Assembly
ASM5214796v1
BioProject PRJNA1297070 · BioSample SAMN48982312
GENOME-RESOLVED EVIDENCE
GCA_052147965.1
Megasphaera coli · Complete Genome
View versioned NCBI assembly →
Quality metadata
Genome size 1822736 bp · GC 50.000%
Completeness —% · contamination —%
Pathway marker completeness
| Module | Markers | Fraction | Call |
|---|---|---|---|
| bcd_etf_module | 1/3 | 0.333 | Partial/absent |
| ethanol_entry_support | 0/1 | 0.000 | Partial/absent |
| fatty_acid_biosynthesis_core | 3/8 | 0.375 | Partial/absent |
| lactate_entry_support | 1/2 | 0.500 | Partial/absent |
| 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 |
|---|---|---|---|---|
| etfBWP_273061686.1 · electron transfer flavoprotein subunit beta/FixA family protein | High | Approved candidatestrong profile and bridge orthogroup support | 343.100 / 1.00000 | Bridge orthogroup OG0001139 |
| fabDWP_302441845.1 · ACP S-malonyltransferase | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 355.300 / 0.97800 | Annotation: gene_symbol |
| fabFWP_441562182.1 · beta-ketoacyl-ACP synthase II | Medium | Approved candidatestrong profile plus independent annotation support: gene_symbol | 609.600 / 0.99300 | Annotation: gene_symbol |
| fabGWP_075572045.1 · 3-oxoacyl-[acyl-carrier-protein] reductase | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 267.700 / 0.98800 | Bridge orthogroup OG0000008 |
| fabZWP_075572022.1 · 3-hydroxyacyl-ACP dehydratase FabZ | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 143.600 / 0.75400 | Bridge orthogroup OG0000074 |
| hbdWP_075572136.1 · 3-hydroxyacyl-CoA dehydrogenase family protein | High | Approved candidatestrong profile and bridge orthogroup support | 305.600 / 0.98900 | Bridge orthogroup OG0000153 |
| lctPWP_075572532.1 · L-lactate permease | High | Approved candidatestrong profile and bridge orthogroup support | 598.400 / 0.98600 | Bridge orthogroup OG0000731 |
| rnfAWP_075572778.1 · electron transport complex protein RnfA | High | Approved candidatestrong profile and bridge orthogroup support | 283.300 / 0.99500 | Bridge orthogroup OG0001169 |
| rnfBWP_441561252.1 · RnfABCDGE type electron transport complex subunit B | High | Approved candidatestrong profile and bridge orthogroup support; annotation support: gene_symbol | 304.200 / 0.94600 | Bridge orthogroup OG0001404 |
| rnfCWP_075572782.1 · electron transport complex subunit RsxC | High | Approved candidatestrong profile and bridge orthogroup support | 402.100 / 0.76400 | Bridge orthogroup OG0001114 |
| rnfDWP_075572781.1 · RnfABCDGE type electron transport complex subunit D | High | Approved candidatestrong profile and bridge orthogroup support | 502.700 / 0.95000 | Bridge orthogroup OG0001182 |
| rnfEWP_075572779.1 · electron transport complex subunit RsxE | High | Approved candidatestrong profile and bridge orthogroup support | 314.200 / 0.97100 | Bridge orthogroup OG0001153 |
| rnfGWP_075572780.1 · RnfABCDGE type electron transport complex subunit G | High | Approved candidatestrong profile and bridge orthogroup support | 199.100 / 0.90700 | Bridge orthogroup OG0001292 |
| thlWP_075572113.1 · acetyl-CoA C-acetyltransferase | High | Approved candidatestrong profile and bridge orthogroup support | 628.200 / 0.99700 | Bridge orthogroup OG0005114 |
| accCWP_075571862.1 · pyruvate carboxylase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 510.800 / 0.98700 | Profile only |
| bcdWP_273061688.1 · acyl-CoA dehydrogenase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 580.400 / 1.00000 | Profile only |
| bcdWP_441561568.1 · acyl-CoA dehydrogenase family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 562.600 / 0.99700 | Profile only |
| bcdWP_075572195.1 · acyl-CoA dehydrogenase family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 465.900 / 0.99500 | Profile only |
| crtWP_075573152.1 · short-chain-enoyl-CoA hydratase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 380.100 / 1.00000 | Annotation: specific_product_name |
| etfAWP_075572444.1 · electron transfer flavoprotein subunit alpha/FixB family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 445.800 / 0.99100 | Profile only |
| etfAWP_441561053.1 · electron transfer flavoprotein subunit alpha/FixB family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 328.300 / 0.97900 | Profile only |
| etfBWP_441561054.1 · electron transfer flavoprotein subunit beta/FixA family protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 255.900 / 0.99600 | Profile only |
| fabGWP_273062150.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 197.800 / 0.98400 | Profile only |
| fabGWP_075572319.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 159.200 / 0.97200 | Profile only |
| fabHWP_075572043.1 · beta-ketoacyl-ACP synthase III | Medium | Needs reviewno bridge-supported orthogroup; require domain, motif, or neighborhood confirmation | 320.100 / 0.99100 | Profile only |
| fabKWP_441562180.1 · NAD(P)H-dependent flavin oxidoreductase | Medium | Needs reviewno bridge-supported orthogroup; require domain, motif, or neighborhood confirmation | 219.800 / 0.93900 | Profile only |
| fabLWP_273062150.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 186.300 / 0.99200 | Profile only |
| fabLWP_075572319.1 · SDR family NAD(P)-dependent oxidoreductase | Medium | Needs reviewextreme per-proteome copy number; profile alone is not function-specific | 155.000 / 0.98800 | Profile only |
| hbdWP_075572358.1 · 3-hydroxybutyryl-CoA dehydrogenase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 401.100 / 0.98600 | Profile only |
| ldhWP_441561701.1 · L-lactate dehydrogenase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 285.100 / 0.98100 | Profile only |
| ldhWP_441562259.1 · lactate/malate family dehydrogenase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 284.100 / 0.98100 | Profile only |
| ldhWP_302441796.1 · L-lactate dehydrogenase | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 276.000 / 0.98700 | Profile only |
| rnfCWP_441561671.1 · 4Fe-4S dicluster domain-containing protein | Medium | Needs reviewretain confidence tier and orthogroup-support fields during import | 531.600 / 0.97700 | Profile only |
| fabLWP_075572045.1 · 3-oxoacyl-[acyl-carrier-protein] reductase | Medium | RejectedSpecific CDD hits identify the sequence as FabG/3-oxoacyl-ACP reductase rather than FabL. | 212.700 / 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.