lppZ Family assigned · medium auto-curated
H37Rv Rv3006 · MTBC0 mtbc0_003195 ·
373 aa · 3386018–3387139 (+) ·
RefSeq NP_217522.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LppZ |
|---|---|
| MTBC0 PGAP re-annotation | sorbosone dehydrogenase family protein |
| Revised (this work) | Sorbosone dehydrogenase family protein. Pfam: GSDH (PF07995.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y293
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved lipoprotein LppZ |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | lppZ |
| eggNOG description | Glucose / Sorbosone dehydrogenase |
| Orthologous group | COG2133 |
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, 6 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 |
|---|---|---|---|---|
GSDH | PF07995.18 | 4.6e-14 | 86–225 | Glucose / Sorbosone dehydrogenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lprC (lipoprotein LprC), medium confidence from genomic context alone (score 664 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0817c lmeA hyp |
hypothetical protein | 702 | 702 ctx | cooccurence:702 |
Rv1109c hyp |
hypothetical protein | 692 | 693 ctx | cooccurence:678 |
Rv0383c ttfA hyp |
hypothetical protein | 672 | 672 ctx | cooccurence:672 |
Rv2468c hyp |
hypothetical protein | 666 | 667 ctx | cooccurence:656 |
Rv2700 cei hyp |
hypothetical protein | 666 | 666 ctx | cooccurence:666 |
Rv1275 lprC |
lipoprotein LprC | 663 | 664 ctx | cooccurence:659 |
Rv2091c |
membrane protein | 633 | 634 ctx | cooccurence:613 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 710 | 629 ctx | cooccurence:627 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 620 | 620 ctx | cooccurence:618 |
Rv3004 cfp6 |
low molecular weight protein antigen 6 | 613 | 614 ctx | cooccurence:591 |
Rv2672 |
protease | 611 | 611 ctx | cooccurence:598 |
Rv3212 hyp |
hypothetical protein | 610 | 610 ctx | cooccurence:605 |
Rv0431 |
tuberculin-like peptide | 694 | 608 ctx | cooccurence:606 |
Rv3244c lpqB |
lipoprotein LpqB | 607 | 608 ctx | cooccurence:605 |
Rv1274 lprB |
lipoprotein LprB | 604 | 605 ctx | cooccurence:599 |
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: lipoprotein LppZ
- MTBC0 PGAP product: sorbosone dehydrogenase family protein
- Pfam (hmmscan --cut_ga): GSDH PF07995.18 (E=5e-14)
- (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_217522.1)
- Domains: Pfam-A via hmmscan --cut_ga — GSDH (PF07995.18)
- 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
COG2133 - Curated reference: UniProt I6Y293 (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 —
76 functional partner(s); context anchor
lprC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003195|Rv3006|lppZ MWTTRLVRSGLAALCAAVLVSSGCARFNDAQSQPFTTEPELRPQPSSTPPPPPPLPPVPFPKECPAPGVMQGCLESTSGLIMGIDSKTALVAERITGAVEEISISAEPKVKTVIPVDPAGDGGLMDIVLSPTYSQDRLMYAYISTPTDNRVVRVADGDIPKDILTGIPKGAAGNTGALIFTSPTTLVVMTGDAGDPALAADPQSLAGKVLRIEQPTTIGQTPPTTALSGIGSGGGLCIDPVDGSLYVADRTPTADRLQRITKNSEVSTVWTWPDKPGVAGCAAMDGTVLVNLINTKLTVAVRLAPSTGAVTGEPDVVRKDTHAHAWALRMSPDGNVWGATVNKTAGDAEKLDDVVFPLFPQGGGFPRNNDDKT