ugpE Family assigned · medium auto-curated
H37Rv Rv2834c · MTBC0 mtbc0_003013 ·
275 aa · 3161153–3161980 (-) ·
RefSeq NP_217350.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sn-glycerol-3-phosphate ABC transporter permease UgpE |
|---|---|
| MTBC0 PGAP re-annotation | carbohydrate ABC transporter permease |
| Revised (this work) | Carbohydrate 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 |
I6Y1U3
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable Sn-glycerol-3-phosphate transport integral membrane protein ABC transporter UgpE |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | ugpE |
| eggNOG description | Binding-protein-dependent transport system inner membrane component |
| Orthologous group | COG0395 |
| KEGG orthology |
K05815
|
| KEGG pathways |
map02010
|
| KEGG modules |
M00198
|
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, 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 |
|---|---|---|---|---|
BPD_transp_1 | PF00528.28 | 7.6e-15 | 86–264 | Binding-protein-dependent transport system inner membrane component |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ugpC (sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 999 | 999 ctx | neighborhood:882 cooccurence:767 coexpression:628 experimental:441 database:900 textmining:574 |
Rv2835c ugpA |
sn-glycerol-3-phosphate ABC transporter permease UgpA | 999 | 999 ctx | neighborhood:882 cooccurence:774 coexpression:602 experimental:412 database:900 textmining:930 |
Rv2833c ugpB |
sn-glycerol-3-phosphate ABC transporter substrate-binding lipoprotein UgpB | 999 | 999 ctx | neighborhood:882 cooccurence:763 coexpression:729 experimental:412 database:800 |
Rv2040c |
sugar ABC transporter permease | 987 | 930 ctx | cooccurence:774 coexpression:486 experimental:412 textmining:830 |
Rv2316 uspA |
sugar ABC transporter permease UspA | 976 | 930 ctx | cooccurence:774 coexpression:482 experimental:412 textmining:673 |
Rv2038c ugpC |
sugar ABC transporter ATP-binding protein | 954 | 929 ctx | cooccurence:762 coexpression:443 experimental:441 |
Rv1236 sugA |
sugar ABC transporter permease SugA | 971 | 922 ctx | cooccurence:751 coexpression:481 experimental:412 textmining:651 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 937 | 920 ctx | cooccurence:759 coexpression:436 experimental:441 |
Rv2041c |
sugar ABC transporter substrate-binding lipoprotein | 929 | 900 ctx | cooccurence:693 coexpression:449 experimental:412 |
Rv2838c rbfA |
ribosome-binding factor RbfA | 782 | 783 ctx | neighborhood:782 |
Rv2839c infB |
translation initiation factor IF-2 | 773 | 773 ctx | neighborhood:773 |
Rv2837c nrnA |
bifunctional oligoribonuclease/PAP phosphatase NrnA | 744 | 744 ctx | neighborhood:743 |
Rv2318 uspC |
sugar ABC transporter substrate-binding lipoprotein UspC | 844 | 738 | coexpression:449 experimental:412 textmining:430 |
Rv1235 lpqY |
trehalose ABC transporter substrate-binding lipoprotein LpqY | 774 | 721 | coexpression:444 experimental:412 |
Rv2836c dinF |
DNA-damage-inducible protein DinF | 673 | 674 ctx | neighborhood:668 |
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: sn-glycerol-3-phosphate ABC transporter permease UgpE
- MTBC0 PGAP product: carbohydrate ABC transporter permease
- Pfam (hmmscan --cut_ga): BPD_transp_1 PF00528.28 (E=8e-15)
- (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_217350.1)
- 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
COG0395 - Curated reference: UniProt I6Y1U3 (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 —
18 functional partner(s); context anchor
ugpC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003013|Rv2834c|ugpE MTPDRLRSSVGYAAMLLVVTLIAGPLLFVFFTSFKDQPDIYAQPTSWWPLRWYPQNYRTATEQIPFWTFLRNSLIITSVLAVVKFTLGVLSAFGLVFVRFPGRTAVFLVIIAALMVPNQITVISNYALISHLGLRNTFAGIILPLAGVAFGTFLMRNHFLSLPAEIIEAARMDGARWWQLLLRVVLPMSRPTMVAVGVITVVNEWNEYLWPFLMSDDESVAPLPIGLTFLQQAEGVTNWGPVMAVTLLAMLPILLVFIALQRQMIKGLTSGAVKG