Assembly
SRRS
BioProject PRJNA1081641 · BioSample SAMN40183110
GENOME-RESOLVED EVIDENCE
GCA_041428845.1
Sporomusa rhizae · Complete Genome
View versioned NCBI assembly →
Quality metadata
Genome size 5829736 bp · GC 43.500%
Completeness —% · contamination —%
Pathway marker completeness
| Module | Markers | Fraction | Call |
|---|---|---|---|
| bcd_etf_module | 3/3 | 1.000 | Complete marker set |
| ethanol_entry_support | 0/1 | 0.000 | Partial/absent |
| fatty_acid_biosynthesis_core | 4/8 | 0.500 | Partial/absent |
| lactate_entry_support | 2/2 | 1.000 | Complete marker set |
| reverse_beta_oxidation_core | 2/4 | 0.500 | Partial/absent |
| rnf_complex | 6/6 | 1.000 | Complete marker set |
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 |
|---|---|---|---|---|
| bcdWP_371367362.1 · acyl-CoA dehydrogenase | Medium | Approved candidateContext-supported Bcd candidate: calibrated profile hit co-localized with independently approved EtfA and EtfB within six CDS positions. | 596.700 / 1.00000 | Annotation: bcd_etfAB_neighborhood |
| bcdWP_371363986.1 · acyl-CoA dehydrogenase | Medium | Approved candidateContext-supported Bcd candidate: calibrated profile hit co-localized with independently approved EtfA and EtfB within six CDS positions. | 592.200 / 1.00000 | Annotation: bcd_etfAB_neighborhood |
| bcdWP_371364468.1 · acyl-CoA dehydrogenase | Medium | Approved candidateContext-supported Bcd candidate: calibrated profile hit co-localized with independently approved EtfA and EtfB within six CDS positions. | 591.400 / 0.99700 | Annotation: bcd_etfAB_neighborhood |
| bcdWP_371367853.1 · acyl-CoA dehydrogenase | Medium | Approved candidateContext-supported Bcd candidate: calibrated profile hit co-localized with independently approved EtfA and EtfB within six CDS positions. | 555.400 / 0.98900 | Annotation: bcd_etfAB_neighborhood |
| bcdWP_371361880.1 · acyl-CoA dehydrogenase | Medium | Approved candidateContext-supported Bcd candidate: calibrated profile hit co-localized with independently approved EtfA and EtfB within six CDS positions. | 540.900 / 0.98900 | Annotation: bcd_etfAB_neighborhood |
| coatWP_371363421.1 · 3-oxoacid CoA-transferase subunit B | Medium | Approved candidatestrong profile plus independent annotation support: specific_product_name | 239.600 / 0.98200 | Annotation: specific_product_name |
| coatWP_371364015.1 · CoA transferase subunit A | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: specific_product_name | 102.500 / 0.70000 | Bridge orthogroup OG0000263 |
| etfAWP_371364464.1 · FAD-binding protein | High | Approved candidatestrong profile and bridge orthogroup support | 467.300 / 0.99400 | Bridge orthogroup OG0001385 |
| etfAWP_371363988.1 · FAD-binding protein | High | Approved candidatestrong profile and bridge orthogroup support | 453.900 / 0.97900 | Bridge orthogroup OG0001385 |
| etfAWP_371361885.1 · FAD-binding protein | High | Approved candidatestrong profile and bridge orthogroup support | 446.200 / 0.99100 | Bridge orthogroup OG0001385 |
| etfAWP_371367366.1 · FAD-binding protein | High | Approved candidatestrong profile and bridge orthogroup support | 442.500 / 0.99100 | Bridge orthogroup OG0001385 |
| etfAWP_371367856.1 · FAD-binding protein | High | Approved candidatestrong profile and bridge orthogroup support | 432.800 / 0.99100 | Bridge orthogroup OG0001385 |
| etfBWP_371364466.1 · electron transfer flavoprotein subunit beta | High | Approved candidatestrong profile and bridge orthogroup support | 396.200 / 1.00000 | Bridge orthogroup OG0001139 |
| etfBWP_371367364.1 · electron transfer flavoprotein subunit beta | High | Approved candidatestrong profile and bridge orthogroup support | 380.900 / 1.00000 | Bridge orthogroup OG0001139 |
| etfBWP_371363987.1 · electron transfer flavoprotein subunit beta | High | Approved candidatestrong profile and bridge orthogroup support | 380.800 / 1.00000 | Bridge orthogroup OG0001139 |
| etfBWP_371361887.1 · electron transfer flavoprotein subunit beta | High | Approved candidatestrong profile and bridge orthogroup support | 380.000 / 1.00000 | Bridge orthogroup OG0001139 |
| etfBWP_371367854.1 · electron transfer flavoprotein subunit beta | High | Approved candidatestrong profile and bridge orthogroup support | 376.300 / 1.00000 | Bridge orthogroup OG0001139 |
| fabDWP_371368896.1 · ACP S-malonyltransferase | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 379.800 / 0.98700 | Annotation: gene_symbol |
| fabFWP_371368902.1 · beta-ketoacyl-ACP synthase II | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 666.500 / 0.99300 | Annotation: gene_symbol |
| fabFWP_371363891.1 · beta-ketoacyl-ACP synthase II | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 582.700 / 0.98800 | Annotation: gene_symbol |
| fabGWP_371368898.1 · 3-oxoacyl-[acyl-carrier-protein] reductase | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 281.600 / 0.99600 | Bridge orthogroup OG0000008 |
| fabHWP_371365476.1 · 3-oxoacyl-ACP synthase III family protein | Medium | Approved candidatestrong profile plus independent annotation support: specific_product_name | 239.400 / 0.99700 | Annotation: specific_product_name |
| fabKWP_371369800.1 · enoyl-[acyl-carrier-protein] reductase FabK | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 449.100 / 0.92700 | Annotation: gene_symbol |
| fabZWP_371363107.1 · 3-hydroxyacyl-ACP dehydratase FabZ | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 164.500 / 0.75400 | Bridge orthogroup OG0000074 |
| fabZWP_371361855.1 · 3-hydroxyacyl-ACP dehydratase FabZ | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 146.600 / 0.74900 | Bridge orthogroup OG0000074 |
| hbdWP_371364461.1 · 3-hydroxyacyl-CoA dehydrogenase family protein | High | Approved candidatestrong profile and bridge orthogroup support | 335.000 / 0.99300 | Bridge orthogroup OG0000153 |
| hbdWP_371364110.1 · 3-hydroxyacyl-CoA dehydrogenase family protein | High | Approved candidatestrong profile and bridge orthogroup support | 259.000 / 0.98900 | Bridge orthogroup OG0000153 |
| lctPWP_371366336.1 · L-lactate permease | High | Approved candidatestrong profile and bridge orthogroup support | 623.100 / 0.98400 | Bridge orthogroup OG0000731 |
| ldhWP_371361716.1 · malate dehydrogenase | High | Approved candidatestrong profile and bridge orthogroup support | 272.100 / 0.97800 | Bridge orthogroup OG0001800 |
| rnfAWP_371368564.1 · electron transport complex protein RnfA | High | Approved candidatestrong profile and bridge orthogroup support | 269.100 / 1.00000 | Bridge orthogroup OG0001169 |
| rnfBWP_371368566.1 · RnfABCDGE type electron transport complex subunit B | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 334.800 / 0.92500 | Bridge orthogroup OG0001404 |
| rnfCWP_371368557.1 · electron transport complex subunit RsxC | High | Approved candidatestrong profile and bridge orthogroup support | 424.700 / 0.75300 | Bridge orthogroup OG0001114 |
| rnfDWP_371368558.1 · RnfABCDGE type electron transport complex subunit D | High | Approved candidatestrong profile and bridge orthogroup support | 497.700 / 0.95900 | Bridge orthogroup OG0001182 |
| rnfEWP_371368562.1 · electron transport complex subunit RsxE | High | Approved candidatestrong profile and bridge orthogroup support | 274.200 / 0.96200 | Bridge orthogroup OG0001153 |
| rnfGWP_371368560.1 · RnfABCDGE type electron transport complex subunit G | High | Approved candidatestrong profile and bridge orthogroup support | 213.500 / 0.91200 | Bridge orthogroup OG0001292 |
| fabGWP_371364245.1 · SDR family oxidoreductase | Low | Excluded: low confidenceprofile hit lacks strong score and bridge orthogroup support | 91.100 / 0.98000 | Profile only |
| fabGWP_371364626.1 · SDR family NAD(P)-dependent oxidoreductase | Low | Excluded: low confidenceprofile hit lacks strong score and bridge orthogroup support | 71.200 / 0.80200 | Profile only |
| accCWP_371362686.1 · acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 594.300 / 0.99300 | Profile only |
| accCWP_371367986.1 · pyruvate carboxylase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 523.400 / 0.98400 | Profile only |
| bcdWP_371369632.1 · acyl-CoA dehydrogenase family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 491.000 / 0.99700 | Profile only |
| bcdWP_371361932.1 · acyl-CoA dehydrogenase family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 411.600 / 0.99500 | Profile only |
| bcdWP_371363423.1 · acyl-CoA dehydrogenase family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 375.000 / 0.94700 | Profile only |
| bcdWP_371361930.1 · acyl-CoA dehydrogenase family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 370.400 / 0.99700 | Profile only |
| crtWP_371367368.1 · short-chain-enoyl-CoA hydratase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 393.600 / 0.99600 | Annotation: specific_product_name |
| crtWP_371364463.1 · short-chain-enoyl-CoA hydratase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 380.900 / 0.99600 | Annotation: specific_product_name |
| crtWP_371367858.1 · short-chain-enoyl-CoA hydratase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 377.300 / 1.00000 | Annotation: specific_product_name |
| crtWP_371361877.1 · short-chain-enoyl-CoA hydratase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 368.500 / 0.99600 | Annotation: specific_product_name |
| etfAWP_371361928.1 · electron transfer flavoprotein subunit alpha/FixB family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 225.400 / 0.95800 | Profile only |
| fabGWP_371363461.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 277.200 / 1.00000 | Profile only |
| fabGWP_371366772.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 212.900 / 0.99200 | Profile only |
| fabGWP_371363844.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 184.400 / 0.98800 | Profile only |
| fabGWP_371366134.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 143.700 / 0.99200 | Profile only |
| fabGWP_371364614.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 104.200 / 0.99200 | Profile only |
| fabHWP_371368894.1 · beta-ketoacyl-ACP synthase III | Medium | Needs reviewno bridge-supported orthogroup; require domain, motif, or neighborhood confirmation | 349.500 / 0.99400 | Profile only |
| fabHWP_371368258.1 · beta-ketoacyl-ACP synthase III | Medium | Needs reviewno bridge-supported orthogroup; require domain, motif, or neighborhood confirmation | 336.500 / 0.99100 | Profile only |
| fabHWP_371364035.1 · beta-ketoacyl-ACP synthase III | Medium | Needs reviewno bridge-supported orthogroup; require domain, motif, or neighborhood confirmation | 219.200 / 0.98500 | Profile only |
| fabKWP_371365735.1 · nitronate monooxygenase | Medium | Needs reviewno bridge-supported orthogroup; require domain, motif, or neighborhood confirmation | 413.300 / 0.98700 | Profile only |
| fabKWP_371368900.1 · NAD(P)H-dependent flavin oxidoreductase | Medium | Needs reviewno bridge-supported orthogroup; require domain, motif, or neighborhood confirmation | 253.500 / 0.93300 | Profile only |
| fabLWP_371363461.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 202.000 / 0.96800 | Profile only |
| fabLWP_371363844.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 188.000 / 0.97200 | Profile only |
| fabLWP_371366772.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 173.600 / 0.98800 | Profile only |
| fabLWP_371366134.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 122.300 / 0.97200 | Profile only |
| fabLWP_371364614.1 · SDR family oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 111.800 / 0.97600 | Profile only |
| hbdWP_371363990.1 · 3-hydroxybutyryl-CoA dehydrogenase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 408.500 / 1.00000 | Profile only |
| hbdWP_371364452.1 · 3-hydroxybutyryl-CoA dehydrogenase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 408.400 / 1.00000 | Profile only |
| rnfCWP_371363804.1 · 4Fe-4S dicluster domain-containing protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 576.800 / 0.98900 | Profile only |
| thlWP_371364450.1 · acetyl-CoA C-acetyltransferase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 615.000 / 0.99700 | Profile only |
| thlWP_371363985.1 · acetyl-CoA C-acetyltransferase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 612.000 / 0.99700 | Profile only |
| fabLWP_371368898.1 · 3-oxoacyl-[acyl-carrier-protein] reductase | Medium | RejectedSpecific CDD hits identify the sequence as FabG/3-oxoacyl-ACP reductase rather than FabL. | 232.300 / 0.97200 | Annotation: CDD_competing_FabG_signature |
Protein-level evidence
| Gene | Protein | Orthogroup | Coordinates | Annotation |
|---|
These are genomic annotation predictions. Experimental activity, expression and metabolite production require separate evidence.