Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C774
  Reference Plasmid   NZ_CP060066.1
  Reference Plasmid Size   148192
  Reference Plasmid GC Content   0.51
  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
M0177462 DHINOAPB_00092 96382 3 Gut 0.11 protein_coding stop_gained HIGH 1484T>G Leu495*






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
DHINOAPB_00006 VFG043568 OmpD 76 2.8e-159 1 365 1.0 1.0083 Adherence phosphoporin PhoE 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
DHINOAPB_00006 Methyl Viologen [class: Paraquat] 76 5.8e-161 1 365 1.0164 1.0249 experiment
DHINOAPB_00043 Nickel (Ni), Cobalt (Co) 79.2 2.6e-115 1 255 1.0000 1.0000 experiment
DHINOAPB_00044 Nickel (Ni), Cobalt (Co) 91.5 4.3e-160 1 318 1.0000 1.0000 experiment
DHINOAPB_00006 Methyl Viologen [class: Paraquat] 92.7 1.9e-197 1 365 1.0192 1.0000 prediction
DHINOAPB_00043 Nickel (Ni), Cobalt (Co) 99.6 8.8e-141 1 255 1.0000 1.0000 prediction
DHINOAPB_00044 Nickel (Ni), Cobalt (Co) 100 1.4e-172 1 318 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
DHINOAPB_00006 PHI:123435 ompD 76 9.8e-160 1 365 1.0000 0.9945 rodents salmonellosis porin OmpD unaffected pathogenicity
DHINOAPB_00037 PHI:6268 lacZ 96.9 0 1 1024 1.0000 1.0000 rodents urinary tract infection beta-galactosidase reduced virulence
DHINOAPB_00043 PHI:8010 fecE 79.2 4.3e-114 1 255 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport ATP-binding protein reduced virulence
DHINOAPB_00044 PHI:8009 fecD 91.5 7.2e-159 1 318 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport system permease protein reduced virulence
DHINOAPB_00045 PHI:8008 fecC 96.7 4e-176 1 332 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport system permease protein reduced virulence
DHINOAPB_00046 PHI:8007 fecB 95.7 2.3e-159 1 300 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate-binding periplasmic protein reduced virulence
DHINOAPB_00047 PHI:8006 fecA 98.6 0 1 762 1.0000 0.9845 even-toed ungulates bovine mastitis ferric citrate outer membrane transporter reduced virulence
DHINOAPB_00048 PHI:8005 fecR 99.1 4.8e-179 1 317 1.0000 1.0000 even-toed ungulates bovine mastitis Fec operon regulator reduced virulence
DHINOAPB_00049 PHI:8004 fecI 97.7 1.6e-91 1 173 1.0000 1.0000 even-toed ungulates bovine mastitis RNA polymerase sigma factor reduced virulence
DHINOAPB_00079 PHI:3317 hsdR 71.4 5.5e-78 17 215 0.9256 0.9853 rodents Glasser's disease involved in pathogenicity reduced virulence
DHINOAPB_00081 PHI:3317 hsdR 75.6 0 1 813 0.9915 0.9853 rodents Glasser's disease involved in pathogenicity reduced virulence
DHINOAPB_00132 PHI:123638 DcuR 88.7 1.7e-123 1 239 1.0000 1.0000 birds pullorum disease two-component system increased virulence (hypervirulence)






        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
DHINOAPB_00004 AXY98589.1|GH24 97.7 1.05e-161 12 229 0.952 1
DHINOAPB_00037 QCC99264.1|GH2 100 0 1 1024 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
DHINOAPB_00003 1.E.64.1.1 97.6 1.3e-38 1 84 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.64 The P7 Phage Holin LydD (LydD) Family
DHINOAPB_00006 1.B.1.1.4 81.1 2.7e-173 1 365 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.1 The General Bacterial Porin (GBP) Family
DHINOAPB_00036 2.A.1.5.1 100 3.3e-228 1 411 1.0000 0.9856 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
DHINOAPB_00043 3.A.1.14.1 79.2 9.7e-114 1 255 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DHINOAPB_00044 3.A.1.14.1 91.5 1.6e-158 1 318 1.0000 1.2471 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DHINOAPB_00045 3.A.1.14.1 96.7 8.9e-176 1 332 1.0000 1.3020 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DHINOAPB_00046 3.A.1.14.1 95.7 5.2e-159 1 300 1.0000 1.1765 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DHINOAPB_00047 1.B.14.1.20 98.6 0 1 762 1.0000 0.9845 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
DHINOAPB_00133 2.A.13.1.2 100 2.4e-245 1 446 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.13 The C<sub>4</sub>-Dicarboxylate Uptake (Dcu) Family