fadD7 Family assigned · medium auto-curated
H37Rv Rv0119 · MTBC0 mtbc0_000130 ·
525 aa · 144215–145792 (+) ·
RefSeq NP_214633.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | fatty-acid--CoA ligase FadD7 |
|---|---|
| MTBC0 PGAP re-annotation | FadD7 family fatty acid--CoA ligase |
| Revised (this work) | FadD7 family fatty acid--CoA ligase. 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 |
O07169
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable fatty-acid-CoA ligase FadD7 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | fadD7 |
| eggNOG description | AMP-binding enzyme C-terminal domain |
| Orthologous group | COG0318 |
| KEGG orthology |
K16029
|
| KEGG pathways |
map01051, map01052
|
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 | 0.241 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 7 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 | 9.0e-73 | 14–386 | AMP-binding enzyme |
AMP-binding_C | PF13193.13 | 1.5e-17 | 437–510 | AMP-binding enzyme C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: oxcA (oxalyl-CoA decarboxylase OxcA), high confidence from genomic context alone (score 893 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0118c oxcA |
oxalyl-CoA decarboxylase OxcA | 895 | 893 ctx | neighborhood:720 coexpression:454 |
Rv0719 rplF |
50S ribosomal protein L6 | 694 | 694 | experimental:402 database:510 |
Rv2947c pks15 |
polyketide synthase | 682 | 682 ctx | fusion:452 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 706 | 681 | |
Rv1527c pks5 |
polyketide synthase | 705 | 680 | |
Rv2048c pks12 |
polyketide synthase | 705 | 680 | |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 704 | 679 | |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 704 | 679 | |
Rv1180 pks3 |
polyketide beta-ketoacyl synthase | 662 | 662 ctx | fusion:414 |
Rv2382c mbtC |
polyketide synthetase | 640 | 637 | |
Rv3800c pks13 |
polyketide synthase | 669 | 636 | |
Rv2946c pks1 |
polyketide synthase | 663 | 631 | |
Rv2932 ppsB |
phthiocerol synthesis polyketide synthase type I PpsB | 651 | 631 | |
Rv0405 pks6 |
membrane bound polyketide synthase | 645 | 628 | |
Rv2380c mbtE |
peptide synthetase | 635 | 619 | experimental:465 |
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 FadD7
- MTBC0 PGAP product: FadD7 family fatty acid--CoA ligase
- Pfam (hmmscan --cut_ga): AMP-binding PF00501.35 (E=9e-73), AMP-binding_C PF13193.13 (E=2e-17)
- (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_214633.1)
- 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 O07169 (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 —
69 functional partner(s); context anchor
oxcA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000130|Rv0119|fadD7 MASDFGPRIADLVEVAATRLPEAPALVVTADRIAISHRDLARLVDELAGQLTRSGLLPGDRVALRMGSNAEFVVALLAASRADLVVVPLDPALPITEQRVRSQAAGARVVLIDADGPHDRAEPTTRWWPLTVNVGGDSGPSGGTLSVHLDAATEPNPATSTPEGLRPDDAMIMFTGGTTGLPKMVPWTHANIASSVRAIITGYRLSPRDATVAVMPLYHGHGLIASLLATLASGGAVSLPARGRFSAHTFWDDIKAVGATWYTAVPTIHQILLERSATEPSGRKPAALRFIRSCSAPLTAQAALALQTEFAAPVVCAFGMTEATHQVTTTQIEGIDQTETPVVSTGLVGRSTGAQIRIVGSDGLPLPAGAVGEIWLRGTTVVRGYLGDPTITAANFTDGWLRTGDLGSLSAAGDLSIRGRIKELINRGGEKISPERVEGVLASHPNVMEAAVFGVPHQLYGEAVAAVIVPRESAPPTREELVQFCRERLAAFEIPASFQEASGLPHTAKGSLDRRAVAERFGHSV