fadD1 Resolved · high auto-curated
H37Rv Rv1750c · MTBC0 mtbc0_001863 ·
532 aa · 1990041–1991639 (-) ·
RefSeq NP_216266.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | fatty-acid--CoA ligase FadD1 |
|---|---|
| MTBC0 PGAP re-annotation | fatty-acid--CoA ligase FadD1 |
| Revised (this work) | Fatty-acid--CoA ligase FadD1. Pfam: AMP-binding (PF00501.35), 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.
Curated reference (UniProt)
| UniProt |
P72007
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Medium/long-chain-fatty-acid--CoA ligase FadD17 |
| EC (curated) |
EC 6.2.1.2, EC 6.2.1.3
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | fadD1 |
| eggNOG description | Activates fatty acids by binding to coenzyme A |
| Orthologous group | COG0318 |
| KEGG orthology |
K00666
|
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 | 0.901 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.20% of strains (287) · 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 |
|---|---|---|---|---|
AMP-binding | PF00501.35 | 2.6e-39 | 18–366 | AMP-binding enzyme |
AMP-binding_C | PF13193.13 | 4.5e-08 | 417–493 | AMP-binding enzyme C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadD18 (fatty-acid--CoA ligase FadD18), high confidence from genomic context alone (score 761 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3513c fadD18 |
fatty-acid--CoA ligase FadD18 | 774 | 761 ctx | cooccurence:760 |
Rv3515c fadD19 |
acyl-CoA synthetase | 816 | 749 ctx | cooccurence:748 |
Rv0719 rplF |
50S ribosomal protein L6 | 695 | 695 | experimental:402 database:510 |
Rv1527c pks5 |
polyketide synthase | 706 | 680 | |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 705 | 680 | |
Rv2048c pks12 |
polyketide synthase | 705 | 680 | |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 705 | 680 | |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 704 | 679 | |
Rv3800c pks13 |
polyketide synthase | 880 | 635 | textmining:685 |
Rv2380c mbtE |
peptide synthetase | 650 | 635 | experimental:465 |
Rv2946c pks1 |
polyketide synthase | 663 | 631 | |
Rv2932 ppsB |
phthiocerol synthesis polyketide synthase type I PpsB | 630 | 608 | |
Rv1661 pks7 |
polyketide synthase | 630 | 608 | |
Rv1181 pks4 |
polyketide beta-ketoacyl synthase | 629 | 608 | |
Rv0405 pks6 |
membrane bound polyketide synthase | 617 | 599 |
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: fatty-acid--CoA ligase FadD1
- MTBC0 PGAP product: fatty-acid--CoA ligase FadD1
- Pfam (hmmscan --cut_ga): AMP-binding PF00501.35 (E=3e-39), AMP-binding_C PF13193.13 (E=4e-08)
- (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_216266.1)
- Domains: Pfam-A via hmmscan --cut_ga — AMP-binding (PF00501.35), 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 P72007 (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 —
94 functional partner(s); context anchor
fadD18 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001863|Rv1750c|fadD1 MTDTIQSLLRQHVSDPTIAVKYGGLQWTWSQYLAESAARAAALITIADPQRPTHIGSLLGNTPEMLAQLAAAGLGGYVLCGLNTTRRGDALAADVRRADCQIVVTDADHRALLDGLDLAGARILDTSTPRWAELVAGDGAFVPYREVDTMDPFMMIFTSGTSGNPKAVPVSHLMATFAGRSLTERFGLTEQDTCYVSMPLFHSNAVVAGWAPAVVSGAAIAPATFSATGFLDDVRRYHATYMNYVGKPLAYILATPERDDDADNPLRVAFGNEANDKDIEEFSRRFGVQVEDGFGSTENAVIVIREPGTPPGSIGRGAHGVAVYNGETVTECAVARFDAHGALTNADEAIGELVNTTGSGFFTGYYNDPEANAERMRHGMYWSGDLAYRDSEGWIYLAGRTADWMRVDGENLTAAPIERILLRYKAINRVAVYAVPDEYVGDQVMAALVLRAGDTFDPDAFEAFLDAQPDLSTKARPRYIRIAADLPSTATHKVLKRQLIDEGTAVGKADTLWVREPRGSAYHHASGPAKAI