Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1182
  Reference Plasmid   NZ_CP129254.1
  Reference Plasmid Size   108578
  Reference Plasmid GC Content   0.49
  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
M0199330 MCBJIKPD_00023 22284 4 Gut 0.40 protein_coding upstream_gene_variant MODIFIER -4601T>C None
M0199331 MCBJIKPD_00030 22501 4 Gut 0.40 protein_coding missense_variant MODERATE 140A>C Glu47Ala
M0199332 MCBJIKPD_00034 24661 4 Gut 0.40 protein_coding stop_lost&splice_region_variant HIGH 1160A>G Ter387Trpext*?
M0199333 MCBJIKPD_00076 73288 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4753T>C None
M0199334 MCBJIKPD_00092 81831 3 Gut 0.30 protein_coding missense_variant MODERATE 56C>T Ala19Val
M0199335 MCBJIKPD_00092 81833 3 Gut 0.30 protein_coding synonymous_variant LOW 54A>C Ile18Ile
M0199336 MCBJIKPD_00106 94803 3 Gut 0.30 protein_coding synonymous_variant LOW 276T>C Arg92Arg
M0199337 MCBJIKPD_00109 96939 3 Gut 0.30 protein_coding missense_variant MODERATE 713G>A Arg238Lys
M0199338 MCBJIKPD_00116 100973 3 Gut 0.30 protein_coding synonymous_variant LOW 547T>C Leu183Leu






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
MCBJIKPD_00068 VFG000843 Hemolysin 99.2 1e-266 1 479 1.0 1 Exotoxin Hemolysin D experiment
MCBJIKPD_00069 VFG000841 Hemolysin 99.7 0 1 705 1.0 0.9986 Exotoxin Hemolysin B experiment
MCBJIKPD_00070 VFG000840 Hemolysin 98.5 0 1 998 1.0 1 Exotoxin Hemolysin A experiment
MCBJIKPD_00071 VFG000842 Hemolysin 98.2 1.3e-99 1 171 1.0 1 Exotoxin Hemolysin C experiment
MCBJIKPD_00100 VFG001827 ShET2 99.5 3e-224 1 391 1.0 1 Exotoxin enterotoxin experiment
MCBJIKPD_00053 VFG043979 Colicin B 99.8 6.2e-290 1 511 1.0 1 Exotoxin colicin B prediction
MCBJIKPD_00068 VFG000843 Hemolysin 99.2 7.6e-266 1 479 1.0 1 Exotoxin Hemolysin D prediction
MCBJIKPD_00069 VFG033882 Hemolysin 99.9 0 1 705 1.0 0.9986 Exotoxin Hemolysin B prediction
MCBJIKPD_00070 VFG033890 Hemolysin 98.6 0 1 998 1.0 1 Exotoxin Hemolysin A prediction
MCBJIKPD_00071 VFG000842 Hemolysin 98.2 9.8e-99 1 171 1.0 1 Exotoxin Hemolysin C prediction
MCBJIKPD_00073 VFG042367 Sab 80.8 0 1 1445 1.0 1.0098 Effector delivery system autotransporter adhesin Sab prediction
MCBJIKPD_00096 VFG043983 Colicin S4 83.6 8.7e-191 3 398 0.995 0.7936 Exotoxin colicin S4 prediction
MCBJIKPD_00100 VFG001827 ShET2 99.5 2.2e-223 1 391 1.0 1 Exotoxin enterotoxin 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






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
MCBJIKPD_00067 PHI:6737 L7052 80.6 3.9e-36 1 93 0.7623 0.9894 nematodes urinary tract infection transcriptional regulator increased virulence (hypervirulence)
MCBJIKPD_00100 PHI:10795 senB 99.2 2.3e-223 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
MCBJIKPD_00101 PHI:10794 cjrC 98.8 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
MCBJIKPD_00102 PHI:10793 cjrB 98.4 9.1e-136 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
MCBJIKPD_00103 PHI:10792 cjrA 98.3 4e-164 1 291 1.0000 1.0000 primates neonatal meningitis iron-regulated protein 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





        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
MCBJIKPD_00053 1.C.1.3.2 99.8 4.9e-290 1 511 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
MCBJIKPD_00056 8.B.24.3.1 96.6 2.6e-61 1 117 1.0000 0.8298 8 Accessory Factors Involved in Transport 8.B Ribosomally synthesized protein/peptide toxins/agonists that target channels and carriers 8.B.24 The Colicin Immunity Protein (ColIP) Functional Family
MCBJIKPD_00069 3.A.1.109.1 73.4 3.4e-302 10 705 0.9872 0.9844 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
MCBJIKPD_00070 1.C.11.1.6 98.7 0 1 998 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.11 The Pore-forming RTX Toxin (RTX-toxin) Family
MCBJIKPD_00087 2.A.8.1.9 71.8 6.7e-152 1 418 0.9905 0.9952 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.8 The Gluconate:H+ Symporter (GntP) Family
MCBJIKPD_00096 1.C.1.3.4 83.6 6.9e-191 3 398 0.9950 0.7956 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
MCBJIKPD_00101 1.B.14.7.1 98.8 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
MCBJIKPD_00102 2.C.1.1.3 98.4 2e-135 1 258 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.C Ion-gradient-driven energizers 2.C.1 The TonB-ExbB-ExbD/TolA-TolQ-TolR Outer Membrane Receptor Energizers and Stabilizers (TonB/TolA) Family
MCBJIKPD_00111 1.E.53.1.11 100 1.1e-21 1 49 1.0000 0.7206 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family