Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C540
  Reference Plasmid   NZ_CP027853.1
  Reference Plasmid Size   395858
  Reference Plasmid GC Content   0.49
  Reference Plasmid Mobility Type   non-mobilizable





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
M0168106 PPKHCNFI_00182 199479 4 Gut 0.50 protein_coding synonymous_variant LOW 279C>G Gly93Gly
M0168107 PPKHCNFI_00182 199614 4 Gut 0.50 protein_coding synonymous_variant LOW 414C>T Ile138Ile
M0168108 PPKHCNFI_00182 199881 4 Gut 0.50 protein_coding synonymous_variant LOW 681C>T Arg227Arg
M0168109 PPKHCNFI_00182 199902 4 Gut 0.50 protein_coding synonymous_variant LOW 702G>T Gly234Gly
M0168110 PPKHCNFI_00178 199917 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4934T>G None
M0168111 PPKHCNFI_00178 199963 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4980C>A None
M0168112 PPKHCNFI_00178 199965 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4982A>G None
M0168113 PPKHCNFI_00181 200002 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1147T>C None
M0168114 PPKHCNFI_00181 200006 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1151G>C None
M0168115 PPKHCNFI_00181 200012 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1157A>G None
M0168116 PPKHCNFI_00181 200051 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1196T>G None
M0168117 PPKHCNFI_00181 200071 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1216T>C None
M0168118 PPKHCNFI_00181 200105 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1250G>T None
M0168119 PPKHCNFI_00181 200147 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1292A>G None
M0168120 PPKHCNFI_00183 200511 4 Gut 0.50 protein_coding synonymous_variant LOW 258A>G Ala86Ala
M0168121 PPKHCNFI_00183 200515 4 Gut 0.50 protein_coding synonymous_variant LOW 262T>C Leu88Leu
M0168122 PPKHCNFI_00178 199149 3 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -4166T>A None
M0168123 PPKHCNFI_00182 199410 3 Gut 0.38 protein_coding synonymous_variant LOW 210C>T Val70Val
M0168124 PPKHCNFI_00182 199503 3 Gut 0.38 protein_coding synonymous_variant LOW 303G>A Leu101Leu
M0168125 PPKHCNFI_00182 199530 3 Gut 0.38 protein_coding synonymous_variant LOW 330G>A Arg110Arg
M0168126 PPKHCNFI_00182 199605 3 Gut 0.38 protein_coding synonymous_variant LOW 405G>A Gly135Gly
M0168127 PPKHCNFI_00182 199608 3 Gut 0.38 protein_coding synonymous_variant LOW 408G>A Ala136Ala
M0168128 PPKHCNFI_00182 199731 3 Gut 0.38 protein_coding synonymous_variant LOW 531A>G Gly177Gly
M0168129 PPKHCNFI_00182 199734 3 Gut 0.38 protein_coding synonymous_variant LOW 534T>C Phe178Phe
M0168130 PPKHCNFI_00182 199740 3 Gut 0.38 protein_coding synonymous_variant LOW 540C>T Cys180Cys
M0168131 PPKHCNFI_00182 199872 3 Gut 0.38 protein_coding synonymous_variant LOW 672T>C Arg224Arg
M0168132 PPKHCNFI_00178 199913 3 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -4930T>C None
M0168133 PPKHCNFI_00178 199945 3 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -4962G>A None
M0168134 PPKHCNFI_00181 200011 3 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -1156C>T None
M0168135 PPKHCNFI_00181 200014 3 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -1159C>T None
M0168136 PPKHCNFI_00181 200021 3 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -1166G>A None
M0168137 PPKHCNFI_00181 200038 3 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -1183A>G None
M0168138 PPKHCNFI_00181 200142 3 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -1287A>G None
M0168139 PPKHCNFI_00183 200418 3 Gut 0.38 protein_coding synonymous_variant LOW 165G>T Val55Val
M0168140 PPKHCNFI_00183 200424 3 Gut 0.38 protein_coding synonymous_variant LOW 171G>A Val57Val
M0168141 PPKHCNFI_00183 200476 3 Gut 0.38 protein_coding missense_variant MODERATE 223A>G Thr75Ala
M0168142 PPKHCNFI_00183 200488 3 Gut 0.38 protein_coding synonymous_variant LOW 235T>C Leu79Leu






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
PPKHCNFI_00029 VFG038367 T6SS secreted effectors 77.8 0 1 669 0.9926 0.7217 Effector delivery system Type VI secretion system effector VgrG1, ADP-ribosyltransferase experiment
PPKHCNFI_00030 VFG038365 T6SS 94.8 3.6e-97 1 172 1.0 1 Effector delivery system HcpA-like protein experiment
PPKHCNFI_00081 VFG038367 T6SS secreted effectors 75.4 2.30000000000092e-312 1 670 0.9911 0.7228 Effector delivery system Type VI secretion system effector VgrG1, ADP-ribosyltransferase experiment
PPKHCNFI_00082 VFG038365 T6SS 95.9 3.3e-98 1 172 1.0 1 Effector delivery system HcpA-like protein experiment
PPKHCNFI_00283 VFG037028 KatA 72.7 9.6e-212 12 483 0.9593 0.9365 Stress survival catalase experiment
PPKHCNFI_00029 VFG038368 T6SS secreted effectors 79 0 1 669 0.9926 0.7225 Effector delivery system Type VI secretion system effector VgrG1, ADP-ribosyltransferase prediction
PPKHCNFI_00030 VFG038370 T6SS 95.3 7.1e-97 1 172 1.0 1 Effector delivery system hemolysin co-regulated protein prediction
PPKHCNFI_00081 VFG038368 T6SS secreted effectors 76.3 0 1 670 0.9911 0.7235 Effector delivery system Type VI secretion system effector VgrG1, ADP-ribosyltransferase prediction
PPKHCNFI_00082 VFG038370 T6SS 96.5 6.4e-98 1 172 1.0 1 Effector delivery system hemolysin co-regulated protein prediction
PPKHCNFI_00283 VFG037029 KatA 72.9 1.9e-211 12 483 0.9593 0.9365 Stress survival catalase 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
PPKHCNFI_00051 Arsenic (As), Antimony (Sb) 77.1 2.5e-59 4 143 0.9790 0.9929 experiment
PPKHCNFI_00050 Arsenic (As) 79.7 2.7e-156 9 357 0.9749 0.9749 prediction
PPKHCNFI_00051 Arsenic (As) 77.7 4.4e-57 4 142 0.9720 0.9720 prediction






        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
PPKHCNFI_00030 PHI:123750 Hcp 94.2 6.1e-96 1 172 1.0000 1.0000 bony fishes furunculosis effector protein effector (plant avirulence determinant)
PPKHCNFI_00082 PHI:123750 Hcp 94.2 2.8e-96 1 172 1.0000 1.0000 bony fishes furunculosis effector protein effector (plant avirulence determinant)
PPKHCNFI_00283 PHI:10648 katA 70.6 2.1e-213 7 485 0.9736 0.9959 rodents opportunistic infection catalase unaffected pathogenicity
PPKHCNFI_00301 PHI:10994 fdoG 84.3 0 1 803 1.0000 0.9833 rodents infection formate dehydrogenase-O major subunit unaffected pathogenicity
PPKHCNFI_00302 PHI:10994 fdoG 89.7 2e-103 1 195 1.0000 0.9833 rodents infection formate dehydrogenase-O major subunit unaffected pathogenicity
PPKHCNFI_00332 PHI:3448 pgaC 75.6 4e-200 1 442 0.9955 1.0000 rodents pneumonia production of poly-b-linkedN-acetylglucosamine 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
PPKHCNFI_00064 AVQ88853.1|GH32 100 0 1 478 1 1
PPKHCNFI_00110 AVQ88889.1|GH2 100 0 1 1040 1 1
PPKHCNFI_00111 AVQ88890.1|GH36 100 0 1 706 1 1
PPKHCNFI_00150 AVQ88917.1|GH2 100 0 1 1034 1 1
PPKHCNFI_00313 AVQ89060.1|GT2 100 2.49e-294 1 400 1 1
PPKHCNFI_00314 AVQ89061.1|GT4 100 4.16e-279 1 377 1 1
PPKHCNFI_00318 AVQ89065.1|GT4 100 2.76e-306 1 416 1 1
PPKHCNFI_00322 AVQ89067.1|GT4 100 7.18e-297 1 406 1 1
PPKHCNFI_00323 AVQ89068.1|GT4 100 0 1 439 1 1
PPKHCNFI_00324 AVQ89069.1|GT4 100 1.47e-266 1 356 1 1
PPKHCNFI_00331 AVQ89073.1|CE4|GH153 100 0 1 674 1 1
PPKHCNFI_00332 AVQ89074.1|GT2 100 0 1 444 1 1
PPKHCNFI_00349 AVQ89089.1|GH103 100 6.02e-268 1 360 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
PPKHCNFI_00033 2.A.21.2.1 86.2 2e-243 1 500 0.9960 0.9960 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.21 The Solute:Sodium Symporter (SSS) Family
PPKHCNFI_00037 2.A.8.1.9 73.6 1.5e-159 1 417 0.9905 0.9952 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.8 The Gluconate:H+ Symporter (GntP) Family
PPKHCNFI_00065 2.A.1.5.6 91 1.1e-207 2 411 0.9976 0.9951 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
PPKHCNFI_00137 2.A.21.3.7 80.5 1.1e-227 1 492 0.9980 0.9743 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.21 The Solute:Sodium Symporter (SSS) Family
PPKHCNFI_00152 2.A.3.7.4 87 6.1e-234 1 476 0.9896 0.9979 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.3 The Amino Acid-Polyamine-Organocation (APC) Family
PPKHCNFI_00215 1.W.5.1.1 73.9 9.4e-228 5 526 0.9849 0.9719 1 Channels/Pores 1.W Phage Portal Protein Subclass 1.W.5 The (Lambda) Phage Portal Protein 5 (PPP5) Family
PPKHCNFI_00301 5.A.3.2.1 76.6 0 1 802 0.9988 0.7901 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
PPKHCNFI_00328 2.A.1.11.3 71 9.9e-153 6 394 0.9581 0.9701 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)