Assembly
ASM1014v1
BioProject PRJDA18979 · BioSample SAMD00060917
GENOME-RESOLVED EVIDENCE
GCA_000010145.1
Limosilactobacillus fermentum IFO 3956 · Complete Genome
View versioned NCBI assembly →
Quality metadata
Genome size 2098685 bp · GC 51.500%
Completeness —% · contamination —%
Pathway marker completeness
| Module | Markers | Fraction | Call |
|---|---|---|---|
| bcd_etf_module | 0/3 | 0.000 | Partial/absent |
| ethanol_entry_support | 1/1 | 1.000 | Complete marker set |
| fatty_acid_biosynthesis_core | 6/8 | 0.750 | Partial/absent |
| lactate_entry_support | 0/2 | 0.000 | 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_012390849.1 · acetyl-CoA carboxylase carboxyltransferase subunit alpha | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 299.400 / 0.95200 | Bridge orthogroup OG0001120 |
| accBWP_003682549.1 · acetyl-CoA carboxylase biotin carboxyl carrier protein | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 122.100 / 0.99400 | Annotation: gene_symbol |
| accCWP_004563306.1 · acetyl-CoA carboxylase biotin carboxylase subunit | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 650.300 / 0.99300 | Annotation: gene_symbol |
| accDWP_004563305.1 · acetyl-CoA carboxylase carboxyltransferase subunit beta | High | Approved candidatestrong profile and bridge orthogroup support | 349.200 / 0.93500 | Bridge orthogroup OG0000844 |
| adhEWP_004562754.1 · bifunctional acetaldehyde-CoA/alcohol dehydrogenase | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 1089.700 / 0.99500 | Bridge orthogroup OG0002334 |
| fabFWP_003682547.1 · beta-ketoacyl-ACP synthase II | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 516.300 / 0.99000 | Annotation: gene_symbol |
| fabGWP_003682544.1 · 3-oxoacyl-ACP reductase family protein | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: specific_product_name | 221.100 / 0.99200 | Bridge orthogroup OG0000008 |
| fabIWP_004563304.1 · enoyl-ACP reductase FabI | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 348.200 / 0.96900 | Annotation: gene_symbol |
| fabZWP_003682551.1 · 3-hydroxyacyl-ACP dehydratase FabZ | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 165.600 / 0.74300 | Bridge orthogroup OG0000074 |
| fabZWP_004563311.1 · 3-hydroxyacyl-ACP dehydratase FabZ | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 122.500 / 0.75400 | Bridge orthogroup OG0000074 |
| thlWP_003682977.1 · acetyl-CoA C-acetyltransferase | High | Approved candidatestrong profile and bridge orthogroup support | 513.200 / 0.99700 | Bridge orthogroup OG0000010 |
| fabGWP_004563304.1 · enoyl-ACP reductase FabI | Low | Excluded: low confidenceprofile hit lacks strong score and bridge orthogroup support | 79.400 / 0.97600 | Profile only |
| accCWP_012391659.1 · acetyl-CoA carboxylase biotin carboxylase subunit | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 540.200 / 0.99100 | Profile only |
| crtWP_003683002.1 · 1,4-dihydroxy-2-naphthoyl-CoA synthase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 151.800 / 0.98800 | Profile only |
| fabGWP_012391768.1 · glucose 1-dehydrogenase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 202.300 / 0.98800 | Profile only |
| fabGWP_012391165.1 · glucose 1-dehydrogenase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 196.900 / 0.99200 | Profile only |
| fabGWP_003681624.1 · (S)-acetoin forming diacetyl reductase | High | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 189.200 / 0.97200 | Bridge orthogroup OG0000008 |
| fabGWP_012391688.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 184.900 / 0.96000 | Profile only |
| fabGWP_171029993.1 · SDR family NAD(P)-dependent oxidoreductase | High | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 171.400 / 0.88700 | Bridge orthogroup OG0000242 |
| fabHWP_004563309.1 · beta-ketoacyl-ACP synthase III | Medium | Needs reviewno bridge-supported orthogroup; require domain, motif, or neighborhood confirmation | 248.400 / 0.97600 | Profile only |
| fabKWP_012391681.1 · NAD(P)H-dependent flavin oxidoreductase | Medium | Needs reviewno bridge-supported orthogroup; require domain, motif, or neighborhood confirmation | 203.500 / 0.95200 | Profile only |
| fabLWP_003681624.1 · (S)-acetoin forming diacetyl reductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 193.100 / 0.99200 | Profile only |
| fabLWP_012391768.1 · glucose 1-dehydrogenase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 183.300 / 0.98000 | Profile only |
| fabLWP_012391688.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 178.300 / 0.96800 | Profile only |
| fabLWP_003682544.1 · 3-oxoacyl-ACP reductase family protein | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 167.200 / 0.97600 | Profile only |
| fabLWP_012391165.1 · glucose 1-dehydrogenase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 165.400 / 0.99200 | Profile only |
| fabLWP_171029993.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 152.900 / 0.77000 | Profile only |
| ldhWP_012391154.1 · L-lactate dehydrogenase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 367.800 / 0.98700 | Profile only |
| ldhWP_012391006.1 · L-lactate dehydrogenase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 233.200 / 0.95900 | Profile only |
| ldhWP_012390864.1 · L-lactate dehydrogenase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 230.900 / 0.96800 | Profile only |
| ldhWP_004563357.1 · L-lactate dehydrogenase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 222.800 / 0.96800 | Profile only |
Protein-level evidence
| Gene | Protein | Orthogroup | Coordinates | Annotation |
|---|
These are genomic annotation predictions. Experimental activity, expression and metabolite production require separate evidence.