Assembly
ASM5539169v1
BioProject PRJDB20344 · BioSample SAMD00887400
GENOME-RESOLVED EVIDENCE
GCA_055391695.1
Clostridium nitrophenolicum · Complete Genome
View versioned NCBI assembly →
Quality metadata
Genome size 5767678 bp · GC 31.500%
Completeness 98.760% · contamination 3.420%
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 | 4/8 | 0.500 | Partial/absent |
| lactate_entry_support | 2/2 | 1.000 | Complete marker set |
| reverse_beta_oxidation_core | 3/4 | 0.750 | Partial/absent |
| rnf_complex | 1/6 | 0.167 | Partial/absent |
Detected markers
| Marker | Function | Copies |
|---|---|---|
| rnfA | Rnf complex subunit A | 1 |
| adhE | bifunctional acetaldehyde-CoA/alcohol dehydrogenase | 2 |
| accB | acetyl-CoA carboxylase biotin carboxyl carrier protein | 1 |
| accC | acetyl-CoA carboxylase biotin carboxylase | 1 |
| fabH | 3-oxoacyl-ACP synthase III | 1 |
| fabZ | 3-hydroxyacyl-ACP dehydratase | 2 |
| lctP | L-lactate permease | 1 |
| ldh | L-lactate dehydrogenase | 1 |
| crt | crotonase/enoyl-CoA hydratase | 2 |
| hbd | 3-hydroxybutyryl-CoA dehydrogenase | 2 |
| thl | acetyl-CoA acetyltransferase/thiolase | 3 |
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 |
|---|---|---|---|---|
| No profile-HMM predictions for this assembly. | ||||
Protein-level evidence
| Gene | Protein | Orthogroup | Coordinates | Annotation |
|---|---|---|---|---|
| accCJCM14030_51810 | BGT46466.1 | OG0000061 | AP042469.1:5562330–5563676 - | acetyl-CoA carboxylase biotin carboxylase subunit [Clostridium nitrophenolicum] |
| ldhJCM14030_22760 | BGT43561.1 | OG0000131 | AP042469.1:2454350–2455297 - | L-lactate dehydrogenase [Clostridium nitrophenolicum] |
| accBJCM14030_51830 | BGT46468.1 | OG0000212 | AP042469.1:5564394–5564915 - | acetyl-CoA carboxylase biotin carboxyl carrier protein [Clostridium nitrophenolicum] |
| hbdJCM14030_06190 | BGT41904.1 | OG0000229 | AP042469.1:696751–697596 + | 3-hydroxybutyryl-CoA dehydrogenase [Clostridium nitrophenolicum] |
| hbdJCM14030_32140 | BGT44499.1 | OG0000229 | AP042469.1:3376848–3377696 - | 3-hydroxybutyryl-CoA dehydrogenase [Clostridium nitrophenolicum] |
| thlJCM14030_06200 | BGT41905.1 | OG0000234 | AP042469.1:697647–698825 + | acetyl-CoA C-acetyltransferase [Clostridium nitrophenolicum] |
| thlJCM14030_32190 | BGT44504.1 | OG0000234 | AP042469.1:3381681–3382856 - | acetyl-CoA C-acetyltransferase [Clostridium nitrophenolicum] |
| thlJCM14030_33310 | BGT44616.1 | OG0000234 | AP042469.1:3502270–3503448 - | acetyl-CoA C-acetyltransferase [Clostridium nitrophenolicum] |
| fabZ_2JCM14030_51820 | BGT46467.1 | OG0000785 | AP042469.1:5563765–5564211 - | 3-hydroxyacyl-ACP dehydratase FabZ [Clostridium nitrophenolicum] |
| adhE_1JCM14030_03040 | BGT41589.1 | OG0001124 | AP042469.1:328661–331291 - | bifunctional acetaldehyde-CoA/alcohol dehydrogenase [Clostridium nitrophenolicum] |
| adhE_2JCM14030_07830 | BGT42068.1 | OG0001124 | AP042469.1:879081–881687 + | bifunctional acetaldehyde-CoA/alcohol dehydrogenase [Clostridium nitrophenolicum] |
| lctPJCM14030_26600 | BGT43945.1 | OG0001228 | AP042469.1:2841075–2842583 - | L-lactate permease [Clostridium nitrophenolicum] |
| rnfAJCM14030_45050 | BGT45790.1 | OG0001328 | AP042469.1:4806510–4807088 - | electron transport complex protein RnfA [Clostridium nitrophenolicum] |
| crtJCM14030_32180 | BGT44503.1 | OG0001394 | AP042469.1:3380870–3381652 - | short-chain-enoyl-CoA hydratase [Clostridium nitrophenolicum] |
| crtJCM14030_06180 | BGT41903.1 | OG0001639 | AP042469.1:695933–696712 + | short-chain-enoyl-CoA hydratase [Clostridium nitrophenolicum] |
| fabHJCM14030_16910 | BGT42976.1 | OG0003311 | AP042469.1:1828868–1829872 - | 3-oxoacyl-ACP synthase III family protein [Clostridium nitrophenolicum] |
| fabZ_1JCM14030_28290 | BGT44114.1 | OG0018560 | AP042469.1:3003887–3004297 - | 3-hydroxyacyl-ACP dehydratase FabZ [Clostridium nitrophenolicum] |
These are genomic annotation predictions. Experimental activity, expression and metabolite production require separate evidence.