fadD11 Resolved · high auto-curated
H37Rv Rv1550 · MTBC0 - ·
571 aa · 1753716–1755431 (+) ·
RefSeq NP_216066.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | fatty-acid--CoA ligase FadD11 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Fatty-acid--CoA ligase FadD11. Pfam: AMP-binding (PF00501.35), AMP-binding_C_3 (PF23562.3). |
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 |
P9WQ53
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Putative fatty-acid--CoA ligase fadD11 |
| EC (curated) |
EC 6.2.1.-
|
UniProt still lists this protein as Putative fatty-acid--CoA ligase fadD11; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | fadD11 |
| eggNOG description | synthetase |
| Orthologous group | COG1022 |
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.405 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 29.48% of strains (42805) · 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 | 1.2e-41 | 126–379 | AMP-binding enzyme |
AMP-binding_C_3 | PF23562.3 | 1.3e-09 | 419–553 | AMP-binding enzyme C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadD11.1 (Possible fatty-acid-CoA ligase FadD11.1 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase); Rv1549, (MTCY48.16c), len: 175 aa. Possible f), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1549 fadD11.1 |
Possible fatty-acid-CoA ligase FadD11.1 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase); Rv1549, (MTCY48.16c), len: 175 aa. Possible f | 999 | 999 ctx | neighborhood:781 fusion:900 cooccurence:745 coexpression:838 |
Rv1551 plsB1 |
acyltransferase PlsB | 972 | 971 ctx | neighborhood:812 coexpression:853 |
Rv2524c fas |
fatty acid synthase | 951 | 932 | database:900 |
Rv2187 fadD15 |
long-chain-fatty-acid--CoA ligase FadD15 | 923 | 923 | database:900 |
Rv0214 fadD4 |
fatty-acid--CoA ligase FadD4 | 924 | 922 | database:900 |
Rv3097c lipY |
triacylglycerol lipase Lip | 809 | 803 | database:800 |
Rv2485c lipQ |
carboxylesterase LipQ | 807 | 800 | coexpression:799 |
Rv0458 |
aldehyde dehydrogenase | 702 | 691 | coexpression:663 |
Rv1389 gmk |
guanylate kinase | 642 | 643 | database:591 |
Rv0270 fadD2 |
fatty-acid--CoA ligase FadD2 | 654 | 642 ctx | cooccurence:627 |
Rv0009 ppiA |
iron-regulated peptidyl-prolyl cis-trans isomerase PpiA | 569 | 568 | database:428 |
Rv0166 fadD5 |
fatty-acid--CoA ligase FadD5 | 561 | 546 | coexpression:410 |
Rv1548c PPE21 |
PPE family protein PPE21 | 528 | 528 ctx | neighborhood:524 |
Rv0526 |
thioredoxin | 509 | 500 | |
Rv2582 ppiB |
peptidyl-prolyl cis-trans isomerase B | 495 | 496 | database:428 |
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 FadD11
- Pfam (hmmscan --cut_ga): AMP-binding PF00501.35 (E=1e-41), AMP-binding_C_3 PF23562.3 (E=1e-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_216066.1)
- Domains: Pfam-A via hmmscan --cut_ga — AMP-binding (PF00501.35), AMP-binding_C_3 (PF23562.3)
- 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
COG1022 - Curated reference: UniProt P9WQ53 (SwissProt, reviewed; 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 —
63 functional partner(s); context anchor
fadD11.1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1550|fadD11 MARLRGAGAAGRCRPGRFGSSARRHGLADDGEPDRVLPARRRCSARRRHLVFGVQHPARRAADLRVRQRGDQGGHLRATVRRSRSRQRCAHRTHRLRRWRAPGTLSLTDLYAAASGDFFDFESTWRAVQPEDIVTLIYTSGTTGNPKGVEMTHANLLFEGYAIDEVLGIRFGDRVTSFLPSAHIADRMTGLYLQEMFGTQVTAVADARTIAAALPDVRPTVWGAVPRVWEKLKAGIEFTVARETDEMKRQALAWAMSVAGKRANALLAGESMSDQLVAEWAKADELVLSKLRERLGFGELRWALSGAAPIPKETLAFFAGIGIPIAEIWGMSELSCVATASHPRDGRLGTVGKLLPGLQGKIAEDGEYLVRGPLVMKGYRKEPAKTAEAIDSDGWLHTGDVFDIDSDGYLRVVDRKKELIINAAGKNMSPANIENTILAACPMVGVMMAIGDGRTYNTALLVFDADSLGPYAAQRGLDASPAALAADPEVIARIAAGVAEGNAKLSRVEQIKRFRILPTLWEPGGDEITLTMKLKRRRIAAKYSAEIEELYASELRPQVYEPAAVPSTQPA