Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C387
  Reference Plasmid   NZ_AP025755.1
  Reference Plasmid Size   215429
  Reference Plasmid GC Content   0.47
  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
M0163717 GJNLHDKI_00249 203584 8 Gut 0.80 protein_coding missense_variant MODERATE 343A>G Thr115Ala
M0163718 GJNLHDKI_00249 203640 8 Gut 0.80 protein_coding missense_variant MODERATE 287C>T Ala96Val
M0163719 GJNLHDKI_00249 203667 8 Gut 0.80 protein_coding missense_variant MODERATE 260T>C Val87Ala
M0163720 GJNLHDKI_00249 203711 8 Gut 0.80 protein_coding synonymous_variant LOW 216T>C Arg72Arg
M0163721 GJNLHDKI_00249 203790 8 Gut 0.80 protein_coding missense_variant MODERATE 137G>A Arg46His
M0163722 GJNLHDKI_00249 203825 8 Gut 0.80 protein_coding synonymous_variant LOW 102G>A Arg34Arg
M0163723 GJNLHDKI_00249 203831 8 Gut 0.80 protein_coding synonymous_variant LOW 96G>A Gln32Gln
M0163724 GJNLHDKI_00249 203834 8 Gut 0.80 protein_coding synonymous_variant LOW 93A>G Gln31Gln
M0163725 GJNLHDKI_00249 203840 8 Gut 0.80 protein_coding synonymous_variant LOW 87T>C His29His
M0163726 GJNLHDKI_00249 203901 8 Gut 0.80 protein_coding missense_variant MODERATE 26A>G Glu9Gly
M0163727 GJNLHDKI_00250 204000 8 Gut 0.80 protein_coding missense_variant MODERATE 253C>T Arg85Cys
M0163728 GJNLHDKI_00250 204016 8 Gut 0.80 protein_coding synonymous_variant LOW 237A>G Glu79Glu
M0163729 GJNLHDKI_00250 204022 8 Gut 0.80 protein_coding synonymous_variant LOW 231A>G Glu77Glu
M0163730 GJNLHDKI_00250 204064 8 Gut 0.80 protein_coding synonymous_variant LOW 189T>A Gly63Gly
M0163731 GJNLHDKI_00250 204078 7 Gut 0.70 protein_coding missense_variant MODERATE 175G>A Gly59Arg
M0163732 GJNLHDKI_00250 204087 8 Gut 0.80 protein_coding synonymous_variant LOW 166A>C Arg56Arg
M0163733 GJNLHDKI_00250 204121 8 Gut 0.80 protein_coding synonymous_variant LOW 132A>G Pro44Pro
M0163734 GJNLHDKI_00250 204124 7 Gut 0.70 protein_coding synonymous_variant LOW 129G>A Thr43Thr
M0163735 GJNLHDKI_00250 204144 7 Gut 0.70 protein_coding missense_variant MODERATE 109G>A Ala37Thr
M0163736 GJNLHDKI_00250 204158 7 Gut 0.70 protein_coding missense_variant MODERATE 95C>T Ala32Val
M0163737 GJNLHDKI_00250 204205 8 Gut 0.80 protein_coding synonymous_variant LOW 48T>C Val16Val
M0163738 GJNLHDKI_00250 204211 8 Gut 0.80 protein_coding synonymous_variant LOW 42C>G Arg14Arg
M0163739 GJNLHDKI_00249 208725 10 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4799G>T None
M0163740 GJNLHDKI_00249 208888 10 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4962T>C None
M0163741 GJNLHDKI_00252 208899 10 Gut 1.00 protein_coding stop_lost&splice_region_variant HIGH 193T>G Ter65Gluext*?
M0163742 GJNLHDKI_00252 208901 10 Gut 1.00 protein_coding stop_gained HIGH 191C>A Ser64*
M0163743 GJNLHDKI_00253 209288 9 Gut 0.90 protein_coding missense_variant MODERATE 205G>A Ala69Thr
M0163744 GJNLHDKI_00253 209372 9 Gut 0.90 protein_coding missense_variant MODERATE 121G>A Gly41Ser






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
GJNLHDKI_00151 VFG001445 TraJ 77.9 1.9e-85 1 195 0.8553 0.9701 Invasion unknown protein experiment
GJNLHDKI_00205 VFG000840 Hemolysin 95 0 1 998 1.0 1 Exotoxin Hemolysin A experiment
GJNLHDKI_00206 VFG000842 Hemolysin 94.2 6.1e-97 1 171 1.0 1 Exotoxin Hemolysin C experiment
GJNLHDKI_00211 VFG002039 Heat-stable toxin (ST) 93.1 1.5e-33 1 72 1.0 1 Exotoxin heat stable enterotoxin I experiment
GJNLHDKI_00251 VFG000844 EspP 91.5 0 1 1301 1.0 1.0008 Effector delivery system autotransporter, serine protease experiment
GJNLHDKI_00015 VFG035429 AAI/SCI-II T6SS 83.8 0 1 842 0.9988 0.9918 Effector delivery system type VI secretion system ATPase TssH prediction
GJNLHDKI_00016 VFG035424 AAI/SCI-II T6SS 75 0 1 1134 1.0 1 Effector delivery system type VI secretion protein prediction
GJNLHDKI_00017 VFG035422 AAI/SCI-II T6SS 70.9 3e-75 1 196 1.0 1 Effector delivery system DotU family type IV/VI secretion system protein prediction
GJNLHDKI_00021 VFG035409 AAI/SCI-II T6SS 76.4 6e-212 1 450 1.0 0.9574 Effector delivery system type VI secretion system baseplate subunit TssK prediction
GJNLHDKI_00022 VFG035404 AAI/SCI-II T6SS 80.3 3e-85 1 183 1.0 1 Effector delivery system type VI secretion lipoprotein TssJ prediction
GJNLHDKI_00023 VFG035399 AAI/SCI-II T6SS 85.2 6.5e-177 1 358 1.0 1 Effector delivery system type VI secretion system protein TssA prediction
GJNLHDKI_00024 VFG035394 AAI/SCI-II T6SS 90.9 1.3e-47 1 99 1.0 1 Effector delivery system PAAR domain-containing protein prediction
GJNLHDKI_00025 VFG035389 AAI/SCI-II T6SS 74.5 4.1e-64 1 153 1.0 0.9871 Effector delivery system hypothetical protein prediction
GJNLHDKI_00026 VFG035384 AAI/SCI-II T6SS 78 3.6e-306 7 660 0.9909 0.9909 Effector delivery system type VI secretion system tip protein VgrG prediction
GJNLHDKI_00027 VFG035379 AAI/SCI-II T6SS 83.5 2.7e-158 10 318 0.9656 0.9968 Effector delivery system type VI secretion system baseplate subunit TssG prediction
GJNLHDKI_00028 VFG035374 AAI/SCI-II T6SS 84.5 4.7e-305 1 600 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssF prediction
GJNLHDKI_00029 VFG035369 AAI/SCI-II T6SS 85 1e-61 1 140 1.0 1 Effector delivery system hypothetical protein prediction
GJNLHDKI_00030 VFG035364 AAI/SCI-II T6SS 73.1 1.8e-65 7 166 0.9639 0.9524 Effector delivery system type VI secretion system protein AaiC/Hcp2 prediction
GJNLHDKI_00031 VFG035359 AAI/SCI-II T6SS 95.9 1.6e-279 1 492 1.0 1 Effector delivery system type VI secretion system contractile sheath large subunit prediction
GJNLHDKI_00032 VFG035354 AAI/SCI-II T6SS 90.5 2.6e-77 1 158 1.0 1 Effector delivery system type VI secretion system contractile sheath small subunit prediction
GJNLHDKI_00033 VFG041000 AAI/SCI-II T6SS 73.2 4.3e-67 1 164 1.0 0.8723 Effector delivery system hypothetical protein prediction
GJNLHDKI_00151 VFG001445 TraJ 77.9 1.4e-84 1 195 0.8553 0.9701 Invasion unknown protein prediction
GJNLHDKI_00205 VFG033890 Hemolysin 95.1 0 1 998 1.0 1 Exotoxin Hemolysin A prediction
GJNLHDKI_00206 VFG000842 Hemolysin 94.2 4.6e-96 1 171 1.0 1 Exotoxin Hemolysin C prediction
GJNLHDKI_00211 VFG002039 Heat-stable toxin (ST) 93.1 1.1e-32 1 72 1.0 1 Exotoxin heat stable enterotoxin I prediction
GJNLHDKI_00236 VFG034602 Adhesive fimbriae 87.9 5.4e-133 1 257 1.0 1 Adherence fimbrial protein FaeJ prediction
GJNLHDKI_00237 VFG043644 CS31A capsule-like antigen 85.8 1.3e-126 1 254 1.0 1 Adherence CS31A minor subunit prediction
GJNLHDKI_00238 VFG043647 CS31A capsule-like antigen 84.8 7e-123 17 272 0.9412 0.9624 Adherence fimbrial protein prediction
GJNLHDKI_00240 VFG042496 Adhesive fimbriae 90.7 6.1e-74 1 162 0.9939 0.9939 Adherence unknown protein prediction
GJNLHDKI_00241 VFG042553 Adhesive fimbriae 92.9 9e-133 1 253 1.0 0.9806 Adherence F4 (K88) fimbrial chaperone FaeE prediction
GJNLHDKI_00242 VFG042494 Adhesive fimbriae 93.1 0 15 814 0.9828 1 Adherence cshB porin (usher) prediction
GJNLHDKI_00243 VFG042533 CS31A capsule-like antigen 93.1 3.5e-81 28 186 0.8548 0.8833 Adherence ClpC prediction
GJNLHDKI_00251 VFG000844 EspP 91.5 0 1 1301 1.0 1.0008 Effector delivery system autotransporter, serine protease prediction
GJNLHDKI_00258 VFG017870 Icm/dot type IVB locus 77.4 1.7e-89 1 208 0.9905 0.9952 Effector delivery system ParA family 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
GJNLHDKI_00030 PHI:123579 Hcp2 73.1 6.4e-66 7 166 0.9639 0.9524 primates avian colibacillosis type VI secretion system protein effector (plant avirulence determinant)
GJNLHDKI_00218 PHI:10997 fdnG 70.3 0 1 1016 1.0000 1.0000 rodents infection formate dehydrogenase, nitrate-inducible, major subunit unaffected pathogenicity






        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
GJNLHDKI_00153 QIC02838.1|GH23 99.1 1.93e-155 1 215 1 1
GJNLHDKI_00228 ANO92402.1|GT4 100 5.58e-290 1 389 1 1
GJNLHDKI_00229 ANP05419.1|GT4 99.8 9.5e-300 1 411 1 1
GJNLHDKI_00230 ANP16064.1|GT1 100 1.43e-270 1 386 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
GJNLHDKI_00107 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
GJNLHDKI_00205 1.C.11.1.6 95.4 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
GJNLHDKI_00218 5.A.3.2.1 70.3 0 1 1016 1.0000 1.0000 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
GJNLHDKI_00224 1.B.13.1.6 100 3.1e-224 59 439 0.8679 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.13 The Alginate Export Porin (AEP) Family
GJNLHDKI_00242 1.B.11.1.1 92 0 5 814 0.9951 0.9975 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family
GJNLHDKI_00251 1.B.12.4.3 91.5 0 1 1301 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family