fadD23 Resolved · high auto-curated
H37Rv Rv3826 · MTBC0 mtbc0_004055 ·
584 aa · 4323922–4325676 (+) ·
RefSeq NP_218343.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | long-chain-fatty-acid--CoA ligase FadD23 |
|---|---|
| MTBC0 PGAP re-annotation | long-chain-fatty-acid--CoA ligase FadD23 |
| Revised (this work) | Long-chain-fatty-acid--CoA ligase FadD23. Pfam: AMP-binding (PF00501.35), AMP-dom_DIP2-like (PF23024.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ47
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Long-chain-fatty-acid--AMP ligase FadD23 |
| EC (curated) |
EC 6.2.1.57
|
| Curated function | Catalyzes the activation of long-chain fatty acids as acyl-adenylates (acyl-AMP), which are then transferred to the multifunctional polyketide synthase (PKS) type III for further chain extension (Probable). Involved in the biosynthesis of sulfolipid 1 (SL-1). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | fadD28 |
| eggNOG description | Activates fatty acids by binding to coenzyme A |
| Orthologous group | COG0318 |
| EC number |
EC 2.7.7.95, EC 6.2.1.51
|
| KEGG orthology |
K00666, K12423, K12425, K12426, K12427, K12428, K21059
|
| Gene Ontology (45) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0006082, GO:0006629, GO:0006631, GO:0006633, GO:0006790, GO:0008150, GO:0008152 +33 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 | 1.248 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 11 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 | PF00501.35 | 2.1e-57 | 12–415 | AMP-binding enzyme |
AMP-dom_DIP2-like | PF23024.2 | 5.0e-09 | 463–571 | Disco-interacting protein 2-like, AMP domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mbtE (peptide synthetase), high confidence from genomic context alone (score 948 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2380c mbtE |
peptide synthetase | 950 | 948 ctx | fusion:631 cooccurence:690 experimental:465 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 942 | 866 ctx | neighborhood:543 textmining:590 |
Rv2379c mbtF |
peptide synthetase | 837 | 836 ctx | cooccurence:657 |
Rv0101 nrp |
peptide synthetase Nrp | 810 | 800 ctx | cooccurence:670 |
Rv2947c pks15 |
polyketide synthase | 786 | 786 ctx | fusion:532 |
Rv2932 ppsB |
phthiocerol synthesis polyketide synthase type I PpsB | 760 | 746 | |
Rv1180 pks3 |
polyketide beta-ketoacyl synthase | 778 | 744 ctx | fusion:418 |
Rv1527c pks5 |
polyketide synthase | 767 | 744 | |
Rv0405 pks6 |
membrane bound polyketide synthase | 754 | 742 | |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 762 | 741 | |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 798 | 739 | |
Rv2383c mbtB |
phenyloxazoline synthase | 764 | 739 ctx | fusion:451 |
Rv2382c mbtC |
polyketide synthetase | 740 | 731 ctx | fusion:438 |
Rv2931 ppsA |
phthiocerol synthesis polyketide synthase type I PpsA | 798 | 718 | |
Rv3800c pks13 |
polyketide synthase | 739 | 714 |
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: long-chain-fatty-acid--CoA ligase FadD23
- MTBC0 PGAP product: long-chain-fatty-acid--CoA ligase FadD23
- Pfam (hmmscan --cut_ga): AMP-binding PF00501.35 (E=2e-57), AMP-dom_DIP2-like PF23024.2 (E=5e-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_218343.1)
- Domains: Pfam-A via hmmscan --cut_ga — AMP-binding (PF00501.35), AMP-dom_DIP2-like (PF23024.2)
- 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 P9WQ47 (SwissProt, reviewed; 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 —
87 functional partner(s); context anchor
mbtE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004055|Rv3826|fadD23 MVSLSIPSMLRQCVNLHPDGTAFTYIDYERDSEGISESLTWSQVYRRTLNVAAEVRRHAAIGDRAVILAPQGLDYIVAFLGALQAGLIAVPLSAPLGGASDERVDAVVRDAKPNVVLTTSAIMGDVVPRVTPPPGIASPPTVAVDQLDLDSPIRSNIVDDSLQTTAYLQYTSGSTRTPAGVMITYKNILANFQQMISAYFADTGAVPPLDLFIMSWLPFYHDMGLVLGVCAPIIVGCGAVLTSPVAFLQRPARWLQLMAREGQAFSAAPNFAFELTAAKAIDDDLAGLDLGRIKTILCGSERVHPATLKRFVDRFSRFNLREFAIRPAYGLAEATVYVATSQAGQPPEIRYFEPHELSAGQAKPCATGAGTALVSYPLPQSPIVRIVDPNTNTECPPGTIGEIWVHGDNVAGGYWEKPDETERTFGGALVAPSAGTPVGPWLRTGDSGFVSEDKFFIIGRIKDLLIVYGRNHSPDDIEATIQEITRGRCAAIAVPSNGVEKLVAIVELNNRGNLDTERLSFVTREVTSAISTSHGLSVSDLVLVAPGSIPITTSGKVRRAECVKLYRHNEFTRLDAKPLQASDL