Basic Information about the Plasmid Cluster
| Cluster Information |
Plasmid Cluster ID |
C747 |
| Reference Plasmid |
NZ_CP054280.1 |
| Reference Plasmid Size |
109094 |
| Reference Plasmid GC Content |
0.53 |
| Reference Plasmid Mobility Type |
conjugative |
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 |
| M0174737 |
BECKBOEM_00076 |
69113 |
4 |
Gut |
1.00 |
protein_coding |
stop_gained |
HIGH |
167G>A |
Trp56* |
| M0174738 |
BECKBOEM_00076 |
69114 |
4 |
Gut |
1.00 |
protein_coding |
missense_variant |
MODERATE |
166T>C |
Trp56Arg |
| M0174739 |
BECKBOEM_00076 |
69117 |
4 |
Gut |
1.00 |
protein_coding |
missense_variant |
MODERATE |
163G>C |
Ala55Pro |
| M0174740 |
BECKBOEM_00076 |
69118 |
4 |
Gut |
1.00 |
protein_coding |
synonymous_variant |
LOW |
162C>A |
Ser54Ser |
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 |
| BECKBOEM_00109 |
VFG034679 |
Ibes |
72.1 |
4.7e-184 |
1 |
459 |
0.9957 |
0.9978 |
Invasion |
Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC |
experiment |
| BECKBOEM_00109 |
VFG034652 |
Ibes |
72.1 |
2.7e-183 |
1 |
459 |
0.9957 |
0.9978 |
Invasion |
Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC |
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 |
| BECKBOEM_00068 |
Arsenic (As), Antimony (Sb) |
99.3 |
3.5e-77 |
1 |
141 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00071 |
Arsenic (As), Antimony (Sb) |
99.1 |
0 |
1 |
583 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00072 |
Arsenic (As), Antimony (Sb) |
98.3 |
1.6e-67 |
1 |
120 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00073 |
Arsenic (As), Antimony (Sb), Bismuth (Bi) |
100 |
8.1e-64 |
1 |
117 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00077 |
Mercury (Hg) |
96.2 |
2.7e-39 |
1 |
78 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00078 |
Mercury (Hg) |
90.1 |
1.6e-54 |
1 |
121 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00079 |
Mercury (Hg) |
92.5 |
8.4e-292 |
1 |
561 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00080 |
Mercury (Hg) |
80.1 |
1.6e-61 |
1 |
141 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00081 |
Mercury (Hg) |
85.7 |
4.5e-38 |
1 |
91 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00082 |
Mercury (Hg) |
99.1 |
6e-62 |
7 |
121 |
0.9504 |
0.9914 |
experiment |
| BECKBOEM_00083 |
Mercury (Hg) |
88.7 |
5.5e-73 |
1 |
151 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00092 |
Copper (Cu), Silver (Ag) |
81.9 |
4.8e-58 |
1 |
144 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00093 |
Copper (Cu) |
90.1 |
2.2e-237 |
1 |
465 |
0.9979 |
0.9979 |
experiment |
| BECKBOEM_00094 |
Copper (Cu) |
94.2 |
1.1e-120 |
1 |
226 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00095 |
Copper (Cu) |
85.4 |
3.9e-142 |
1 |
309 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00096 |
Copper (Cu) |
93.7 |
2.5e-63 |
1 |
126 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00097 |
Copper (Cu) |
84.5 |
1.3e-150 |
3 |
297 |
0.9966 |
1.0000 |
experiment |
| BECKBOEM_00098 |
Copper (Cu) |
94.6 |
1.1e-287 |
1 |
496 |
1.0000 |
0.8198 |
experiment |
| BECKBOEM_00104 |
Silver (Ag) |
86.4 |
0 |
1 |
813 |
0.9963 |
0.9879 |
experiment |
| BECKBOEM_00106 |
Silver (Ag) |
97.1 |
0 |
1 |
1048 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00107 |
Silver (Ag) |
93 |
9.7e-232 |
1 |
430 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00108 |
Silver (Ag) |
83.3 |
7.4e-41 |
28 |
117 |
0.7692 |
0.9375 |
experiment |
| BECKBOEM_00109 |
Silver (Ag) |
92.4 |
4e-239 |
1 |
461 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00110 |
Copper (Cu), Silver (Ag) |
88.9 |
8.7e-115 |
1 |
225 |
0.9956 |
0.9912 |
experiment |
| BECKBOEM_00111 |
Silver (Ag) |
84.6 |
4.7e-230 |
1 |
489 |
1.0020 |
0.9920 |
experiment |
| BECKBOEM_00112 |
Silver (Ag) |
76.2 |
4e-57 |
1 |
143 |
1.0000 |
1.0000 |
experiment |
| BECKBOEM_00068 |
Arsenic (As) |
100 |
1.6e-75 |
1 |
141 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00071 |
Arsenic (As), Antimony (Sb) |
100 |
0 |
1 |
583 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00072 |
Arsenic (As) |
100 |
4.4e-66 |
1 |
120 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00073 |
Arsenic (As) |
100 |
1.9e-61 |
1 |
117 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00077 |
Mercury (Hg) |
98.7 |
5.1e-39 |
1 |
78 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00078 |
Mercury (Hg) |
100 |
3.1e-59 |
1 |
121 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00079 |
Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] |
99.8 |
0 |
1 |
561 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00080 |
Mercury (Hg) |
80.9 |
3.2e-60 |
1 |
141 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00081 |
Mercury (Hg) |
94.5 |
9.1e-40 |
1 |
91 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00082 |
Mercury (Hg) |
100 |
1.2e-63 |
1 |
121 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00083 |
Mercury (Hg) |
99.3 |
7.9e-81 |
1 |
151 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00092 |
Copper (Cu), Silver (Ag) |
84.7 |
2.4e-58 |
1 |
144 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00093 |
Copper (Cu) |
98.9 |
3.2e-258 |
1 |
466 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00094 |
Copper (Cu) |
100 |
3e-124 |
1 |
226 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00095 |
Copper (Cu) |
100 |
4.2e-161 |
1 |
309 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00096 |
Copper (Cu) |
100 |
3.9e-65 |
1 |
126 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00097 |
Copper (Cu) |
84.9 |
7.1e-150 |
1 |
297 |
1.0034 |
1.0000 |
prediction |
| BECKBOEM_00098 |
Copper (Cu) |
100 |
3.4e-298 |
1 |
496 |
1.0000 |
0.8198 |
prediction |
| BECKBOEM_00104 |
Silver (Ag) |
87.8 |
0 |
1 |
813 |
0.9951 |
1.0000 |
prediction |
| BECKBOEM_00106 |
Silver (Ag) |
100 |
0 |
1 |
1048 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00107 |
Silver (Ag) |
100 |
3.8e-245 |
1 |
430 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00108 |
Silver (Ag) |
87.2 |
9.2e-53 |
1 |
117 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00109 |
Silver (Ag) |
100 |
3.7e-254 |
1 |
461 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00110 |
Silver (Ag) |
96.9 |
4.8e-122 |
1 |
226 |
1.0000 |
1.0000 |
prediction |
| BECKBOEM_00111 |
Silver (Ag) |
88.7 |
1.4e-243 |
1 |
486 |
0.9878 |
0.9898 |
prediction |
| BECKBOEM_00112 |
Silver (Ag) |
79 |
4.4e-57 |
1 |
143 |
1.0000 |
1.0000 |
prediction |
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 |
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 |
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.
| Gene Name |
cazy_id |
identity |
evalue |
qstart |
qend |
query_coverage |
subject_coverage |
| BECKBOEM_00023 |
APB48007.1|GH23 |
100 |
2.97e-105 |
1 |
151 |
1 |
1 |
| BECKBOEM_00057 |
QLV33194.1|GT2 |
100 |
3.48e-241 |
1 |
331 |
1 |
1 |
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 |
| BECKBOEM_00059 |
2.A.53.3.1 |
90.9 |
3.1e-249 |
1 |
492 |
1.0000 |
1.0000 |
2 |
Electrochemical Potential-driven Transporters |
2.A |
Porters (uniporters, symporters, antiporters) |
2.A.53 |
The Sulfate Permease (SulP) Family |
| BECKBOEM_00071 |
3.A.4.1.1 |
85.7 |
5e-283 |
1 |
581 |
0.9966 |
1.3543 |
3 |
Primary Active Transporters |
3.A |
P-P-bond-hydrolysis-driven transporters |
3.A.4 |
The Arsenite-Antimonite (ArsAB) Efflux Family |
| BECKBOEM_00077 |
1.A.72.5.1 |
80.8 |
7.5e-33 |
1 |
78 |
1.0000 |
1.0000 |
1 |
Channels/Pores |
1.A |
α-Type Channels |
1.A.72 |
The Mercuric Ion Pore (Mer) Superfamily |
| BECKBOEM_00081 |
1.A.72.3.1 |
85.7 |
1.7e-36 |
1 |
91 |
1.0000 |
1.0000 |
1 |
Channels/Pores |
1.A |
α-Type Channels |
1.A.72 |
The Mercuric Ion Pore (Mer) Superfamily |
| BECKBOEM_00082 |
1.A.72.3.1 |
93 |
4.4e-56 |
7 |
121 |
0.9504 |
1.2637 |
1 |
Channels/Pores |
1.A |
α-Type Channels |
1.A.72 |
The Mercuric Ion Pore (Mer) Superfamily |
| BECKBOEM_00095 |
9.B.62.1.1 |
85.4 |
1.5e-140 |
1 |
309 |
1.0000 |
1.0000 |
9 |
Incompletely Characterized Transport Systems |
9.B |
Putative transport proteins |
9.B.62 |
The Copper Resistance (CopD) Family |
| BECKBOEM_00097 |
1.B.76.1.5 |
84.5 |
4.9e-149 |
3 |
297 |
0.9933 |
1.0000 |
1 |
Channels/Pores |
1.B |
β-Barrel Porins |
1.B.76 |
The Copper Resistance Putative Porin (CopB) Family |
| BECKBOEM_00102 |
1.A.34.1.3 |
85.8 |
8.2e-118 |
1 |
246 |
1.0000 |
1.0000 |
1 |
Channels/Pores |
1.A |
α-Type Channels |
1.A.34 |
The <i>Bacillus</i> Gap Junction-like Channel-forming Complex (GJ-CC) Family |
| BECKBOEM_00104 |
3.A.3.5.4 |
86.4 |
0 |
1 |
813 |
0.9951 |
0.9879 |
3 |
Primary Active Transporters |
3.A |
P-P-bond-hydrolysis-driven transporters |
3.A.3 |
The P-type ATPase (P-ATPase) Superfamily |
| BECKBOEM_00106 |
2.A.6.1.3 |
97.1 |
0 |
1 |
1048 |
1.0000 |
1.0000 |
2 |
Electrochemical Potential-driven Transporters |
2.A |
Porters (uniporters, symporters, antiporters) |
2.A.6 |
The Resistance-Nodulation-Cell Division (RND) Superfamily |
| BECKBOEM_00109 |
1.B.17.3.4 |
92.4 |
1.5e-237 |
1 |
461 |
1.0000 |
1.0000 |
1 |
Channels/Pores |
1.B |
β-Barrel Porins |
1.B.17 |
The Outer Membrane Factor (OMF) Family |