Assembly
ASM34148v2
BioProject PRJNA186449 · BioSample SAMN02951877
GENOME-RESOLVED EVIDENCE
GCA_000341485.2
Bordetella holmesii H558 · Complete Genome
View versioned NCBI assembly →
Quality metadata
Genome size 3696428 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 | 0/2 | 0.000 | Partial/absent |
| reverse_beta_oxidation_core | 2/4 | 0.500 | 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_005014792.1 · acetyl-CoA carboxylase carboxyltransferase subunit alpha | High | Approved candidatestrong profile and bridge orthogroup support | 342.600 / 0.98900 | Bridge orthogroup OG0001120 |
| accBWP_005018492.1 · acetyl-CoA carboxylase biotin carboxyl carrier protein | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 137.000 / 0.98100 | Annotation: gene_symbol |
| accCWP_005018494.1 · acetyl-CoA carboxylase biotin carboxylase subunit | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 586.600 / 0.99600 | Annotation: gene_symbol |
| accDWP_005012146.1 · acetyl-CoA carboxylase, carboxyltransferase subunit beta | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 320.500 / 0.90100 | Bridge orthogroup OG0000844 |
| coatWP_005018897.1 · CoA transferase subunit B | Medium | Approved candidatestrong profile plus independent annotation support: specific_product_name | 212.800 / 0.94000 | Annotation: specific_product_name |
| coatWP_005016616.1 · 3-oxoacid CoA-transferase subunit B | Medium | Approved candidatestrong profile plus independent annotation support: specific_product_name | 166.200 / 0.92200 | Annotation: specific_product_name |
| fabFWP_005012192.1 · beta-ketoacyl-ACP synthase II | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 639.000 / 0.99000 | Annotation: gene_symbol |
| fabGWP_005012188.1 · 3-oxoacyl-ACP reductase FabG | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 246.500 / 0.99200 | Bridge orthogroup OG0000008 |
| fabIWP_005018647.1 · enoyl-ACP reductase FabI | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 378.900 / 0.97300 | Annotation: gene_symbol |
| fabZWP_005013907.1 · 3-hydroxyacyl-ACP dehydratase FabZ | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 120.000 / 0.76000 | Bridge orthogroup OG0000074 |
| hbdWP_005016624.1 · 3-hydroxyacyl-CoA dehydrogenase family protein | High | Approved candidatestrong profile and bridge orthogroup support | 293.900 / 0.98600 | Bridge orthogroup OG0000153 |
| thlWP_005017444.1 · acetyl-CoA C-acetyltransferase | High | Approved candidatestrong profile and bridge orthogroup support | 449.900 / 0.98700 | Bridge orthogroup OG0000010 |
| thlWP_005019101.1 · 3-oxoadipyl-CoA thiolase | High | Approved candidatestrong profile and bridge orthogroup support | 414.500 / 0.99200 | Bridge orthogroup OG0000010 |
| thlWP_005012984.1 · acetyl-CoA C-acyltransferase | High | Approved candidatestrong profile and bridge orthogroup support | 384.000 / 0.99000 | Bridge orthogroup OG0000010 |
| fabGWP_005014509.1 · SDR family oxidoreductase | Low | Excluded: low confidenceprofile hit lacks strong score and bridge orthogroup support | 89.400 / 0.78200 | Profile only |
| fabGWP_005018248.1 · SDR family oxidoreductase | Low | Excluded: low confidenceprofile hit lacks strong score and bridge orthogroup support | 83.200 / 0.99200 | Profile only |
| fabGWP_005013696.1 · SDR family NAD(P)-dependent oxidoreductase | Low | Excluded: low confidenceprofile hit lacks strong score and bridge orthogroup support | 77.300 / 0.69800 | Profile only |
| bcdWP_005020377.1 · acyl-CoA dehydrogenase family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 381.500 / 0.97900 | Profile only |
| bcdWP_005017445.1 · isovaleryl-CoA dehydrogenase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 373.100 / 0.99500 | Profile only |
| bcdWP_005017813.1 · acyl-CoA dehydrogenase family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 358.900 / 0.98200 | Profile only |
| bcdWP_005019767.1 · acyl-CoA dehydrogenase family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 349.700 / 0.98200 | Profile only |
| bcdWP_005018421.1 · acyl-CoA dehydrogenase family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 291.500 / 0.91300 | Profile only |
| bcdWP_005016779.1 · acyl-CoA dehydrogenase family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 282.600 / 0.84400 | Profile only |
| bcdWP_005014081.1 · acyl-CoA dehydrogenase family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 257.200 / 0.94200 | Profile only |
| bcdWP_005013477.1 · acyl-CoA dehydrogenase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 255.200 / 0.98400 | Profile only |
| crtWP_005020370.1 · enoyl-CoA hydratase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 265.500 / 0.97700 | Annotation: specific_product_name |
| crtWP_005015374.1 · enoyl-CoA hydratase/isomerase family protein | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 207.700 / 0.95000 | Annotation: specific_product_name |
| crtWP_005016532.1 · crotonase/enoyl-CoA hydratase family protein | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 202.100 / 0.98100 | Annotation: specific_product_name |
| crtWP_005015618.1 · enoyl-CoA hydratase/isomerase family protein | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 179.000 / 0.99200 | Annotation: specific_product_name |
| crtWP_005015660.1 · enoyl-CoA hydratase/isomerase family protein | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 178.200 / 0.97700 | Annotation: specific_product_name |
| crtWP_005012517.1 · 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase PaaG | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 167.500 / 0.99600 | Profile only |
| crtWP_005016227.1 · enoyl-CoA hydratase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 155.500 / 0.98500 | Annotation: specific_product_name |
| crtWP_005020403.1 · enoyl-CoA hydratase family protein | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 149.700 / 0.96100 | Annotation: specific_product_name |
| crtWP_005014973.1 · enoyl-CoA hydratase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 135.700 / 0.97700 | Annotation: specific_product_name |
| crtWP_005020177.1 · enoyl-CoA hydratase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 127.400 / 0.96100 | Annotation: specific_product_name |
| crtWP_005018034.1 · enoyl-CoA hydratase-related protein | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 124.600 / 0.94600 | Annotation: specific_product_name |
| crtWP_005018030.1 · enoyl-CoA hydratase/isomerase family protein | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 124.200 / 0.95800 | Annotation: specific_product_name |
| etfAWP_005012460.1 · electron transfer flavoprotein subunit alpha/FixB family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 236.900 / 0.94300 | Profile only |
| fabGWP_005012386.1 · acetoacetyl-CoA reductase | High | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 219.200 / 0.98000 | Bridge orthogroup OG0000008 |
| fabGWP_005014361.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 198.100 / 0.98800 | Profile only |
| fabGWP_005018417.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 193.200 / 0.97600 | Profile only |
| fabGWP_005013789.1 · acetoacetyl-CoA reductase | High | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 179.400 / 0.96000 | Bridge orthogroup OG0000008 |
| fabGWP_003814011.1 · 3-hydroxybutyrate dehydrogenase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 178.400 / 0.98800 | Profile only |
| fabGWP_005018961.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 176.100 / 0.96400 | Profile only |
| fabGWP_005017130.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 175.300 / 0.98000 | Profile only |
| fabGWP_017685416.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 173.100 / 0.99200 | Profile only |
| fabGWP_005016704.1 · 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 164.700 / 0.98400 | Profile only |
| fabGWP_005015678.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 164.400 / 0.98400 | Profile only |
| fabGWP_005015670.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 160.500 / 0.98400 | Profile only |
| fabGWP_101558050.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 157.900 / 0.91500 | Profile only |
| fabGWP_005014089.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 155.700 / 0.87500 | Profile only |
| fabGWP_017685749.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 154.500 / 0.97600 | Profile only |
| fabGWP_005016620.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 152.500 / 0.95600 | Profile only |
| fabGWP_005017827.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 150.800 / 0.96800 | Profile only |
| fabGWP_005013046.1 · 3-oxoacyl-ACP reductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 145.000 / 0.99600 | Annotation: specific_product_name |
| fabGWP_005012817.1 · 3-hydroxyacyl-CoA dehydrogenase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 135.900 / 0.98800 | Profile only |
| fabGWP_005014910.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 131.900 / 0.99600 | Profile only |
| fabGWP_005013105.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 126.300 / 0.97200 | Profile only |
| fabGWP_005015672.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 113.900 / 0.96000 | Profile only |
| fabGWP_005015806.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 111.100 / 0.75000 | Profile only |
| fabGWP_005015120.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 107.600 / 0.96400 | Profile only |
| fabGWP_005013515.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 98.400 / 0.75000 | Profile only |
| fabHWP_005012185.1 · beta-ketoacyl-ACP synthase III | Medium | Needs reviewno bridge-supported orthogroup; require domain, motif, or neighborhood confirmation | 276.500 / 0.98800 | Profile only |
| fabLWP_005018961.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 230.700 / 0.96000 | Profile only |
| fabLWP_005012188.1 · 3-oxoacyl-ACP reductase FabG | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 194.500 / 0.97200 | Profile only |
| fabLWP_005015670.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 186.400 / 0.99600 | Profile only |
| fabLWP_005017130.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 186.100 / 0.98400 | Profile only |
| fabLWP_005015678.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 181.400 / 0.96800 | Profile only |
| fabLWP_005018417.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 181.000 / 0.98800 | Profile only |
| fabLWP_005013046.1 · 3-oxoacyl-ACP reductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 180.300 / 0.96800 | Profile only |
| fabLWP_101558050.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 179.100 / 0.90900 | Profile only |
| fabLWP_005017827.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 177.800 / 0.96000 | Profile only |
| fabLWP_005016704.1 · 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 172.400 / 0.98400 | Profile only |
| fabLWP_005014361.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 169.000 / 0.96800 | Profile only |
| fabLWP_003814011.1 · 3-hydroxybutyrate dehydrogenase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 165.700 / 0.97600 | Profile only |
| fabLWP_017685416.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 157.600 / 0.98800 | Profile only |
| fabLWP_005013789.1 · acetoacetyl-CoA reductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 155.500 / 0.96400 | Profile only |
| fabLWP_005012386.1 · acetoacetyl-CoA reductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 154.700 / 0.97600 | Profile only |
| fabLWP_005014910.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 140.700 / 0.98400 | Profile only |
| fabLWP_005014089.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 139.000 / 0.89300 | Profile only |
| fabLWP_005016620.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 134.400 / 0.96400 | Profile only |
| fabLWP_005013105.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 130.900 / 0.98800 | Profile only |
| fabLWP_017685749.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 129.000 / 0.99200 | Profile only |
| fabLWP_005015672.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 120.800 / 0.96400 | Profile only |
| fabLWP_005015120.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 108.900 / 0.99200 | Profile only |
| fabLWP_005015806.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 107.900 / 0.76200 | Profile only |
| hbdWP_005018043.1 · 3-hydroxyacyl-CoA dehydrogenase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 265.700 / 0.98900 | Profile only |
Protein-level evidence
| Gene | Protein | Orthogroup | Coordinates | Annotation |
|---|
These are genomic annotation predictions. Experimental activity, expression and metabolite production require separate evidence.