ltp4 Family assigned · low auto-curated
H37Rv Rv3522 · MTBC0 mtbc0_003738 ·
354 aa · 3982125–3983189 (+) ·
RefSeq NP_218039.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipid transfer protein |
|---|---|
| MTBC0 PGAP re-annotation | thiolase domain-containing protein |
| Revised (this work) | Thiolase domain-containing protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53567
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible lipid transfer protein or keto acyl-CoA thiolase Ltp4 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | ltp4 |
| eggNOG description | lipid-transfer protein |
| Orthologous group | COG0183 |
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 | 0.211 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ltp3 (lipid carrier protein), high confidence from genomic context alone (score 917 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3521 hyp |
hypothetical protein | 996 | 989 ctx | neighborhood:863 cooccurence:774 coexpression:453 experimental:415 textmining:705 |
Rv0860 fadB |
fatty oxidation protein FadB | 967 | 966 | coexpression:697 experimental:804 database:447 |
Rv3542c chsH2 hyp |
hypothetical protein | 940 | 920 ctx | cooccurence:770 coexpression:438 experimental:415 |
Rv3523 ltp3 |
lipid carrier protein | 966 | 917 ctx | neighborhood:861 textmining:618 |
Rv3550 echA20 |
enoyl-CoA hydratase EchA20 | 928 | 909 ctx | cooccurence:649 database:447 |
Rv3541c chsH1 hyp |
hypothetical protein | 885 | 860 ctx | cooccurence:773 |
Rv3504 fadE26 |
acyl-CoA dehydrogenase FadE26 | 894 | 843 ctx | cooccurence:733 |
Rv3516 echA19 |
enoyl-CoA hydratase EchA19 | 970 | 840 | database:447 textmining:826 |
Rv3543c fadE29 |
acyl-CoA dehydrogenase FadE29 | 968 | 838 ctx | cooccurence:721 textmining:815 |
Rv3573c fadE34 |
acyl-CoA dehydrogenase FadE34 | 901 | 826 ctx | cooccurence:704 textmining:456 |
Rv3552 |
CoA-transferase subunit beta | 824 | 816 ctx | cooccurence:761 |
Rv3520c |
coenzyme F420-dependent oxidoreductase | 943 | 815 ctx | neighborhood:760 textmining:705 |
Rv3551 |
CoA-transferase subunit alpha | 815 | 807 ctx | cooccurence:755 |
Rv3562 fadE31 |
acyl-CoA dehydrogenase FadE31 | 834 | 802 ctx | cooccurence:664 |
Rv3544c fadE28 |
acyl-CoA dehydrogenase FadE28 | 897 | 789 ctx | cooccurence:642 textmining:535 |
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: thiolase domain-containing protein
- (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_218039.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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 O53567 (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 —
150 functional partner(s); context anchor
ltp3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003738|Rv3522|ltp4 MSVRDIAVVGFAHAPHVRRTDGTTNGVEMLMPCFAQLYDELGITKADIGFWCSGSSDYLAGRAFSFISAIDSIGAVPPINESHVEMDAAWALYEAYIKLLTGEVDTALVYGFGKSSAGTLRRVLSRQTDPYTVAPLWPDSVSMAGLQARLGLDSGKWTHEQMARVAFDSFTNARRVDSVEPPITVGELLARPFFADPLRRHDIAPITDGAAAVVLAADNRARELRENPAWITGIEHRIESPALGARDITESPSTKLAAKIATGGHTGDIDVAEIHGPFTHQHLIVAEAIRIPGKTKVNPSGGPLAANPMFAAGLERIGFAAQHIWDGSARRVLAHATSGPALQQNLVAVMEGRG