Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C501
  Reference Plasmid   NZ_CP024237.1
  Reference Plasmid Size   152713
  Reference Plasmid GC Content   0.48
  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
M0167491 PPJPOBPJ_00066 50803 3 Gut 0.08 protein_coding synonymous_variant LOW 42T>A Arg14Arg
M0167492 PPJPOBPJ_00066 50806 3 Gut 0.08 protein_coding synonymous_variant LOW 39T>C Gly13Gly
M0167493 PPJPOBPJ_00066 50809 3 Gut 0.08 protein_coding synonymous_variant LOW 36C>A Val12Val
M0167494 PPJPOBPJ_00066 50812 3 Gut 0.08 protein_coding synonymous_variant LOW 33T>C Leu11Leu
M0167495 PPJPOBPJ_00059 50849 3 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -4519T>A None
M0167496 PPJPOBPJ_00059 50850 3 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -4520T>C None
M0167497 PPJPOBPJ_00067 50951 3 Gut 0.08 protein_coding missense_variant MODERATE 43A>C Asn15His
M0167498 PPJPOBPJ_00060 51374 3 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -4580A>G None
M0167499 PPJPOBPJ_00069 52655 3 Gut 0.08 protein_coding synonymous_variant LOW 987T>C Thr329Thr
M0167500 PPJPOBPJ_00069 52886 3 Gut 0.08 protein_coding synonymous_variant LOW 756C>T Ser252Ser
M0167501 PPJPOBPJ_00069 52889 3 Gut 0.08 protein_coding synonymous_variant LOW 753G>A Gly251Gly






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
PPJPOBPJ_00153 VFG036068 Heat-labile toxin (LT) 98.4 2.6e-65 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) experiment
PPJPOBPJ_00154 VFG036066 Heat-labile toxin (LT) 99.5 5.3e-130 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) experiment
PPJPOBPJ_00180 VFG034541 EtpA 70.9 0 1 1511 0.9967 0.9818 Adherence Two-partner secreted adhesin EtpA experiment
PPJPOBPJ_00181 VFG042382 EtpA 98.8 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB experiment
PPJPOBPJ_00006 VFG035924 Dispersin 77.8 1.7e-89 1 207 0.9952 0.9952 Others ATP-binding protein AatC prediction
PPJPOBPJ_00007 VFG035917 Dispersin 99.6 7.5e-143 3 257 0.9922 1 Others AatB prediction
PPJPOBPJ_00008 VFG035910 Dispersin 100 2.4e-220 1 400 1.0 1 Others outer membrane protein AatA prediction
PPJPOBPJ_00009 VFG035903 Dispersin 100 7.3e-195 4 379 0.9921 1 Others permease AatP prediction
PPJPOBPJ_00020 VFG042470 Adhesive fimbriae 100 1.7e-82 1 168 1.0 1 Adherence CS3 pilin precursor polypeptide (AA -22 to 146) prediction
PPJPOBPJ_00022 VFG042469 Adhesive fimbriae 100 0 260 810 0.6769 0.9616 Adherence unknown protein prediction
PPJPOBPJ_00023 VFG042468 Adhesive fimbriae 99.2 1.4e-138 1 241 1.0 1 Adherence unknown protein prediction
PPJPOBPJ_00040 VFG020186 VirK 98.7 4.2e-188 1 316 1.0 1 Others virulence factor VirK prediction
PPJPOBPJ_00041 VFG013087 MsbB2 97.1 7.8e-162 1 279 1.0 0.8885 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase prediction
PPJPOBPJ_00092 VFG033834 Pic 99.8 0 1 1364 1.0 0.9985 Effector delivery system Pic serine protease precursor, autotransporter prediction
PPJPOBPJ_00104 VFG020186 VirK 98.7 4.2e-188 1 316 1.0 1 Others virulence factor VirK prediction
PPJPOBPJ_00105 VFG013087 MsbB2 97.1 7.8e-162 1 279 1.0 0.8885 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase prediction
PPJPOBPJ_00153 VFG036068 Heat-labile toxin (LT) 98.4 2e-64 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) prediction
PPJPOBPJ_00154 VFG036065 Heat-labile toxin (LT) 100 1.1e-129 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) prediction
PPJPOBPJ_00166 VFG043747 Heat-stable toxin (ST) 98.6 1.2e-34 1 72 1.0 1 Exotoxin unknown protein prediction
PPJPOBPJ_00180 VFG034541 EtpA 70.9 0 1 1511 0.9967 0.9818 Adherence Two-partner secreted adhesin EtpA prediction
PPJPOBPJ_00181 VFG042382 EtpA 98.8 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB prediction
PPJPOBPJ_00188 VFG035930 Dispersin 100 8.1e-235 15 428 0.9673 1 Others AatD 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
PPJPOBPJ_00039 PHI:10400 Sfgtr4 (ORF186) 95.6 7.3e-208 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) reduced virulence
PPJPOBPJ_00088 PHI:3113 stbA 97.9 2.8e-182 1 326 1.0000 1.0000 rodents neonatal meningitis stability protein for the plasmid reduced virulence
PPJPOBPJ_00103 PHI:10400 Sfgtr4 (ORF186) 95.6 7.3e-208 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) reduced virulence
PPJPOBPJ_00153 PHI:699 CtxB 79 7.9e-53 1 124 1.0000 1.0000 primates cholera Cholera toxin (CT) reduced virulence
PPJPOBPJ_00154 PHI:698 CtxA 80.7 2.9e-106 1 218 1.0000 0.8450 primates cholera Cholera toxin (CT) 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.

Gene Name cazy_id identity evalue qstart qend query_coverage subject_coverage
PPJPOBPJ_00039 AOT35667.1|GT4 100 7.65e-272 1 362 1 1
PPJPOBPJ_00103 AOT35667.1|GT4 100 7.65e-272 1 362 1 1
PPJPOBPJ_00139 APG37898.1|GH23 100 4.96e-124 1 169 1 1
PPJPOBPJ_00178 APG37925.1|GT41 100 0 1 636 1 0.9984





        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
PPJPOBPJ_00154 1.C.72.4.1 99.5 3.1e-129 1 218 1.0000 0.8450 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.72 The Pertussis Toxin (PTX) Family
PPJPOBPJ_00177 9.B.127.1.3 100 1.4e-94 1 164 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.127 The DUF2919 (PF11143) Family
PPJPOBPJ_00181 1.B.20.3.3 98.8 0 1 603 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.20 The Two-Partner Secretion (TPS) Family