ltp3 Family assigned · medium auto-curated
H37Rv Rv3523 · MTBC0 mtbc0_003739 ·
394 aa · 3983206–3984390 (+) ·
RefSeq NP_218040.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipid carrier protein |
|---|---|
| MTBC0 PGAP re-annotation | thiolase domain-containing protein |
| Revised (this work) | Thiolase domain-containing protein. Pfam: Thiolase_C_1 (PF22691.3). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YGD8
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable lipid carrier protein or keto acyl-CoA thiolase Ltp3 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | ltp3 |
| eggNOG description | Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation |
| Orthologous group | COG0183 |
| EC number |
EC 2.3.1.9
|
| KEGG orthology |
K00626
|
| KEGG pathways |
map00071, map00072, map00280, map00310, map00362, map00380, map00620, map00630, map00640, map00650, map00720, map00900, map01100, map01110, map01120, map01130, map01200, map01212, map02020
|
| KEGG modules |
M00088, M00095, M00373, M00374, M00375
|
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) pseudogene candidate
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 4 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 7.00% of strains (10170) · 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 |
|---|---|---|---|---|
Thiolase_C_1 | PF22691.3 | 2.5e-29 | 253–377 | Thiolase C-terminal domain-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ltp4 (lipid transfer protein), high confidence from genomic context alone (score 917 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 |
Rv3521 hyp |
hypothetical protein | 996 | 986 ctx | neighborhood:844 cooccurence:763 coexpression:428 experimental:415 textmining:787 |
Rv1715 fadB3 |
3-hydroxybutyryl-CoA dehydrogenase FadB | 966 | 965 | coexpression:428 experimental:412 database:900 |
Rv0468 fadB2 |
3-hydroxybutyryl-CoA dehydrogenase | 966 | 964 | coexpression:424 experimental:412 database:900 |
Rv3667 acs |
acetyl-CoAsynthetase | 943 | 941 | coexpression:411 database:900 |
Rv0914c |
lipid carrier protein or keto acyl-CoA thiolase | 928 | 928 | database:900 |
Rv2790c ltp1 |
lipid-transfer protein | 929 | 927 | database:900 |
Rv3542c chsH2 hyp |
hypothetical protein | 953 | 924 ctx | cooccurence:740 coexpression:434 experimental:508 textmining:416 |
Rv1837c glcB |
malate synthase | 927 | 924 | database:900 |
Rv3710 leuA |
2-isopropylmalate synthase | 926 | 923 | database:900 |
Rv2503c scoB |
succinyl-CoA:3-ketoacid-CoA transferase subunit B | 926 | 921 | database:900 |
Rv2504c scoA |
succinyl-CoA:3-ketoacid-CoA transferase subunit A | 924 | 920 | database:900 |
Rv3522 ltp4 |
lipid transfer protein | 966 | 917 ctx | neighborhood:861 textmining:618 |
Rv3546 fadA5 |
acetyl-CoA acetyltransferase FadA | 972 | 913 | database:900 textmining:691 |
Rv0753c mmsA |
methylmalonate-semialdehyde dehydrogenase | 914 | 910 | 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 carrier protein
- MTBC0 PGAP product: thiolase domain-containing protein
- Pfam (hmmscan --cut_ga): Thiolase_C_1 PF22691.3 (E=2e-29)
- (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_218040.1)
- Domains: Pfam-A via hmmscan --cut_ga — Thiolase_C_1 (PF22691.3)
- 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 I6YGD8 (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 —
164 functional partner(s); context anchor
ltp4 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003739|Rv3523|ltp3 MAGKLAAVLGTGQTKYVAKRQDVSMNGLVREAIDRALADSGSTFDDIDAVVVGKAPDFFEGVMMPELFMADAMGATGKPLIRVHTAGSVGGSTGVVAASLVQSGKYRRVLALAWEKQSESNAMWALSIPVPFTKPVGAGAGGYFAPHVRAYIRRSGAPAHIGAMVAVKDRLNGSRNPLAHLQQPDITLEKVMASQMLWDPIRFDETCPSSDGACAVVVGDEEIADARLAQGHPVAWIHGTALRTEPLAFAGRDQVNPQAGRDAAAALWKAAGITSPIDEIDAAEIYVPFSWFEPMWLENLGFAREGEGWKLTEAGETAIGGRLPVNPSGGVLSANPIGASGLIRFAEAAIQVMGKAEARQVPGARKALGHAYGGGSQYFSMWVVGCEKPKQAAA