Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C121
  Reference Plasmid   CP063571.1
  Reference Plasmid Size   18047
  Reference Plasmid GC Content   0.34
  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
M0144676 LPCPCAHJ_00005 2011 3 Gut 1.00 protein_coding missense_variant MODERATE 559G>A Glu187Lys
M0144677 LPCPCAHJ_00007 3687 3 Gut 1.00 protein_coding synonymous_variant LOW 162A>C Gly54Gly
M0144678 LPCPCAHJ_00007 3756 3 Gut 1.00 protein_coding synonymous_variant LOW 93T>C Phe31Phe
M0144679 LPCPCAHJ_00007 3792 3 Gut 1.00 protein_coding synonymous_variant LOW 57A>G Leu19Leu
M0144680 LPCPCAHJ_00007 3814 3 Gut 1.00 protein_coding missense_variant MODERATE 35C>A Ala12Asp
M0144681 LPCPCAHJ_00007 3830 3 Gut 1.00 protein_coding missense_variant MODERATE 19A>T Thr7Ser
M0144682 LPCPCAHJ_00008 3878 3 Gut 1.00 protein_coding synonymous_variant LOW 1038C>T Gly346Gly
M0144683 LPCPCAHJ_00008 3919 3 Gut 1.00 protein_coding missense_variant MODERATE 997A>G Asn333Asp
M0144684 LPCPCAHJ_00008 3926 3 Gut 1.00 protein_coding synonymous_variant LOW 990G>A Lys330Lys
M0144685 LPCPCAHJ_00008 3939 3 Gut 1.00 protein_coding missense_variant MODERATE 977G>A Gly326Asp
M0144686 LPCPCAHJ_00008 3977 3 Gut 1.00 protein_coding synonymous_variant LOW 939A>G Gly313Gly
M0144687 LPCPCAHJ_00008 4028 3 Gut 1.00 protein_coding synonymous_variant LOW 888A>C Gly296Gly
M0144688 LPCPCAHJ_00008 4055 3 Gut 1.00 protein_coding synonymous_variant LOW 861G>A Thr287Thr
M0144689 LPCPCAHJ_00008 4079 3 Gut 1.00 protein_coding synonymous_variant LOW 837G>A Ala279Ala
M0144690 LPCPCAHJ_00008 4127 3 Gut 1.00 protein_coding synonymous_variant LOW 789G>A Lys263Lys
M0144691 LPCPCAHJ_00008 4139 3 Gut 1.00 protein_coding synonymous_variant LOW 777C>T Asn259Asn
M0144692 LPCPCAHJ_00008 4148 3 Gut 1.00 protein_coding synonymous_variant LOW 768C>T Ser256Ser
M0144693 LPCPCAHJ_00008 4149 3 Gut 1.00 protein_coding missense_variant MODERATE 767G>A Ser256Asn
M0144694 LPCPCAHJ_00008 4160 3 Gut 1.00 protein_coding synonymous_variant LOW 756A>G Glu252Glu
M0144695 LPCPCAHJ_00008 4199 3 Gut 1.00 protein_coding synonymous_variant LOW 717T>C Phe239Phe
M0144696 LPCPCAHJ_00008 4232 3 Gut 1.00 protein_coding synonymous_variant LOW 684C>T His228His
M0144697 LPCPCAHJ_00008 4244 3 Gut 1.00 protein_coding synonymous_variant LOW 672A>C Gly224Gly
M0144698 LPCPCAHJ_00008 4259 3 Gut 1.00 protein_coding synonymous_variant LOW 657C>T Ile219Ile
M0144699 LPCPCAHJ_00008 4274 3 Gut 1.00 protein_coding synonymous_variant LOW 642G>T Pro214Pro
M0144700 LPCPCAHJ_00008 4280 3 Gut 1.00 protein_coding synonymous_variant LOW 636C>T Asp212Asp
M0144701 LPCPCAHJ_00008 4337 3 Gut 1.00 protein_coding synonymous_variant LOW 579C>T His193His
M0144702 LPCPCAHJ_00008 4352 3 Gut 1.00 protein_coding synonymous_variant LOW 564A>G Gln188Gln
M0144703 LPCPCAHJ_00009 5185 3 Gut 1.00 protein_coding synonymous_variant LOW 1077T>A Gly359Gly
M0144704 LPCPCAHJ_00009 5548 3 Gut 1.00 protein_coding synonymous_variant LOW 714G>A Gly238Gly
M0144705 LPCPCAHJ_00009 5563 3 Gut 1.00 protein_coding synonymous_variant LOW 699T>C Gly233Gly
M0144706 LPCPCAHJ_00009 5812 3 Gut 1.00 protein_coding synonymous_variant LOW 450G>A Leu150Leu
M0144707 LPCPCAHJ_00009 5851 3 Gut 1.00 protein_coding synonymous_variant LOW 411C>T Asn137Asn
M0144708 LPCPCAHJ_00009 5924 3 Gut 1.00 protein_coding missense_variant MODERATE 338A>G His113Arg
M0144709 LPCPCAHJ_00009 6136 3 Gut 1.00 protein_coding synonymous_variant LOW 126C>T Asn42Asn
M0144710 LPCPCAHJ_00009 6178 3 Gut 1.00 protein_coding synonymous_variant LOW 84G>T Pro28Pro
M0144711 LPCPCAHJ_00009 6202 3 Gut 1.00 protein_coding synonymous_variant LOW 60T>C Tyr20Tyr
M0144712 LPCPCAHJ_00009 6226 3 Gut 1.00 protein_coding synonymous_variant LOW 36A>G Leu12Leu
M0144713 LPCPCAHJ_00009 6228 3 Gut 1.00 protein_coding missense_variant MODERATE 34T>A Leu12Ile
M0144714 LPCPCAHJ_00009 6229 3 Gut 1.00 protein_coding synonymous_variant LOW 33A>G Lys11Lys
M0144715 LPCPCAHJ_00009 6253 3 Gut 1.00 protein_coding synonymous_variant LOW 9G>A Glu3Glu
M0144716 LPCPCAHJ_00009 6258 3 Gut 1.00 protein_coding missense_variant MODERATE 4A>G Lys2Glu
M0144717 LPCPCAHJ_00010 6355 3 Gut 1.00 protein_coding missense_variant MODERATE 340G>C Ala114Pro
M0144718 LPCPCAHJ_00010 6358 3 Gut 1.00 protein_coding missense_variant MODERATE 337G>A Ala113Thr
M0144719 LPCPCAHJ_00010 6365 3 Gut 1.00 protein_coding synonymous_variant LOW 330T>A Val110Val
M0144720 LPCPCAHJ_00010 6376 3 Gut 1.00 protein_coding synonymous_variant LOW 319C>T Leu107Leu
M0144721 LPCPCAHJ_00010 6530 3 Gut 1.00 protein_coding synonymous_variant LOW 165C>T Gly55Gly
M0144722 LPCPCAHJ_00010 6546 3 Gut 1.00 protein_coding missense_variant MODERATE 149T>C Val50Ala
M0144723 LPCPCAHJ_00010 6567 3 Gut 1.00 protein_coding missense_variant MODERATE 128T>C Val43Ala
M0144724 LPCPCAHJ_00010 6568 3 Gut 1.00 protein_coding missense_variant MODERATE 127G>A Val43Ile
M0144725 LPCPCAHJ_00011 6821 3 Gut 1.00 protein_coding missense_variant MODERATE 290G>C Ser97Thr
M0144726 LPCPCAHJ_00011 6853 3 Gut 1.00 protein_coding missense_variant MODERATE 258G>C Glu86Asp
M0144727 LPCPCAHJ_00011 7084 3 Gut 1.00 protein_coding synonymous_variant LOW 27G>A Gln9Gln
M0144728 LPCPCAHJ_00011 7106 3 Gut 1.00 protein_coding missense_variant MODERATE 5T>C Val2Ala
M0144729 LPCPCAHJ_00011 7107 3 Gut 1.00 protein_coding missense_variant MODERATE 4G>A Val2Ile
M0144730 LPCPCAHJ_00012 7122 3 Gut 1.00 protein_coding synonymous_variant LOW 288G>A Val96Val
M0144731 LPCPCAHJ_00012 7172 3 Gut 1.00 protein_coding missense_variant MODERATE 238A>G Ile80Val
M0144732 LPCPCAHJ_00012 7211 3 Gut 1.00 protein_coding missense_variant MODERATE 199G>A Ala67Thr
M0144733 LPCPCAHJ_00012 7221 3 Gut 1.00 protein_coding synonymous_variant LOW 189A>G Lys63Lys
M0144734 LPCPCAHJ_00012 7233 3 Gut 1.00 protein_coding synonymous_variant LOW 177C>T Ala59Ala
M0144735 LPCPCAHJ_00012 7245 3 Gut 1.00 protein_coding synonymous_variant LOW 165G>T Ala55Ala
M0144736 LPCPCAHJ_00012 7253 3 Gut 1.00 protein_coding missense_variant MODERATE 157C>A Gln53Lys
M0144737 LPCPCAHJ_00012 7260 3 Gut 1.00 protein_coding synonymous_variant LOW 150G>C Thr50Thr
M0144738 LPCPCAHJ_00012 7275 3 Gut 1.00 protein_coding synonymous_variant LOW 135T>C Asn45Asn
M0144739 LPCPCAHJ_00012 7296 3 Gut 1.00 protein_coding synonymous_variant LOW 114A>G Leu38Leu
M0144740 LPCPCAHJ_00012 7317 3 Gut 1.00 protein_coding synonymous_variant LOW 93C>T Gly31Gly
M0144741 LPCPCAHJ_00012 7370 3 Gut 1.00 protein_coding missense_variant MODERATE 40A>T Thr14Ser
M0144742 LPCPCAHJ_00013 7466 3 Gut 1.00 protein_coding synonymous_variant LOW 495A>C Gly165Gly
M0144743 LPCPCAHJ_00013 7516 3 Gut 1.00 protein_coding missense_variant MODERATE 445G>A Asp149Asn
M0144744 LPCPCAHJ_00013 7577 3 Gut 1.00 protein_coding synonymous_variant LOW 384C>T Pro128Pro
M0144745 LPCPCAHJ_00013 7586 3 Gut 1.00 protein_coding synonymous_variant LOW 375A>G Lys125Lys
M0144746 LPCPCAHJ_00013 7844 3 Gut 1.00 protein_coding synonymous_variant LOW 117G>A Val39Val
M0144747 LPCPCAHJ_00013 7926 3 Gut 1.00 protein_coding missense_variant MODERATE 35T>G Val12Gly
M0144748 LPCPCAHJ_00014 8380 3 Gut 1.00 protein_coding synonymous_variant LOW 423C>A Thr141Thr
M0144749 LPCPCAHJ_00014 8410 3 Gut 1.00 protein_coding synonymous_variant LOW 393A>C Val131Val
M0144750 LPCPCAHJ_00014 8584 3 Gut 1.00 protein_coding synonymous_variant LOW 219A>G Glu73Glu
M0144751 LPCPCAHJ_00016 10008 3 Gut 1.00 protein_coding missense_variant MODERATE 1594G>A Asp532Asn
M0144752 LPCPCAHJ_00016 10011 3 Gut 1.00 protein_coding synonymous_variant LOW 1591T>C Leu531Leu
M0144753 LPCPCAHJ_00017 11727 3 Gut 1.00 protein_coding synonymous_variant LOW 1215T>A Ser405Ser
M0144754 LPCPCAHJ_00018 13222 3 Gut 1.00 protein_coding synonymous_variant LOW 24G>C Ala8Ala
M0144755 LPCPCAHJ_00019 13547 3 Gut 1.00 protein_coding missense_variant MODERATE 136A>G Ile46Val
M0144756 LPCPCAHJ_00019 13608 3 Gut 1.00 protein_coding synonymous_variant LOW 75A>T Val25Val
M0144757 LPCPCAHJ_00019 13662 3 Gut 1.00 protein_coding missense_variant MODERATE 21T>G Ile7Met
M0144758 LPCPCAHJ_00019 13677 3 Gut 1.00 protein_coding synonymous_variant LOW 6C>T Asp2Asp
M0144759 LPCPCAHJ_00020 13752 3 Gut 1.00 protein_coding synonymous_variant LOW 1665G>A Leu555Leu
M0144760 LPCPCAHJ_00021 16031 3 Gut 1.00 protein_coding synonymous_variant LOW 228G>A Gln76Gln
M0144761 LPCPCAHJ_00021 16067 3 Gut 1.00 protein_coding synonymous_variant LOW 192T>C Phe64Phe
M0144762 LPCPCAHJ_00021 16112 3 Gut 1.00 protein_coding missense_variant MODERATE 147A>C Arg49Ser
M0144763 LPCPCAHJ_00021 16145 3 Gut 1.00 protein_coding synonymous_variant LOW 114G>A Arg38Arg
M0144764 LPCPCAHJ_00021 16202 3 Gut 1.00 protein_coding synonymous_variant LOW 57G>A Lys19Lys
M0144765 LPCPCAHJ_00021 16211 3 Gut 1.00 protein_coding synonymous_variant LOW 48C>T Ile16Ile
M0144766 LPCPCAHJ_00022 16399 3 Gut 1.00 protein_coding synonymous_variant LOW 315T>A Val105Val
M0144767 LPCPCAHJ_00022 16425 3 Gut 1.00 protein_coding missense_variant MODERATE 289A>G Asn97Asp
M0144768 LPCPCAHJ_00022 16453 3 Gut 1.00 protein_coding synonymous_variant LOW 261C>T Asn87Asn
M0144769 LPCPCAHJ_00022 16465 3 Gut 1.00 protein_coding synonymous_variant LOW 249G>A Lys83Lys
M0144770 LPCPCAHJ_00022 16576 3 Gut 1.00 protein_coding synonymous_variant LOW 138C>T Tyr46Tyr
M0144771 LPCPCAHJ_00022 16584 3 Gut 1.00 protein_coding synonymous_variant LOW 130C>T Leu44Leu
M0144772 LPCPCAHJ_00023 16852 3 Gut 1.00 protein_coding missense_variant MODERATE 167G>A Ser56Asn
M0144773 LPCPCAHJ_00023 16853 3 Gut 1.00 protein_coding missense_variant MODERATE 166A>G Ser56Gly
M0144774 LPCPCAHJ_00023 16979 3 Gut 1.00 protein_coding missense_variant MODERATE 40G>A Glu14Lys
M0144775 LPCPCAHJ_00023 17014 3 Gut 1.00 protein_coding missense_variant MODERATE 5C>T Ala2Val
M0144776 LPCPCAHJ_00017 17038 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4097T>A None
M0144777 LPCPCAHJ_00017 17042 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4101T>C None
M0144778 LPCPCAHJ_00017 17100 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4159G>A None






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






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
LPCPCAHJ_00006 CAD7757511.1|GH25 96.9 7.41e-221 1 292 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