fadD18 Resolved · high auto-curated
H37Rv Rv3513c · MTBC0 - ·
218 aa · 3945092–3945748 (-) ·
RefSeq NP_218030.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | fatty-acid--CoA ligase FadD18 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Fatty-acid--CoA ligase FadD18. Pfam: AMP-binding_C (PF13193.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
I6YGC8
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable fatty-acid-CoA ligase FadD18 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | fadD19 |
| eggNOG description | COG0318 Acyl-CoA synthetases (AMP-forming) AMP-acid ligases II |
| Orthologous group | COG0318 |
| EC number |
EC 6.2.1.42
|
| KEGG orthology |
K18688
|
| Gene Ontology (17) |
GO:0003674, GO:0005488, GO:0005515, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005777, GO:0042579, GO:0043226, GO:0043227, GO:0043229 +5 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 | 0.49 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 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 |
|---|---|---|---|---|
AMP-binding_C | PF13193.13 | 2.4e-16 | 116–191 | AMP-binding enzyme C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadD22 (p-hydroxybenzoyl--AMP ligase), high confidence from genomic context alone (score 769 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2948c fadD22 |
p-hydroxybenzoyl--AMP ligase | 769 | 769 ctx | cooccurence:769 |
Rv0099 fadD10 |
fatty-acid--CoA ligase FadD10 | 767 | 767 ctx | cooccurence:767 |
Rv3506 fadD17 |
long-chain-fatty-acid--CoA ligase FadD17 | 853 | 765 ctx | cooccurence:764 textmining:402 |
Rv1750c fadD1 |
fatty-acid--CoA ligase FadD1 | 774 | 761 ctx | cooccurence:760 |
Rv0719 rplF |
50S ribosomal protein L6 | 695 | 695 | experimental:402 database:510 |
Rv1527c pks5 |
polyketide synthase | 782 | 681 | |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 705 | 680 | |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 705 | 680 | |
Rv2048c pks12 |
polyketide synthase | 705 | 680 | |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 704 | 679 | |
Rv3800c pks13 |
polyketide synthase | 670 | 637 | |
Rv2380c mbtE |
peptide synthetase | 651 | 636 | experimental:465 |
Rv2946c pks1 |
polyketide synthase | 663 | 631 | |
Rv1661 pks7 |
polyketide synthase | 631 | 610 | |
Rv2932 ppsB |
phthiocerol synthesis polyketide synthase type I PpsB | 628 | 606 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): fatty-acid--CoA ligase FadD18
- Pfam (hmmscan --cut_ga): AMP-binding_C PF13193.13 (E=2e-16)
- (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_218030.1)
- Domains: Pfam-A via hmmscan --cut_ga — AMP-binding_C (PF13193.13)
- 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
COG0318 - Curated reference: UniProt I6YGC8 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
86 functional partner(s); context anchor
fadD22 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3513c|fadD18 MAASLSENLSCHSSNMCRLSGNAATNLERPGEEPPGDRCTRRQAVRPARTLAKKGNIPVGYYKDEKKTAETFRTINGVRYAIPGDYAQVEEDGTVTMLGRGSVSINSGGEKVYPEEVEAALKGHPDVFDALVVGVPDPRYGQQVAAVVQARPGCRPSLAELDSFVRSEIAGYKVPRSLWFVDEVKRSPAGKPDYRWAKEQTEARPADDVHAGHVTSGS