ltp1 Resolved · high auto-curated
H37Rv Rv2790c · MTBC0 mtbc0_002969 ·
401 aa · 3121379–3122584 (-) ·
RefSeq NP_217306.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipid-transfer protein |
|---|---|
| MTBC0 PGAP re-annotation | lipid-transfer protein |
| Revised (this work) | Lipid-transfer protein. Pfam: Thiolase_N (PF00108.30), Thiolase_C_1 (PF22691.3), Thiolase_C (PF02803.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33332
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | propanoyl-CoA C-acyltransferase |
| EC (curated) |
EC 2.3.1.176
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | ltp1 |
| eggNOG description | Belongs to the thiolase family |
| Orthologous group | COG0183 |
| EC number |
EC 2.3.1.16
|
| KEGG orthology |
K00632
|
| KEGG pathways |
map00071, map00280, map00281, map00362, map00592, map00642, map01100, map01110, map01120, map01130, map01212
|
| KEGG modules |
M00087, M00113
|
| Gene Ontology (71) |
GO:0003674, GO:0003676, GO:0003723, GO:0003729, GO:0003824, GO:0003988, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005739 +59 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 | 0.053 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 12 synonymous, 2 missense, 0 nonsense, 7 frameshift |
| Disruption | 7 distinct premature-stop/frameshift site(s); most common in 0.87% of strains (1270) · convergent |
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 |
|---|---|---|---|---|
Thiolase_N | PF00108.30 | 3.0e-22 | 10–234 | Thiolase, N-terminal domain |
Thiolase_C_1 | PF22691.3 | 7.4e-33 | 269–391 | Thiolase C-terminal domain-like |
Thiolase_C | PF02803.25 | 4.3e-09 | 275–373 | Thiolase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE21 (acyl-CoA dehydrogenase FadE21), high confidence from genomic context alone (score 977 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0860 fadB |
fatty oxidation protein FadB | 996 | 996 | coexpression:696 experimental:804 database:942 |
Rv2789c fadE21 |
acyl-CoA dehydrogenase FadE21 | 977 | 977 ctx | neighborhood:847 coexpression:839 |
Rv0231 fadE4 |
acyl-CoA dehydrogenase FadE4 | 953 | 951 | database:900 |
Rv3140 fadE23 |
acyl-CoA dehydrogenase FadE23 | 945 | 942 | database:900 |
Rv0400c fadE7 |
acyl-CoA dehydrogenase FadE7 | 943 | 942 | database:900 |
Rv0154c fadE2 |
acyl-CoA dehydrogenase FadE2 | 943 | 942 | database:900 |
Rv0975c fadE13 |
acyl-CoA dehydrogenase FadE13 | 943 | 941 | database:900 |
Rv0131c fadE1 |
acyl-CoA dehydrogenase FadE1 | 943 | 941 | database:900 |
Rv3280 accD5 |
propionyl-CoA carboxylase subunit beta | 931 | 928 | database:900 |
Rv2247 accD6 |
acetyl-/propionyl-CoA carboxylase subunit beta | 930 | 927 | database:900 |
Rv3523 ltp3 |
lipid carrier protein | 929 | 927 | database:900 |
Rv0914c |
lipid carrier protein or keto acyl-CoA thiolase | 926 | 927 | database:900 |
Rv2501c accA1 |
acetyl/propionyl-CoA carboxylase subuit alpha | 928 | 925 | database:900 |
Rv0973c accA2 |
acetyl/propionyl-CoA carboxylase subuit alpha | 928 | 925 | database:900 |
Rv3285 accA3 |
bifunctional protein acetyl-/propionyl-CoA carboxylase subunit alpha AccA | 928 | 925 | database:900 |
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: lipid-transfer protein
- MTBC0 PGAP product: lipid-transfer protein
- Pfam (hmmscan --cut_ga): Thiolase_N PF00108.30 (E=3e-22), Thiolase_C_1 PF22691.3 (E=7e-33), Thiolase_C PF02803.25 (E=4e-09)
- (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_217306.3)
- Domains: Pfam-A via hmmscan --cut_ga — Thiolase_N (PF00108.30), Thiolase_C_1 (PF22691.3), Thiolase_C (PF02803.25)
- 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
COG0183 - Curated reference: UniProt O33332 (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 —
153 functional partner(s); context anchor
fadE21 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002969|Rv2790c|ltp1 MPNQGSSNKVYVIGVGMTKFEKPGRREGWDYPDMARESGTKALRDAGIDYREVEQGYVGYVYGESTSGQRALYELGMTGIPIVNVNNNCSTGSTALYLGAQAIRGGLADCVLALGFEKMQPGALGGGADDRESPLGRHVKALAEIDEFGFPVAPWMFGAAGREHMKKYGTTAEHFAKIGYKNHKHSVNNPYAQFQDEYTLDDILASKMISDPLTKLQCSPTSDGSAAVVLASEDYLANHNLAGRAVEIVGQAMTTDFASTFDGSARNIIGYDMTVQAAQRVYQQSGLGPKDFGVIELHDCFSANELLLYEALGLCGPGEAPELIDDNQTTYGGRWVVNPSGGLISKGHPLGATGLAQCAELTWQLRGTAEARQVDNVTAALQHNIGLGGAAVVTAYQRAER