Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C477
  Reference Plasmid   NZ_CP020859.1
  Reference Plasmid Size   264403
  Reference Plasmid GC Content   0.32
  Reference Plasmid Mobility Type   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
M0167078 PFPLPDNJ_00006 5397 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -521T>C None
M0167079 PFPLPDNJ_00008 5751 3 Gut 0.14 protein_coding synonymous_variant LOW 384C>T Asn128Asn
M0167080 PFPLPDNJ_00009 6313 3 Gut 0.14 protein_coding missense_variant MODERATE 389T>C Ile130Thr
M0167081 PFPLPDNJ_00010 6926 3 Gut 0.14 protein_coding synonymous_variant LOW 1068A>C Thr356Thr
M0167082 PFPLPDNJ_00010 7732 3 Gut 0.14 protein_coding missense_variant MODERATE 262A>G Thr88Ala
M0167083 PFPLPDNJ_00012 8808 3 Gut 0.14 protein_coding missense_variant MODERATE 1324G>A Ala442Thr
M0167084 PFPLPDNJ_00015 11581 3 Gut 0.14 protein_coding missense_variant MODERATE 2441G>A Gly814Asp
M0167085 PFPLPDNJ_00015 12023 3 Gut 0.14 protein_coding missense_variant MODERATE 1999A>G Lys667Glu
M0167086 PFPLPDNJ_00015 12263 3 Gut 0.14 protein_coding missense_variant MODERATE 1759T>C Tyr587His
M0167087 PFPLPDNJ_00015 13465 3 Gut 0.14 protein_coding missense_variant MODERATE 557C>T Ala186Val
M0167088 PFPLPDNJ_00015 13736 3 Gut 0.14 protein_coding missense_variant MODERATE 286G>A Ala96Thr
M0167089 PFPLPDNJ_00016 14169 3 Gut 0.14 protein_coding missense_variant MODERATE 2722A>G Thr908Ala
M0167090 PFPLPDNJ_00016 14285 3 Gut 0.14 protein_coding missense_variant MODERATE 2606G>A Gly869Asp
M0167091 PFPLPDNJ_00016 14902 3 Gut 0.14 protein_coding synonymous_variant LOW 1989C>T Asp663Asp
M0167092 PFPLPDNJ_00017 17793 3 Gut 0.14 protein_coding missense_variant MODERATE 1578G>A Met526Ile
M0167093 PFPLPDNJ_00017 18214 3 Gut 0.14 protein_coding missense_variant MODERATE 1157C>A Ala386Glu
M0167094 PFPLPDNJ_00017 18471 3 Gut 0.14 protein_coding synonymous_variant LOW 900T>C Ile300Ile
M0167095 PFPLPDNJ_00026 29587 3 Gut 0.14 protein_coding missense_variant MODERATE 2749T>G Ser917Ala
M0167096 PFPLPDNJ_00026 31115 3 Gut 0.14 protein_coding synonymous_variant LOW 1221G>A Gly407Gly
M0167097 PFPLPDNJ_00026 32191 3 Gut 0.14 protein_coding missense_variant MODERATE 145A>G Lys49Glu
M0167098 PFPLPDNJ_00028 32985 3 Gut 0.14 protein_coding missense_variant MODERATE 728T>C Leu243Ser
M0167099 PFPLPDNJ_00180 174113 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -1914A>G None
M0167100 PFPLPDNJ_00180 174489 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -2290C>T None
M0167101 PFPLPDNJ_00180 174569 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -2370G>A None
M0167102 PFPLPDNJ_00180 174577 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -2378C>T None
M0167103 PFPLPDNJ_00185 174768 3 Gut 0.14 protein_coding synonymous_variant LOW 2394A>G Lys798Lys
M0167104 PFPLPDNJ_00185 175313 3 Gut 0.14 protein_coding missense_variant MODERATE 1849C>T Arg617Cys
M0167105 PFPLPDNJ_00185 175422 3 Gut 0.14 protein_coding synonymous_variant LOW 1740A>G Glu580Glu
M0167106 PFPLPDNJ_00185 175574 3 Gut 0.14 protein_coding missense_variant MODERATE 1588G>A Val530Ile
M0167107 PFPLPDNJ_00185 175650 3 Gut 0.14 protein_coding synonymous_variant LOW 1512T>C Ala504Ala
M0167108 PFPLPDNJ_00185 175655 3 Gut 0.14 protein_coding missense_variant MODERATE 1507T>G Ser503Ala
M0167109 PFPLPDNJ_00185 175676 3 Gut 0.14 protein_coding missense_variant MODERATE 1486A>G Asn496Asp
M0167110 PFPLPDNJ_00185 175683 3 Gut 0.14 protein_coding synonymous_variant LOW 1479T>C Asp493Asp
M0167111 PFPLPDNJ_00185 175698 3 Gut 0.14 protein_coding synonymous_variant LOW 1464A>G Thr488Thr
M0167112 PFPLPDNJ_00185 175763 3 Gut 0.14 protein_coding missense_variant MODERATE 1399A>G Asn467Asp
M0167113 PFPLPDNJ_00185 175773 3 Gut 0.14 protein_coding synonymous_variant LOW 1389C>T Gly463Gly
M0167114 PFPLPDNJ_00185 175785 3 Gut 0.14 protein_coding synonymous_variant LOW 1377A>G Gln459Gln
M0167115 PFPLPDNJ_00185 175799 3 Gut 0.14 protein_coding missense_variant MODERATE 1363G>A Val455Ile
M0167116 PFPLPDNJ_00185 175833 3 Gut 0.14 protein_coding synonymous_variant LOW 1329C>T Val443Val
M0167117 PFPLPDNJ_00185 175856 3 Gut 0.14 protein_coding synonymous_variant LOW 1306C>T Leu436Leu
M0167118 PFPLPDNJ_00185 175923 3 Gut 0.14 protein_coding synonymous_variant LOW 1239C>T Gly413Gly
M0167119 PFPLPDNJ_00185 175952 3 Gut 0.14 protein_coding missense_variant MODERATE 1210G>A Glu404Lys
M0167120 PFPLPDNJ_00185 175953 3 Gut 0.14 protein_coding synonymous_variant LOW 1209T>C Phe403Phe
M0167121 PFPLPDNJ_00185 175979 3 Gut 0.14 protein_coding synonymous_variant LOW 1183T>C Leu395Leu
M0167122 PFPLPDNJ_00185 175983 3 Gut 0.14 protein_coding missense_variant MODERATE 1179A>T Glu393Asp
M0167123 PFPLPDNJ_00185 175989 3 Gut 0.14 protein_coding synonymous_variant LOW 1173T>C Gly391Gly
M0167124 PFPLPDNJ_00185 176106 3 Gut 0.14 protein_coding synonymous_variant LOW 1056C>T Gly352Gly
M0167125 PFPLPDNJ_00185 176240 3 Gut 0.14 protein_coding synonymous_variant LOW 922T>C Leu308Leu
M0167126 PFPLPDNJ_00185 176244 3 Gut 0.14 protein_coding synonymous_variant LOW 918T>C Asp306Asp
M0167127 PFPLPDNJ_00185 176268 3 Gut 0.14 protein_coding synonymous_variant LOW 894C>T Asp298Asp
M0167128 PFPLPDNJ_00185 176340 3 Gut 0.14 protein_coding synonymous_variant LOW 822T>C Asn274Asn
M0167129 PFPLPDNJ_00185 176568 3 Gut 0.14 protein_coding synonymous_variant LOW 594T>C Ser198Ser
M0167130 PFPLPDNJ_00185 176589 3 Gut 0.14 protein_coding synonymous_variant LOW 573C>T Ser191Ser
M0167131 PFPLPDNJ_00185 176687 3 Gut 0.14 protein_coding missense_variant MODERATE 475A>G Met159Val
M0167132 PFPLPDNJ_00185 176715 3 Gut 0.14 protein_coding synonymous_variant LOW 447G>A Glu149Glu
M0167133 PFPLPDNJ_00185 176890 3 Gut 0.14 protein_coding missense_variant MODERATE 272T>C Phe91Ser
M0167134 PFPLPDNJ_00185 176953 3 Gut 0.14 protein_coding missense_variant MODERATE 209G>A Ser70Asn
M0167135 PFPLPDNJ_00185 177029 3 Gut 0.14 protein_coding missense_variant MODERATE 133A>G Thr45Ala
M0167136 PFPLPDNJ_00185 177069 3 Gut 0.14 protein_coding synonymous_variant LOW 93A>G Gly31Gly
M0167137 PFPLPDNJ_00185 177079 3 Gut 0.14 protein_coding missense_variant MODERATE 83C>T Thr28Ile
M0167138 PFPLPDNJ_00185 177084 3 Gut 0.14 protein_coding synonymous_variant LOW 78A>G Lys26Lys
M0167139 PFPLPDNJ_00185 177093 3 Gut 0.14 protein_coding synonymous_variant LOW 69T>C Asn23Asn
M0167140 PFPLPDNJ_00185 177129 3 Gut 0.14 protein_coding synonymous_variant LOW 33C>T Phe11Phe
M0167141 PFPLPDNJ_00181 177240 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -4896G>A None
M0167142 PFPLPDNJ_00181 177247 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -4903A>T None
M0167143 PFPLPDNJ_00181 177264 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -4920C>G None
M0167144 PFPLPDNJ_00181 177265 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -4921A>T None
M0167145 PFPLPDNJ_00181 177319 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -4975A>G None
M0167146 PFPLPDNJ_00181 177321 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -4977G>A None
M0167147 PFPLPDNJ_00185 177346 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -185A>C None
M0167148 PFPLPDNJ_00185 177347 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -186T>A None
M0167149 PFPLPDNJ_00185 177349 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -188C>T None
M0167150 PFPLPDNJ_00185 177355 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -194T>A None
M0167151 PFPLPDNJ_00185 177358 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -197A>C None
M0167152 PFPLPDNJ_00185 177372 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -211A>T None
M0167153 PFPLPDNJ_00185 177373 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -212A>T None
M0167154 PFPLPDNJ_00185 177383 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -222G>A None
M0167155 PFPLPDNJ_00186 177454 3 Gut 0.14 protein_coding missense_variant MODERATE 28T>A Ser10Thr
M0167156 PFPLPDNJ_00186 177504 3 Gut 0.14 protein_coding synonymous_variant LOW 78G>A Lys26Lys
M0167157 PFPLPDNJ_00186 177515 3 Gut 0.14 protein_coding missense_variant MODERATE 89G>T Trp30Leu
M0167158 PFPLPDNJ_00186 177537 3 Gut 0.14 protein_coding synonymous_variant LOW 111G>A Leu37Leu
M0167159 PFPLPDNJ_00186 177547 3 Gut 0.14 protein_coding missense_variant MODERATE 121G>A Val41Ile
M0167160 PFPLPDNJ_00186 177582 3 Gut 0.14 protein_coding missense_variant MODERATE 156G>A Met52Ile
M0167161 PFPLPDNJ_00186 177707 3 Gut 0.14 protein_coding missense_variant MODERATE 281A>G Tyr94Cys
M0167162 PFPLPDNJ_00186 177734 3 Gut 0.14 protein_coding missense_variant MODERATE 308A>G Asn103Ser
M0167163 PFPLPDNJ_00186 177744 3 Gut 0.14 protein_coding synonymous_variant LOW 318T>C Asn106Asn
M0167164 PFPLPDNJ_00186 177761 3 Gut 0.14 protein_coding missense_variant MODERATE 335T>C Val112Ala
M0167165 PFPLPDNJ_00186 177786 3 Gut 0.14 protein_coding missense_variant MODERATE 360G>A Met120Ile
M0167166 PFPLPDNJ_00186 177846 3 Gut 0.14 protein_coding synonymous_variant LOW 420A>G Ser140Ser
M0167167 PFPLPDNJ_00186 177861 3 Gut 0.14 protein_coding synonymous_variant LOW 435G>A Lys145Lys
M0167168 PFPLPDNJ_00186 177870 3 Gut 0.14 protein_coding synonymous_variant LOW 444A>G Leu148Leu
M0167169 PFPLPDNJ_00186 177881 3 Gut 0.14 protein_coding missense_variant MODERATE 455C>T Ala152Val
M0167170 PFPLPDNJ_00186 177930 3 Gut 0.14 protein_coding synonymous_variant LOW 504T>C Tyr168Tyr
M0167171 PFPLPDNJ_00186 177936 3 Gut 0.14 protein_coding synonymous_variant LOW 510C>T Ser170Ser
M0167172 PFPLPDNJ_00186 177948 3 Gut 0.14 protein_coding synonymous_variant LOW 522C>T Ser174Ser
M0167173 PFPLPDNJ_00186 177957 3 Gut 0.14 protein_coding synonymous_variant LOW 531G>A Val177Val
M0167174 PFPLPDNJ_00186 178137 3 Gut 0.14 protein_coding synonymous_variant LOW 711C>T Ser237Ser
M0167175 PFPLPDNJ_00186 178181 3 Gut 0.14 protein_coding missense_variant MODERATE 755G>A Gly252Glu
M0167176 PFPLPDNJ_00186 178357 3 Gut 0.14 protein_coding missense_variant MODERATE 931G>A Val311Ile
M0167177 PFPLPDNJ_00186 178381 3 Gut 0.14 protein_coding missense_variant MODERATE 955G>A Ala319Thr
M0167178 PFPLPDNJ_00186 178425 3 Gut 0.14 protein_coding synonymous_variant LOW 999G>A Ala333Ala
M0167179 PFPLPDNJ_00186 178473 3 Gut 0.14 protein_coding synonymous_variant LOW 1047A>G Glu349Glu
M0167180 PFPLPDNJ_00186 178563 3 Gut 0.14 protein_coding synonymous_variant LOW 1137A>G Lys379Lys
M0167181 PFPLPDNJ_00037 49047 3 Gut 0.14 protein_coding stop_lost&splice_region_variant HIGH 307T>C Ter103Glnext*?
M0167182 PFPLPDNJ_00037 49062 3 Gut 0.14 protein_coding missense_variant MODERATE 292T>C Tyr98His
M0167183 PFPLPDNJ_00037 49282 3 Gut 0.14 protein_coding synonymous_variant LOW 72G>A Arg24Arg
M0167184 PFPLPDNJ_00041 50472 3 Gut 0.14 protein_coding missense_variant MODERATE 1504G>A Val502Ile
M0167185 PFPLPDNJ_00041 51298 3 Gut 0.14 protein_coding synonymous_variant LOW 678A>G Glu226Glu
M0167186 PFPLPDNJ_00041 51894 3 Gut 0.14 protein_coding missense_variant MODERATE 82A>G Lys28Glu






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







        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
PFPLPDNJ_00239 ARO:3002626 100 9.66e-218 1 287 1.0000 1.0000 aminoglycoside antibiotic ANT(6) antibiotic inactivation
PFPLPDNJ_00243 ARO:3002597 100 0 1 479 1.0000 1.0000 aminoglycoside antibiotic aminoglycoside bifunctional resistance protein 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






        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
PFPLPDNJ_00060 CCO10203.2|GH1 87.9 8.11e-247 1 388 0.9949 0.9949
PFPLPDNJ_00242 CCO10203.2|GH1 86.9 1.56e-244 1 390 1 1
PFPLPDNJ_00245 CCO10203.2|GH1 86.9 1.56e-244 1 390 1 1
PFPLPDNJ_00246 CCO11850.2|GH4 79.8 3.76e-121 222 439 0.4966 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
PFPLPDNJ_00132 2.A.21.3.20 74.5 7.1e-209 1 498 0.9940 0.9960 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.21 The Solute:Sodium Symporter (SSS) Family
PFPLPDNJ_00204 2.A.1.1.74 71.2 2.2e-171 1 417 0.9952 0.9953 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)