SPECIES · STRAIN AND FUNCTION PROFILE
Clostridium gelidum
Reported/putative producer
Imported from the NCBI assembly data report; MCFA production is not implied.
1strain profiles1assemblies12MCFA marker genes67%strain metadata coverage
Name, taxonomy and strain identifiers
Curation status: Exact match imported · Strain designation · checked 2026-07-29. Exact strain-level match; curated BacDive fields imported.
Taxonomic record
- Scientific name
- Clostridium gelidum
- Rank
- species
- NCBI Taxonomy
- Not resolved at this level
- Database role
- Reported/putative producer
C5S11 Type strain
- Full name
- Clostridium gelidum
- Culture collections
- DSM 112608, NBRC 114689
- History
- DSMZ <- A. Ueki, Yamagata Univ., Tsuruoka, Japan; C5S11 <- S Homma; {2009}
- BacDive
- Strain 169423
Morphology and observable traits
| Strain | Gram stain | Cell shape | Motility | Spore formation | Colony morphology |
|---|
| C5S11 | Not curated | Not curated | Not curated | Not curated | Not curated |
Culture and growth conditions
| Strain | Medium | Temperature | pH | Atmosphere/result |
|---|
| C5S11 | PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)DSMZ Medium 104 · Name: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)
Composition:
Yeast extract 10.0 g/l
D-Glucose 5.0 g/l
Trypticase peptone 5.0 g/l
Meat peptone 5.0 g/l
Na2CO3 1.0 g/l
L-Cysteine HCl x H2O 0.5 g/l
NaHCO3 0.4 g/l
NaCl 0.08 g/l
K2HPO4 0.04 g/l
KH2PO4 0.04 g/l
MgSO4 x 7 H2O 0.02 g/l
CaCl2 x 2 H2O 0.01 g/l
Sodium resazurin 0.0005 g/l
Distilled water | 10.00 °C | — | — · yes |
Documented condition ranges
| Profile | pH | Temperature | Electron donors | Substrates/reactor |
|---|
| BacDive documented cultivation conditions | ?–?; optimum ? | 10.00–10.00 °C; optimum ? | Not curated | —; culture-collection cultivation |
| Species-level documented cultivation conditions | ?–?; optimum ? | 10.00–10.00 °C; optimum ? | Not curated | —; species-level culture records |
Physiology and metabolism
Documented substrates and products
Only approved assertions are shown. Results may be strain- and condition-specific.
| Relationship | Compound/source term | Evidence | Confidence | Condition |
|---|
| No approved strain-level phenotype assertions yet. |
Predicted metabolic capabilities
Genome-derived hypotheses requiring review—not demonstrated substrates or products.
| Capability | Basis/status | Confidence | Assemblies | Limitation |
|---|
| reverse beta-oxidation potential | Genomic prediction · Needs review | 0.600 | GCA_019977655.1 | Complete marker-rule set; not evidence of expression, flux, or product formation. |
| lactate transport potential | Genomic prediction · Needs review | 0.450 | GCA_019977655.1 | Transporter annotation supports uptake potential but not utilization. |
| lactate metabolism potential | Genomic prediction · Needs review | 0.400 | GCA_019977655.1 | LDH presence does not establish reaction direction or growth on lactate. |
Isolation, environment and safety
| Strain | Isolation source | Category/location | Oxygen tolerance | Biosafety | GC content |
|---|
| C5S11 | rice paddy field soil | —; Japan | Not curated | Not curated | 29.000% |
Sequence information
Genome assemblies
| Accession | Source | Level | Size/GC | Quality | BioProject |
|---|
| GCA_019977655.1 | NCBI GenBank | Complete Genome | 6041432 bp / 29.000% | 99.070% complete; 0.540% contamination | PRJDB11893 |
Marker and ribosomal sequences
| Strain | Type | Accession | Length | Description |
|---|
| C5S11 | 16S rRNA | AB539905 | 1419 bp | Clostridium gelidum gene for 16S ribosomal RNA, partial sequence |
| C5S11 | Genome | GCA_019977655 | — bp | ASM1997765v1 assembly for Clostridium gelidum C5S11 |
MCFA pathways and genes
Show 12 annotation-derived MCFA genes
| Gene | Locus | Function | Protein | Orthogroup |
|---|
| crt | psyc5s11_03820 | 3-hydroxybutyryl-CoA dehydratase (4.2.1.55) | BCZ44315.1 | OG0001394 |
| hbd | psyc5s11_03860 | 3-hydroxybutyryl-CoA dehydrogenase (1.1.1.157) | BCZ44319.1 | OG0000229 |
| thl | psyc5s11_05700 | Acetyl-CoA acetyltransferase (2.3.1.9) | BCZ44503.1 | OG0000234 |
| bcd | psyc5s11_10980 | Butyryl-CoA dehydrogenase (1.3.8.1) | BCZ45031.1 | OG0000229 |
| glcA | psyc5s11_17910 | L-lactate permease [Clostridium gelidum] | BCZ45724.1 | OG0001228 |
| bcd2_1 | psyc5s11_17930 | Butyryl-CoA dehydrogenase (1.3.8.1) | BCZ45726.1 | OG0000034 |
| bcd2_2 | psyc5s11_17990 | Butyryl-CoA dehydrogenase (1.3.8.1) | BCZ45732.1 | OG0000034 |
| accC | psyc5s11_43320 | Acetyl-CoA carboxylase (6.4.1.2) | BCZ48265.1 | OG0000061 |
| ldh1 | psyc5s11_44040 | L-lactate dehydrogenase (1.1.1.27) | BCZ48337.1 | OG0000131 |
| ldh | psyc5s11_46120 | L-lactate dehydrogenase (1.1.1.27) | BCZ48545.1 | OG0000131 |
| ldh3 | psyc5s11_48330 | L-lactate dehydrogenase (1.1.1.27) | BCZ48766.1 | OG0000131 |
| thil | psyc5s11_54680 | Acetyl-CoA acetyltransferase (2.3.1.9) | BCZ49401.1 | OG0000234 |
Curator-approved marker pathway assessments
These summaries use approved candidate predictions only and update after every review decision.
| Assembly | Pathway rule | Approved markers | Status |
|---|
| No approved-marker pathway assessments. |
Profile-HMM marker predictions
Approved candidates and unresolved review calls are genomic hypotheses, not evidence of expression or MCFA production.
| Marker | Assembly / protein | Confidence and status | Support | Review history |
|---|
| No active marker predictions for this organism. |
Literature and provenance
| Study | DOI | Public data |
|---|
| No organism-linked literature indexed yet. |
Profile evidence
External databases can change. mcfaKB records source links and separates experimentally reported, curator-entered and predicted information.