Annotation Categories of the Plasmid Cluster
Summary of the plasmid cluster
Basic Information about the Plasmid Cluster
| Cluster Information |
Plasmid Cluster ID |
C890 |
| Reference Plasmid |
NZ_CP072882.1 |
| Reference Plasmid Size |
183270 |
| Reference Plasmid GC Content |
0.36 |
| Reference Plasmid Mobility Type |
non-mobilizable |
Mutation sites in the plasmid cluster
The table lists mutations identified in the plasmid cluster.
Note: Mutations identified in this plasmid cluster are listed below. Click on a mutation ID to view full details..
| mutid |
gname |
pos |
count |
tissue |
frequnt |
biotype |
consequence |
impact |
nucchange |
aachange |
| M0188177 |
MCPBPDFC_00107 |
104181 |
3 |
Gut |
0.50 |
protein_coding |
missense_variant |
MODERATE |
371G>T |
Ser124Ile |
| M0188178 |
MCPBPDFC_00107 |
104289 |
3 |
Gut |
0.50 |
protein_coding |
missense_variant |
MODERATE |
263A>G |
Lys88Arg |
| M0188179 |
MCPBPDFC_00108 |
104692 |
3 |
Gut |
0.50 |
protein_coding |
missense_variant |
MODERATE |
3124G>A |
Val1042Ile |
| M0188180 |
MCPBPDFC_00108 |
104720 |
3 |
Gut |
0.50 |
protein_coding |
synonymous_variant |
LOW |
3096C>A |
Ala1032Ala |
Analysis of virulence factors contributing to bacterial pathogenicity
This table presents virulence factors identified within the plasmid cluster.
Note: Virulence factor analysis was performed using VFDB. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known virulence factors are listed.
| Gene Name |
vf_gene_id |
vf_name |
identity |
evalue |
qstart |
qend |
query_coverage |
subject_coverage |
vf_category |
gene_description |
condition |
| MCPBPDFC_00006 |
VFG042989 |
PilA-type pili (PGS1, pilin gene clusters 1) |
99.1 |
1e-124 |
1 |
223 |
1.0 |
1 |
Adherence |
putative housekeeping sortase |
prediction |
| MCPBPDFC_00009 |
VFG042985 |
PilA-type pili (PGS1, pilin gene clusters 1) |
98.8 |
4.9e-38 |
1 |
86 |
1.0 |
1 |
Adherence |
hypothetical hydrophobic peptide |
prediction |
Analysis of biocide and heavy metal resistance genes to assess antimicrobial risk and environmental impact
This table presents biocides and heavy metals resistance genes identified within the plasmid cluster.
Note: Analyzing biocide and heavy metal resistance genes based on BacMet to evaluate bacterial resistance risk and the potential impact of environmental heavy metal contamination. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, E-value < 1e-5) to known biocide and heavy metal resistance genes are listed.
| Gene Name |
compound |
identity |
evalue |
qstart |
qend |
query_coverage |
subject_coverage |
group |
Analyzing antimicrobial resistance genes to assess bacterial resistance to antibiotics and other antimicrobial agents
This table presents antimicrobial resistance genes identified within the plasmid cluster.
Note: Antimicrobial resistance was performed using CARD. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known antimicrobial resistance genes are listed.
| Gene Name |
aro_accession |
identity |
evalue |
qstart |
qend |
query_coverage |
subject_coverage |
drug_class |
amr_gene_family |
resistance_mechanism |
| MCPBPDFC_00167 |
ARO:3000375 |
98.8 |
4.8e-175 |
1 |
245 |
1.0000 |
0.9879 |
macrolide antibiotic |
Erm 23S ribosomal RNA methyltransferase |
antibiotic target alteration |
| MCPBPDFC_00179 |
ARO:3000375 |
98.8 |
4.8e-175 |
1 |
245 |
1.0000 |
0.9879 |
macrolide antibiotic |
Erm 23S ribosomal RNA methyltransferase |
antibiotic target alteration |
Analysis of pathogenicity genes to explore pathogen-host interactions
This table presents host pathogen-host interactions within the plasmid cluster.
Note: Analyzing pathogenicity-related genes using PHI-base to understand pathogen virulence mechanisms and their impact on host interactions. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e-5) to known pathogenicity-related genes are listed.
| Gene Name |
phi_molconn_id |
host gene_name |
identity |
evalue |
qstart |
qend |
query_coverage |
subject_coverage |
host_descripton |
disease_name |
function |
phenotype_of_mutant |
| MCPBPDFC_00017 |
PHI:5205 |
HMPREF0351_10118 (WxL locusC) |
75 |
1.5e-174 |
1 |
392 |
0.9899 |
1.0000 |
rodents |
endocarditis |
involved in bile salt stress and endocarditis pathogenesis |
reduced virulence |
| MCPBPDFC_00083 |
PHI:7637 |
CspA |
76.9 |
7.4e-26 |
1 |
65 |
1.0000 |
0.9848 |
bony fishes |
listeriosis |
cold shock protein |
reduced virulence |
| MCPBPDFC_00120 |
PHI:5205 |
HMPREF0351_10118 (WxL locusC) |
75 |
1.5e-174 |
1 |
392 |
0.9899 |
1.0000 |
rodents |
endocarditis |
involved in bile salt stress and endocarditis pathogenesis |
reduced virulence |
Analyzing carbohydrate-active enzyme genes to uncover mechanisms of nutrient degradation
This table presents carbohydrate-active enzyme genes identified within the plasmid cluster.
Note: Annotation of carbohydrate-active enzyme genes was performed using CAZy to explore mechanisms of nutrient breakdown and utilization. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known CAZyme genes are listed.
Analyzing transport proteins to understand bacterial strategies for substrate uptake and detoxification
This table presents transport proteins within the plasmid cluster.
Note: Investigation of transport proteins based on TCDB to uncover bacterial mechanisms of substrate transport and environmental detoxification. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known transport protein entries are listed.
| Gene Name |
tcid |
identity |
evalue |
qstart |
qend |
query_coverage |
subject_coverage |
class_field |
class_term |
subclass |
subclass_term |
family |
family_term |
| MCPBPDFC_00171 |
3.A.1.126.5 |
100 |
1.9e-163 |
61 |
353 |
0.8300 |
1.0000 |
3 |
Primary Active Transporters |
3.A |
P-P-bond-hydrolysis-driven transporters |
3.A.1 |
The ATP-binding Cassette (ABC) Superfamily |