lpqY Family assigned · medium auto-curated
H37Rv Rv1235 · MTBC0 mtbc0_001324 ·
468 aa · 1385968–1387374 (+) ·
RefSeq NP_215751.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | trehalose ABC transporter substrate-binding lipoprotein LpqY |
|---|---|
| MTBC0 PGAP re-annotation | trehalose ABC transporter substrate-binding protein LpqY |
| Revised (this work) | Trehalose ABC transporter substrate-binding protein LpqY. 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 |
P9WGU9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Trehalose-binding lipoprotein LpqY |
| 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. No binding affinity for maltose. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | lpqY |
| eggNOG description | Extracellular solute-binding protein |
| Orthologous group | COG1653 |
| KEGG orthology |
K02027
|
| KEGG modules |
M00207
|
| 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 | 0.23 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 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 |
|---|---|---|---|---|
SBP_bac_1 | PF01547.31 | 2.0e-33 | 42–373 | Bacterial extracellular solute-binding protein |
SBP_bac_8 | PF13416.12 | 3.6e-16 | 50–404 | Bacterial extracellular solute-binding protein |
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:451 experimental:997 textmining:902 |
Rv1236 sugA |
sugar ABC transporter permease SugA | 999 | 996 ctx | neighborhood:881 cooccurence:772 coexpression:453 experimental:788 textmining:936 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 999 | 995 ctx | neighborhood:881 cooccurence:477 coexpression:469 experimental:870 textmining:964 |
Rv1234 |
transmembrane protein | 855 | 855 ctx | neighborhood:853 |
Rv2316 uspA |
sugar ABC transporter permease UspA | 826 | 766 | coexpression:428 experimental:412 |
Rv2317 uspB |
sugar ABC transporter permease UspB | 831 | 759 | coexpression:445 experimental:412 |
Rv2039c |
sugar ABC transporter permease | 823 | 750 | coexpression:446 experimental:412 |
Rv2040c |
sugar ABC transporter permease | 758 | 744 | coexpression:429 experimental:412 |
Rv2835c ugpA |
sn-glycerol-3-phosphate ABC transporter permease UgpA | 749 | 729 | coexpression:426 experimental:412 |
Rv2834c ugpE |
sn-glycerol-3-phosphate ABC transporter permease UgpE | 774 | 721 | coexpression:444 experimental:412 |
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 857 | 720 | coexpression:465 experimental:469 textmining:513 |
Rv2038c ugpC |
sugar ABC transporter ATP-binding protein | 817 | 720 | coexpression:466 experimental:469 |
Rv1233c hyp |
hypothetical protein | 508 | 509 ctx | neighborhood:502 |
Rv1231c |
membrane protein | 427 | 427 ctx | neighborhood:423 |
Rv1232c hyp |
hypothetical protein | 412 | 411 ctx | neighborhood:404 |
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: trehalose ABC transporter substrate-binding lipoprotein LpqY
- MTBC0 PGAP product: trehalose ABC transporter substrate-binding protein LpqY
- Pfam (hmmscan --cut_ga): SBP_bac_1 PF01547.31 (E=2e-33), SBP_bac_8 PF13416.12 (E=4e-16)
- (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_215751.1)
- 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 P9WGU9 (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 —
19 functional partner(s); context anchor
sugB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001324|Rv1235|lpqY MVMSRGRIPRLGAAVLVALTTAAAACGADSQGLVVSFYTPATDGATFTAIAQRCNQQFGGRFTIAQVSLPRSPNEQRLQLARRLTGNDRTLDVMALDVVWTAEFAEAGWALPLSDDPAGLAENDAVADTLPGPLATAGWNHKLYAAPVTTNTQLLWYRPDLVNSPPTDWNAMIAEAARLHAAGEPSWIAVQANQGEGLVVWFNTLLVSAGGSVLSEDGRHVTLTDTPAHRAATVSALQILKSVATTPGADPSITRTEEGSARLAFEQGKAALEVNWPFVFASMLENAVKGGVPFLPLNRIPQLAGSINDIGTFTPSDEQFRIAYDASQQVFGFAPYPAVAPGQPAKVTIGGLNLAVAKTTRHRAEAFEAVRCLRDQHNQRYVSLEGGLPAVRASLYSDPQFQAKYPMHAIIRQQLTDAAVRPATPVYQALSIRLAAVLSPITEIDPESTADELAAQAQKAIDGMGLLP