugpE |
sn-glycerol-3-phosphate ABC transporter permease UgpE | 844 | 738 | coexpression:449 experimental:412 textmining:430 |
Rv2313c hyp |
hypothetical protein | 719 | 720 ctx | neighborhood:719 |
Rv1236 sugA |
sugar ABC transporter permease SugA | 916 | 694 | coexpression:432 experimental:412 textmining:739 |
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 936 | 673 | coexpression:476 textmining:814 |
Rv1237 sugB |
sugar ABC transporter permease SugB | 825 | 673 | coexpression:449 experimental:412 textmining:487 |
Rv2038c ugpC |
sugar ABC transporter ATP-binding protein | 879 | 670 | coexpression:471 textmining:650 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 887 | 669 | coexpression:469 textmining:675 |
Rv1510 hyp |
hypothetical protein | 549 | 533 ctx | cooccurence:530 |
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 substrate-binding lipoprotein UspC
- MTBC0 PGAP product: sugar ABC transporter substrate-binding protein
- Pfam (hmmscan --cut_ga): SBP_bac_1 PF01547.31 (E=3e-39), SBP_bac_8 PF13416.12 (E=8e-23)
- (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_216834.1)
- Domains: Pfam-A via hmmscan --cut_ga — SBP_bac_1 (PF01547.31), SBP_bac_8 (PF13416.12)
- 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
COG1653 - Curated reference: UniProt P71894 (TrEMBL, unreviewed; 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 —
21 functional partner(s); context anchor
uspB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002466|Rv2318|uspC MTRPRQSTLVATALVLVAILLGVTAVLLGLSAEPRGGKIVVTVRLWDEPIAAAYRQSFAAFTRSHPDIEVRTNLVAYSTYFETLRTDVAGGSADDIFWLSNAYFAAYADSGRLMKIQTDAADWEPAVVDQFTRSGVLWGVPQLTDAGIAVFYNADLLAAAGVDPTQVDNLRWSRGDDDTLRPMLARLTVDADGRTANTPGFDARRVRQWGYNAANDPQAIYLNYIGSAGGVFQRDGKFAFDNPGAIEAFRYLVGLINDDHVAPPASDTNDNGDFSRNQFLAGKMALFQSGTYSLAPVARDALFHWGVAMLPAGPAGRVSVTNGIAAAGNSASKHPDAVRQVLAWMGSTEGNSYLGRHGAAIPAVLSAQPVYFDYWSARGVDVTPFFAVLNGPRIAAPGGAGFAAGQQALEPYFDEMFLGRGDVTTTLRQAQAAANAATQR