Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C601
  Reference Plasmid   NZ_CP035847.1
  Reference Plasmid Size   141411
  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
M0169229 KFLMNJPH_00032 22961 4 Gut 0.18 protein_coding missense_variant MODERATE 313A>G Ser105Gly
M0169230 KFLMNJPH_00033 23353 4 Gut 0.18 protein_coding synonymous_variant LOW 936T>C Tyr312Tyr
M0169231 KFLMNJPH_00033 23355 4 Gut 0.18 protein_coding missense_variant MODERATE 934T>C Tyr312His
M0169232 KFLMNJPH_00036 26525 4 Gut 0.18 protein_coding missense_variant MODERATE 488A>G Tyr163Cys
M0169233 KFLMNJPH_00032 22766 3 Gut 0.14 protein_coding missense_variant MODERATE 508G>A Val170Ile
M0169234 KFLMNJPH_00032 23007 3 Gut 0.14 protein_coding synonymous_variant LOW 267T>C Ala89Ala
M0169235 KFLMNJPH_00032 23012 3 Gut 0.14 protein_coding missense_variant MODERATE 262C>T Leu88Phe
M0169236 KFLMNJPH_00032 23034 3 Gut 0.14 protein_coding synonymous_variant LOW 240G>A Arg80Arg
M0169237 KFLMNJPH_00030 23336 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -1973A>G None
M0169238 KFLMNJPH_00033 23521 3 Gut 0.14 protein_coding synonymous_variant LOW 768G>A Gly256Gly






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
KFLMNJPH_00089 VFG042382 EtpA 98.7 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB experiment
KFLMNJPH_00114 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
KFLMNJPH_00115 VFG036068 Heat-labile toxin (LT) 98.4 2.6e-65 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) experiment
KFLMNJPH_00033 VFG020186 VirK 98.1 3e-186 1 316 1.0 1 Others virulence factor VirK prediction
KFLMNJPH_00053 VFG042468 Adhesive fimbriae 99.2 1.4e-138 1 241 1.0 1 Adherence unknown protein prediction
KFLMNJPH_00054 VFG042469 Adhesive fimbriae 100 0 260 810 0.6769 0.9616 Adherence unknown protein prediction
KFLMNJPH_00056 VFG042470 Adhesive fimbriae 100 1.7e-82 1 168 1.0 1 Adherence CS3 pilin precursor polypeptide (AA -22 to 146) prediction
KFLMNJPH_00067 VFG035903 Dispersin 100 7.3e-195 4 379 0.9921 1 Others permease AatP prediction
KFLMNJPH_00068 VFG035910 Dispersin 100 2.4e-220 1 400 1.0 1 Others outer membrane protein AatA prediction
KFLMNJPH_00069 VFG035917 Dispersin 99.6 7.5e-143 3 257 0.9922 1 Others AatB prediction
KFLMNJPH_00070 VFG035924 Dispersin 77.8 1.7e-89 1 207 0.9952 0.9952 Others ATP-binding protein AatC prediction
KFLMNJPH_00079 VFG035930 Dispersin 100 8.1e-235 15 428 0.9673 1 Others AatD prediction
KFLMNJPH_00089 VFG042382 EtpA 98.7 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB prediction
KFLMNJPH_00102 VFG043747 Heat-stable toxin (ST) 98.6 1.2e-34 1 72 1.0 1 Exotoxin unknown protein prediction
KFLMNJPH_00114 VFG036065 Heat-labile toxin (LT) 100 1.1e-129 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) prediction
KFLMNJPH_00115 VFG036068 Heat-labile toxin (LT) 98.4 2e-64 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) prediction
KFLMNJPH_00164 VFG013087 MsbB2 97.5 1.4e-183 1 314 1.0 1 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase prediction
KFLMNJPH_00165 VFG020186 VirK 98.4 7.9e-187 1 316 1.0 1 Others virulence factor VirK prediction
KFLMNJPH_00178 VFG033834 Pic 99.9 0 1 1364 1.0 0.9985 Effector delivery system Pic serine protease precursor, autotransporter prediction
KFLMNJPH_00183 VFG041000 AAI/SCI-II T6SS 87.1 5.7e-66 15 153 0.9085 0.7394 Effector delivery system hypothetical 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






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
KFLMNJPH_00034 PHI:10400 Sfgtr4 (ORF186) 95.3 1.6e-207 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) reduced virulence
KFLMNJPH_00114 PHI:698 CtxA 80.7 2.9e-106 1 218 1.0000 0.8450 primates cholera Cholera toxin (CT) reduced virulence
KFLMNJPH_00115 PHI:699 CtxB 79 7.9e-53 1 124 1.0000 1.0000 primates cholera Cholera toxin (CT) reduced virulence
KFLMNJPH_00166 PHI:10400 Sfgtr4 (ORF186) 95.3 1.6e-207 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) reduced virulence
KFLMNJPH_00184 PHI:3113 stbA 97.9 2.8e-182 1 326 1.0000 1.0000 rodents neonatal meningitis stability protein for the plasmid 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
KFLMNJPH_00034 AOT35667.1|GT4 99.7 2.19e-271 1 362 1 1
KFLMNJPH_00094 APG37925.1|GT41 100 0 1 636 1 0.9984
KFLMNJPH_00130 APG37898.1|GH23 100 4.96e-124 1 169 1 1
KFLMNJPH_00166 AOT35667.1|GT4 99.7 2.19e-271 1 362 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
KFLMNJPH_00089 1.B.20.3.3 98.7 0 1 603 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.20 The Two-Partner Secretion (TPS) Family
KFLMNJPH_00095 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
KFLMNJPH_00114 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