ugpB Family assigned · medium auto-curated
H37Rv Rv2833c · MTBC0 mtbc0_003012 ·
436 aa · 3159840–3161150 (-) ·
RefSeq NP_217349.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sn-glycerol-3-phosphate ABC transporter substrate-binding lipoprotein UgpB |
|---|---|
| MTBC0 PGAP re-annotation | ABC transporter substrate-binding protein |
| Revised (this work) | 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 |
P71619
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable Sn-glycerol-3-phosphate-binding lipoprotein UgpB |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | ugpB |
| eggNOG description | Bacterial extracellular solute-binding protein |
| Orthologous group | COG1653 |
| KEGG orthology |
K05813
|
| 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 | 1.285 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 14 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.64% of strains (928) · clonal |
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 | 2.3e-38 | 50–335 | Bacterial extracellular solute-binding protein |
SBP_bac_8 | PF13416.12 | 7.6e-40 | 59–356 | Bacterial extracellular solute-binding protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ugpE (sn-glycerol-3-phosphate ABC transporter permease UgpE), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2834c ugpE |
sn-glycerol-3-phosphate ABC transporter permease UgpE | 999 | 999 ctx | neighborhood:882 cooccurence:763 coexpression:729 experimental:412 database:800 |
Rv2835c ugpA |
sn-glycerol-3-phosphate ABC transporter permease UgpA | 999 | 998 ctx | neighborhood:882 cooccurence:769 coexpression:498 experimental:412 database:800 textmining:817 |
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 999 | 996 ctx | neighborhood:882 coexpression:580 experimental:469 database:800 textmining:825 |
Rv1237 sugB |
sugar ABC transporter permease SugB | 976 | 961 | coexpression:446 experimental:914 textmining:424 |
Rv1236 sugA |
sugar ABC transporter permease SugA | 934 | 907 | coexpression:428 experimental:788 |
Rv2317 uspB |
sugar ABC transporter permease UspB | 937 | 862 ctx | cooccurence:586 coexpression:448 experimental:412 textmining:565 |
Rv2039c |
sugar ABC transporter permease | 931 | 851 ctx | cooccurence:551 coexpression:451 experimental:412 textmining:561 |
Rv2316 uspA |
sugar ABC transporter permease UspA | 907 | 851 ctx | cooccurence:558 coexpression:440 experimental:412 textmining:403 |
Rv2040c |
sugar ABC transporter permease | 864 | 835 ctx | cooccurence:520 coexpression:431 experimental:412 |
Rv2038c ugpC |
sugar ABC transporter ATP-binding protein | 919 | 800 | coexpression:478 experimental:469 textmining:613 |
Rv2838c rbfA |
ribosome-binding factor RbfA | 782 | 783 ctx | neighborhood:782 |
Rv2839c infB |
translation initiation factor IF-2 | 778 | 773 ctx | neighborhood:773 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 843 | 758 | coexpression:466 experimental:469 |
Rv2837c nrnA |
bifunctional oligoribonuclease/PAP phosphatase NrnA | 743 | 744 ctx | neighborhood:743 |
Rv2836c dinF |
DNA-damage-inducible protein DinF | 668 | 668 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 substrate-binding lipoprotein UgpB
- MTBC0 PGAP product: ABC transporter substrate-binding protein
- Pfam (hmmscan --cut_ga): SBP_bac_1 PF01547.31 (E=2e-38), SBP_bac_8 PF13416.12 (E=8e-40)
- (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_217349.1)
- 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 P71619 (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 —
22 functional partner(s); context anchor
ugpE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003012|Rv2833c|ugpB MDPLNRRQFLALAAAAAGVTAGCAGMGGGGSVKSGSGPIDFWSSHPGQSSAAERELIGRFQDRFPTLSVKLIDAGKDYDEVAQKFNAALIGTDVPDVVLLDDRWWFHFALSGVLTALDDLFGQVGVDTTDYVDSLLADYEFNGRHYAVPYARSTPLFYYNKAAWQQAGLPDRGPQSWSEFDEWGPELQRVVGAGRSAHGWANADLISWTFQGPNWAFGGAYSDKWTLTLTEPATIAAGNFYRNSIHGKGYAAVANDIANEFATGILASAVASTGSLAGITASARFDFGAAPLPTGPDAAPACPTGGAGLAIPAKLSEERKVNALKFIAFVTNPTNTAYFSQQTGYLPVRKSAVDDASERHYLADNPRARVALDQLPHTRTQDYARVFLPGGDRIISAGLESIGLRGADVTKTFTNIQKRLQVILDRQIMRKLAGHG