fadB Resolved · high auto-curated
H37Rv Rv0860 · MTBC0 mtbc0_000915 ·
720 aa · 959443–961605 (+) ·
RefSeq NP_215375.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | fatty oxidation protein FadB |
|---|---|
| MTBC0 PGAP re-annotation | fatty oxidation protein FadB |
| Revised (this work) | Fatty oxidation protein FadB. Pfam: ECH_1 (PF00378.26), ECH_2 (PF16113.11), 3HCDH_N (PF02737.25), 3HCDH (PF00725.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53872
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable fatty oxidation protein FadB |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | fadB |
| eggNOG description | 3-hydroxyacyl-CoA dehydrogenase |
| Orthologous group | COG1024 |
| EC number |
EC 1.1.1.35, EC 4.2.1.17, EC 5.1.2.3
|
| KEGG orthology |
K01782
|
| KEGG pathways |
map00071, map00280, map00281, map00310, map00362, map00380, map00410, map00640, map00650, map00903, map00930, map01040, map01100, map01110, map01120, map01130, map01200, map01212
|
| KEGG modules |
M00032, M00087
|
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 | 0.238 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 5 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 |
|---|---|---|---|---|
ECH_1 | PF00378.26 | 1.1e-31 | 13–213 | Enoyl-CoA hydratase/isomerase |
ECH_2 | PF16113.11 | 6.1e-20 | 18–193 | Enoyl-CoA hydratase/isomerase |
3HCDH_N | PF02737.25 | 5.5e-63 | 328–505 | 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain |
3HCDH | PF00725.28 | 3.5e-19 | 508–607 | 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadA (acyltransferase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0859 fadA |
acyltransferase | 999 | 1000 ctx | neighborhood:882 cooccurence:730 coexpression:955 experimental:980 database:942 textmining:949 |
Rv0243 fadA2 |
acetyl-CoA acetyltransferase FadA | 998 | 998 | coexpression:697 experimental:804 database:942 |
Rv1323 fadA4 |
acetyl-CoA acetyltransferase | 998 | 996 | coexpression:698 experimental:804 database:942 textmining:580 |
Rv3556c fadA6 |
acetyl-CoA acetyltransferase FadA | 997 | 996 | coexpression:697 experimental:804 database:942 |
Rv1867 hyp |
hypothetical protein | 996 | 996 | coexpression:697 experimental:804 database:942 |
Rv3523 ltp3 |
lipid carrier protein | 996 | 996 | coexpression:696 experimental:804 database:942 |
Rv2790c ltp1 |
lipid-transfer protein | 996 | 996 | coexpression:696 experimental:804 database:942 |
Rv1074c fadA3 |
beta-ketoacyl CoA thiolase FadA | 996 | 996 | coexpression:697 experimental:804 database:942 |
Rv3546 fadA5 |
acetyl-CoA acetyltransferase FadA | 996 | 996 | coexpression:697 experimental:804 database:942 |
Rv0914c |
lipid carrier protein or keto acyl-CoA thiolase | 996 | 996 | coexpression:697 experimental:804 database:942 |
Rv1627c |
nonspecific lipid-transfer protein | 970 | 966 | coexpression:699 experimental:804 database:447 |
Rv1135A |
Rv1135A, len: 80 aa. Possible acetyl-CoA acetyltransferase (possible gene fragment), highly similar to other acetyl-CoA acetyltransferases e | 970 | 966 | coexpression:695 experimental:804 database:447 |
Rv3540c ltp2 |
lipid transfer protein | 969 | 966 | coexpression:697 experimental:804 database:447 |
Rv3522 ltp4 |
lipid transfer protein | 967 | 966 | coexpression:697 experimental:804 database:447 |
Rv2503c scoB |
succinyl-CoA:3-ketoacid-CoA transferase subunit B | 946 | 939 | database:900 |
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 oxidation protein FadB
- MTBC0 PGAP product: fatty oxidation protein FadB
- Pfam (hmmscan --cut_ga): ECH_1 PF00378.26 (E=1e-31), ECH_2 PF16113.11 (E=6e-20), 3HCDH_N PF02737.25 (E=6e-63), 3HCDH PF00725.28 (E=4e-19)
- (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_215375.1)
- Domains: Pfam-A via hmmscan --cut_ga — ECH_1 (PF00378.26), ECH_2 (PF16113.11), 3HCDH_N (PF02737.25), 3HCDH (PF00725.28)
- 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
COG1024 - Curated reference: UniProt O53872 (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 —
272 functional partner(s); context anchor
fadA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000915|Rv0860|fadB MPDNTIQWDKDADGIVTLTMDDPSGSTNVMNEAYIESMGKAVDRLVAEKDSITGVVVASAKKTFFAGGDVKTMIQARPEDAGDVFNTVETIKRQLRTLETLGKPVVAAINGAALGGGLEIALACHHRIAADVKGSQLGLPEVTLGLLPGGGGVTRTVRMFGIQNAFVSVLAQGTRFKPAKAKEIGLVDELVATVEELVPAAKAWIKEELKANPDGAGVQPWDKKGYKMPGGTPSSPGLAAILPSFPSNLRKQLKGAPMPAPRAILAAAVEGAQVDFDTASRIESRYFASLVTGQVAKNMMQAFFFDLQAINAGGSRPEGIGKTPIKRIGVLGAGMMGAGIAYVSAKAGYEVVLKDVSLEAAAKGKGYSEKLEAKALERGRTTQERSDALLARITPTADAADFKGVDFVIEAVFENQELKHKVFGEIEDIVEPNAILGSNTSTLPITGLATGVKRQEDFIGIHFFSPVDKMPLVEIIKGEKTSDEALARVFDYTLAIGKTPIVVNDSRGFFTSRVIGTFVNEALAMLGEGVEPASIEQAGSQAGYPAPPLQLSDELNLELMHKIAVATRKGVEDAGGTYQPHPAEAVVEKMIELGRSGRLKGAGFYEYADGKRSGLWPGLRETFKSGSSQPPLQDMIDRMLFAEALETQKCLDEGVLTSTADANIGSIMGIGFPPWTGGSAQFIVGYSGPAGTGKAAFVARARELAAAYGDRFLPPESLLS