Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1162
  Reference Plasmid   NZ_CP124472.1
  Reference Plasmid Size   134675
  Reference Plasmid GC Content   0.52
  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
M0198591 PIBEDNMJ_00151 122885 4 Gut 0.67 protein_coding missense_variant MODERATE 178A>G Thr60Ala
M0198592 PIBEDNMJ_00152 123591 3 Gut 0.50 protein_coding synonymous_variant LOW 447A>C Ala149Ala
M0198593 PIBEDNMJ_00152 123679 3 Gut 0.50 protein_coding synonymous_variant LOW 535C>T Leu179Leu
M0198594 PIBEDNMJ_00152 123762 4 Gut 0.67 protein_coding synonymous_variant LOW 618A>G Gln206Gln
M0198595 PIBEDNMJ_00152 123847 4 Gut 0.67 protein_coding missense_variant MODERATE 703A>T Ser235Cys
M0198596 PIBEDNMJ_00152 123855 3 Gut 0.50 protein_coding synonymous_variant LOW 711C>T Ser237Ser
M0198597 PIBEDNMJ_00152 123866 4 Gut 0.67 protein_coding missense_variant MODERATE 722T>C Val241Ala
M0198598 PIBEDNMJ_00152 123870 3 Gut 0.50 protein_coding synonymous_variant LOW 726A>G Pro242Pro
M0198599 PIBEDNMJ_00152 124002 4 Gut 0.67 protein_coding synonymous_variant LOW 858T>C Cys286Cys
M0198600 PIBEDNMJ_00152 124084 3 Gut 0.50 protein_coding missense_variant MODERATE 940T>C Ser314Pro
M0198601 PIBEDNMJ_00152 124121 3 Gut 0.50 protein_coding missense_variant MODERATE 977C>A Pro326Gln
M0198602 PIBEDNMJ_00152 124132 3 Gut 0.50 protein_coding missense_variant MODERATE 988T>C Ser330Pro
M0198603 PIBEDNMJ_00152 124133 3 Gut 0.50 protein_coding missense_variant MODERATE 989C>G Ser330Cys
M0198604 PIBEDNMJ_00148 124198 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -2407T>C None
M0198605 PIBEDNMJ_00154 126112 3 Gut 0.50 protein_coding missense_variant MODERATE 673A>T Thr225Ser






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
PIBEDNMJ_00022 VFG001827 ShET2 99.7 7.9e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
PIBEDNMJ_00117 VFG001445 TraJ 100 6e-116 1 200 0.8772 0.995 Invasion unknown protein experiment
PIBEDNMJ_00022 VFG036084 Enterotoxin SenB/TieB 100 1.2e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB prediction
PIBEDNMJ_00117 VFG001445 TraJ 100 4.5e-115 1 200 0.8772 0.995 Invasion unknown protein 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
PIBEDNMJ_00057 ARO:3003839 100 4.74e-272 1 412 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
PIBEDNMJ_00058 ARO:3000316 100 1e-217 1 301 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
PIBEDNMJ_00060 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
PIBEDNMJ_00061 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
PIBEDNMJ_00062 ARO:3002660 99.3 4.37e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
PIBEDNMJ_00064 ARO:3000165 99.7 7.17e-278 1 390 0.9774 0.9198 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
PIBEDNMJ_00069 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation






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
PIBEDNMJ_00022 PHI:10795 senB 100 4.2e-225 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
PIBEDNMJ_00023 PHI:10794 cjrC 100 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
PIBEDNMJ_00024 PHI:10793 cjrB 100 1.7e-137 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
PIBEDNMJ_00025 PHI:10792 cjrA 99.6 2.7e-134 1 235 1.0000 0.8076 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
PIBEDNMJ_00119 AML12690.1|GH23 100 7.04e-124 1 169 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
PIBEDNMJ_00023 1.B.14.7.1 100 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
PIBEDNMJ_00024 2.C.1.1.3 100 3.7e-137 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
PIBEDNMJ_00044 2.A.108.2.10 100 5e-101 3 175 0.9886 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
PIBEDNMJ_00045 2.A.108.2.10 99.8 0 1 646 1.0000 3.7341 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
PIBEDNMJ_00053 2.A.51.1.7 99.5 5.1e-210 1 376 0.9377 0.9666 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.51 The Chromate Ion Transporter (CHR) Family
PIBEDNMJ_00064 2.A.1.2.4 100 2.4e-223 1 399 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
PIBEDNMJ_00065 2.A.7.3.67 99.7 1.7e-154 1 286 1.0000 0.9728 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily