Assembly
ASM400621v1
BioProject PRJNA287884 · BioSample SAMN06350661
GENOME-RESOLVED EVIDENCE
GCA_004006215.1
Bordetella sp. J329 · Complete Genome
View versioned NCBI assembly →
Quality metadata
Genome size 3925525 bp · GC 62.500%
Completeness —% · contamination —%
Pathway marker completeness
| Module | Markers | Fraction | Call |
|---|---|---|---|
| bcd_etf_module | 0/3 | 0.000 | Partial/absent |
| ethanol_entry_support | 0/1 | 0.000 | Partial/absent |
| fatty_acid_biosynthesis_core | 6/8 | 0.750 | Partial/absent |
| lactate_entry_support | 1/2 | 0.500 | Partial/absent |
| reverse_beta_oxidation_core | 1/4 | 0.250 | Partial/absent |
| rnf_complex | 0/6 | 0.000 | Partial/absent |
Detected markers
| Marker | Function | Copies |
|---|
Profile-HMM marker predictions
Approved candidates and review records are genomic predictions, not evidence of expression or MCFA production. Excluded matches remain visible for audit.
| Marker / protein | Confidence | Review status | Score / coverage | Supporting evidence |
|---|---|---|---|---|
| accAWP_068370343.1 · acetyl-CoA carboxylase carboxyltransferase subunit alpha | High | Approved candidatestrong profile and bridge orthogroup support | 350.600 / 0.98200 | Bridge orthogroup OG0001120 |
| accBWP_068372736.1 · acetyl-CoA carboxylase biotin carboxyl carrier protein | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 133.700 / 0.98100 | Annotation: gene_symbol |
| accCWP_068372735.1 · acetyl-CoA carboxylase biotin carboxylase subunit | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 579.700 / 0.99600 | Annotation: gene_symbol |
| accDWP_127775052.1 · acetyl-CoA carboxylase, carboxyltransferase subunit beta | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 321.600 / 0.88700 | Bridge orthogroup OG0000844 |
| coatWP_068366632.1 · 3-oxoacid CoA-transferase subunit B | Medium | Approved candidatestrong profile plus independent annotation support: specific_product_name | 209.500 / 0.94000 | Annotation: specific_product_name |
| fabFWP_127775038.1 · beta-ketoacyl-ACP synthase II | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 638.400 / 0.99000 | Annotation: gene_symbol |
| fabGWP_127775039.1 · 3-oxoacyl-ACP reductase FabG | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 238.400 / 0.99600 | Bridge orthogroup OG0000008 |
| fabIWP_127775253.1 · enoyl-ACP reductase FabI | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 379.100 / 0.97700 | Annotation: gene_symbol |
| fabIWP_127774517.1 · enoyl-ACP reductase FabI | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 301.900 / 0.96900 | Annotation: gene_symbol |
| fabZWP_068372276.1 · 3-hydroxyacyl-ACP dehydratase FabZ | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 129.300 / 0.75400 | Bridge orthogroup OG0000074 |
| lctPWP_127773193.1 · L-lactate permease | High | Approved candidatestrong profile and bridge orthogroup support | 407.400 / 0.99000 | Bridge orthogroup OG0000731 |
| thlWP_127773295.1 · 3-oxoadipyl-CoA thiolase | High | Approved candidatestrong profile and bridge orthogroup support | 412.400 / 0.99700 | Bridge orthogroup OG0000010 |
| thlWP_127773099.1 · acetyl-CoA C-acyltransferase | High | Approved candidatestrong profile and bridge orthogroup support | 375.500 / 0.99200 | Bridge orthogroup OG0000010 |
| thlWP_127774780.1 · thiolase family protein | High | Approved candidatestrong profile and bridge orthogroup support | 344.500 / 0.99500 | Bridge orthogroup OG0000010 |
| thlWP_127773096.1 · acetyl-CoA C-acetyltransferase | High | Approved candidatestrong profile and bridge orthogroup support | 302.400 / 0.98700 | Bridge orthogroup OG0000010 |
| fabGWP_068370723.1 · 3-phenylpropionate-dihydrodiol/cinnamic acid-dihydrodiol dehydrogenase | Low | Excluded: low confidenceprofile hit lacks strong score and bridge orthogroup support | 93.100 / 0.98000 | Profile only |
| fabGWP_068371413.1 · SDR family oxidoreductase | Low | Excluded: low confidenceprofile hit lacks strong score and bridge orthogroup support | 80.300 / 0.95600 | Profile only |
| accCWP_127774937.1 · urea carboxylase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 466.700 / 0.98900 | Profile only |
| accCWP_127773472.1 · biotin carboxylase N-terminal domain-containing protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 462.500 / 0.96400 | Profile only |
| crtWP_127773287.1 · 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase PaaG | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 183.000 / 0.98100 | Profile only |
| crtWP_068368342.1 · crotonase/enoyl-CoA hydratase family protein | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 147.300 / 0.98100 | Annotation: specific_product_name |
| crtWP_127773274.1 · crotonase/enoyl-CoA hydratase family protein | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 146.700 / 0.95800 | Annotation: specific_product_name |
| etfAWP_127774968.1 · FAD-binding protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 238.600 / 0.94600 | Profile only |
| fabGWP_127774510.1 · beta-ketoacyl-ACP reductase | High | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 217.700 / 0.98000 | Bridge orthogroup OG0000008 |
| fabGWP_127773135.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 208.700 / 0.97600 | Profile only |
| fabGWP_068370149.1 · acetoacetyl-CoA reductase | High | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 205.400 / 0.98000 | Bridge orthogroup OG0000008 |
| fabGWP_127774307.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 194.700 / 0.98800 | Profile only |
| fabGWP_127775076.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 194.400 / 0.99200 | Profile only |
| fabGWP_127775328.1 · SDR family NAD(P)-dependent oxidoreductase | High | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 191.300 / 0.97600 | Bridge orthogroup OG0000008 |
| fabGWP_068374083.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 187.000 / 0.98800 | Profile only |
| fabGWP_127773537.1 · 3-hydroxybutyrate dehydrogenase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 182.900 / 0.99600 | Profile only |
| fabGWP_068367379.1 · glucose 1-dehydrogenase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 181.600 / 0.97200 | Profile only |
| fabGWP_127775330.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 180.500 / 0.96000 | Profile only |
| fabGWP_127774872.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 175.600 / 0.98400 | Profile only |
| fabGWP_127775490.1 · 3-oxoacyl-ACP reductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 156.900 / 0.98400 | Annotation: specific_product_name |
| fabGWP_127774165.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 150.100 / 0.98800 | Profile only |
| fabGWP_127774488.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 148.500 / 0.96000 | Profile only |
| fabGWP_127773216.1 · SDR family NAD(P)-dependent oxidoreductase | High | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 145.200 / 0.98000 | Bridge orthogroup OG0000008 |
| fabGWP_127773731.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 144.700 / 0.98800 | Profile only |
| fabGWP_278859070.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 144.000 / 0.97600 | Profile only |
| fabGWP_278858539.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 143.500 / 0.98400 | Profile only |
| fabGWP_127774477.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 142.300 / 0.98800 | Profile only |
| fabGWP_127773065.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 139.300 / 0.96800 | Profile only |
| fabGWP_127774873.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 135.900 / 0.94000 | Profile only |
| fabGWP_127773206.1 · 3-ketoacyl-ACP reductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 128.200 / 0.96400 | Profile only |
| fabGWP_321197281.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 124.600 / 0.97600 | Profile only |
| fabGWP_068374565.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 123.700 / 0.97200 | Profile only |
| fabGWP_127773601.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 121.100 / 0.98400 | Profile only |
| fabGWP_127773643.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 119.700 / 0.88300 | Profile only |
| fabGWP_127774874.1 · SDR family NAD(P)-dependent oxidoreductase | High | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 116.600 / 0.98400 | Bridge orthogroup OG0000008 |
| fabGWP_068370578.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 115.300 / 0.97600 | Profile only |
| fabGWP_127775646.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 111.800 / 0.99200 | Profile only |
| fabHWP_127775041.1 · beta-ketoacyl-ACP synthase III | Medium | Needs reviewno bridge-supported orthogroup; require domain, motif, or neighborhood confirmation | 267.400 / 0.98800 | Profile only |
| fabKWP_127774651.1 · nitronate monooxygenase family protein | Medium | Needs reviewno bridge-supported orthogroup; require domain, motif, or neighborhood confirmation | 231.500 / 0.96200 | Profile only |
| fabLWP_127775076.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 205.000 / 0.99200 | Profile only |
| fabLWP_127774307.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 198.800 / 0.98400 | Profile only |
| fabLWP_068371413.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 197.000 / 0.97600 | Profile only |
| fabLWP_127774165.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 193.200 / 0.98400 | Profile only |
| fabLWP_127775646.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 187.400 / 0.99200 | Profile only |
| fabLWP_127773135.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 186.800 / 0.97600 | Profile only |
| fabLWP_127775039.1 · 3-oxoacyl-ACP reductase FabG | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 186.700 / 0.97600 | Profile only |
| fabLWP_127774872.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 182.300 / 0.97200 | Profile only |
| fabLWP_127775490.1 · 3-oxoacyl-ACP reductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 181.200 / 0.97200 | Profile only |
| fabLWP_127773065.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 181.100 / 0.95600 | Profile only |
| fabLWP_068367379.1 · glucose 1-dehydrogenase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 178.600 / 0.97600 | Profile only |
| fabLWP_068374083.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 172.800 / 0.99200 | Profile only |
| fabLWP_127775330.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 161.500 / 0.96400 | Profile only |
| fabLWP_127773537.1 · 3-hydroxybutyrate dehydrogenase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 159.700 / 0.98000 | Profile only |
| fabLWP_278858539.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 159.100 / 0.96800 | Profile only |
| fabLWP_127774510.1 · beta-ketoacyl-ACP reductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 154.600 / 0.99200 | Profile only |
| fabLWP_127775328.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 153.100 / 0.98800 | Profile only |
| fabLWP_127774477.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 151.900 / 0.99200 | Profile only |
| fabLWP_068370149.1 · acetoacetyl-CoA reductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 150.300 / 0.99200 | Profile only |
| fabLWP_127773216.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 146.600 / 0.99200 | Profile only |
| fabLWP_127773601.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 131.900 / 0.96800 | Profile only |
| fabLWP_127774873.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 131.500 / 0.96400 | Profile only |
| fabLWP_127774488.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 130.200 / 0.99200 | Profile only |
| fabLWP_127773206.1 · 3-ketoacyl-ACP reductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 128.800 / 0.97200 | Profile only |
| fabLWP_068370578.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 123.200 / 0.97600 | Profile only |
| fabLWP_278859070.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 122.700 / 0.97200 | Profile only |
| fabLWP_127773643.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 120.100 / 0.91300 | Profile only |
| fabLWP_321197281.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 118.500 / 0.97600 | Profile only |
| fabLWP_068374565.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 110.900 / 0.73400 | Profile only |
| hbdWP_127773292.1 · 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 201.600 / 0.98200 | Profile only |
| thlWP_127774520.1 · acetyl-CoA C-acetyltransferase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 596.800 / 0.99700 | Profile only |
Protein-level evidence
| Gene | Protein | Orthogroup | Coordinates | Annotation |
|---|
These are genomic annotation predictions. Experimental activity, expression and metabolite production require separate evidence.