lipB Resolved · high auto-curated
H37Rv Rv2217 · MTBC0 mtbc0_002353 ·
230 aa · 2510741–2511433 (+) ·
RefSeq NP_216733.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | octanoyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | lipoyl(octanoyl) transferase LipB |
| Revised (this work) | Lipoyl(octanoyl) transferase LipB. Pfam: LplA-B_cat (PF21948.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK83
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Octanoyltransferase |
| EC (curated) |
EC 2.3.1.181
|
| Curated function | Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | lipB |
| eggNOG description | Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate |
| Orthologous group | COG0321 |
| EC number |
EC 2.3.1.181
|
| KEGG orthology |
K03801
|
| KEGG pathways |
map00785, map01100
|
| Gene Ontology (63) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0006082, GO:0006464, GO:0006629, GO:0006631, GO:0006633, GO:0006732, GO:0006790 +51 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 | 0.787 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
LplA-B_cat | PF21948.2 | 1.4e-45 | 21–206 | Lipoyl protein ligase A/B catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lipA (lipoyl synthase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2218 lipA |
lipoyl synthase | 999 | 1000 ctx | neighborhood:882 fusion:900 cooccurence:762 database:900 textmining:892 |
Rv2215 dlaT |
pyruvate dehydrogenase E2 component dihydrolipoamide acyltransferase | 943 | 916 ctx | neighborhood:808 cooccurence:505 |
Rv1826 gcvH |
glycine cleavage system protein H | 954 | 891 | database:844 textmining:596 |
Rv2219 |
transmembrane protein | 846 | 847 ctx | neighborhood:843 |
Rv2524c fas |
fatty acid synthase | 847 | 827 | database:800 |
Rv2216 |
epimerase family protein | 871 | 817 ctx | neighborhood:808 |
Rv2946c pks1 |
polyketide synthase | 710 | 667 | database:574 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 707 | 663 | database:574 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 707 | 663 | database:574 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 706 | 663 | database:574 |
Rv1527c pks5 |
polyketide synthase | 706 | 662 | database:574 |
Rv2048c pks12 |
polyketide synthase | 706 | 662 | database:574 |
Rv1181 pks4 |
polyketide beta-ketoacyl synthase | 686 | 650 | database:574 |
Rv1661 pks7 |
polyketide synthase | 685 | 649 | database:574 |
Rv2932 ppsB |
phthiocerol synthesis polyketide synthase type I PpsB | 678 | 645 | database:574 |
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: octanoyltransferase
- MTBC0 PGAP product: lipoyl(octanoyl) transferase LipB
- Pfam (hmmscan --cut_ga): LplA-B_cat PF21948.2 (E=1e-45)
- (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_216733.1)
- Domains: Pfam-A via hmmscan --cut_ga — LplA-B_cat (PF21948.2)
- 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
COG0321 - Curated reference: UniProt P9WK83 (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 —
46 functional partner(s); context anchor
lipA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002353|Rv2217|lipB MTGSIRSKLSAIDVRQLGTVDYRTAWQLQRELADARVAGGADTLLLLEHPAVYTAGRRTETHERPIDGTPVVDTDRGGKITWHGPGQLVGYPIIGLAEPLDVVNYVRRLEESLIQVCADLGLHAGRVDGRSGVWLPGRPARKVAAIGVRVSRATTLHGFALNCDCDLAAFTAIVPCGISDAAVTSLSAELGRTVTVDEVRATVAAAVCAALDGVLPVGDRVPSHAVPSPL