Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C915
  Reference Plasmid   NZ_CP077338.1
  Reference Plasmid Size   221423
  Reference Plasmid GC Content   0.41
  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
M0104710 PCLCBLIG_00072 70159 4 Skin 0.12 protein_coding synonymous_variant LOW 330A>C Ala110Ala
M0104711 PCLCBLIG_00072 70164 4 Skin 0.12 protein_coding missense_variant MODERATE 325G>T Ala109Ser
M0104712 PCLCBLIG_00072 70201 4 Skin 0.12 protein_coding synonymous_variant LOW 288A>C Ser96Ser
M0104713 PCLCBLIG_00072 70216 4 Skin 0.12 protein_coding synonymous_variant LOW 273T>C Gly91Gly
M0104714 PCLCBLIG_00069 70533 4 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3110A>G None
M0104715 PCLCBLIG_00069 70542 4 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3119T>A None
M0104716 PCLCBLIG_00071 69312 3 Skin 0.09 protein_coding synonymous_variant LOW 141T>C Ile47Ile
M0104717 PCLCBLIG_00071 69346 3 Skin 0.09 protein_coding missense_variant MODERATE 107A>G Asn36Ser
M0104718 PCLCBLIG_00071 69369 3 Skin 0.09 protein_coding synonymous_variant LOW 84G>A Leu28Leu
M0104719 PCLCBLIG_00071 69378 3 Skin 0.09 protein_coding synonymous_variant LOW 75T>C Pro25Pro
M0104720 PCLCBLIG_00071 69405 3 Skin 0.09 protein_coding synonymous_variant LOW 48G>A Leu16Leu
M0104721 PCLCBLIG_00072 69580 3 Skin 0.09 protein_coding missense_variant MODERATE 909C>A Asp303Glu
M0104722 PCLCBLIG_00072 69609 3 Skin 0.09 protein_coding missense_variant MODERATE 880T>A Tyr294Asn
M0104723 PCLCBLIG_00072 69610 3 Skin 0.09 protein_coding synonymous_variant LOW 879C>T Phe293Phe
M0104724 PCLCBLIG_00072 69615 3 Skin 0.09 protein_coding missense_variant MODERATE 874G>C Glu292Gln
M0104725 PCLCBLIG_00072 69618 3 Skin 0.09 protein_coding missense_variant MODERATE 871T>C Ser291Pro
M0104726 PCLCBLIG_00072 69697 3 Skin 0.09 protein_coding synonymous_variant LOW 792A>G Pro264Pro
M0104727 PCLCBLIG_00072 69722 3 Skin 0.09 protein_coding missense_variant MODERATE 767G>A Arg256Gln
M0104728 PCLCBLIG_00072 69788 3 Skin 0.09 protein_coding missense_variant MODERATE 701C>A Pro234Gln
M0104729 PCLCBLIG_00072 69796 3 Skin 0.09 protein_coding synonymous_variant LOW 693A>T Ala231Ala
M0104730 PCLCBLIG_00072 69817 3 Skin 0.09 protein_coding synonymous_variant LOW 672C>A Val224Val
M0104731 PCLCBLIG_00072 69838 3 Skin 0.09 protein_coding synonymous_variant LOW 651A>T Ile217Ile
M0104732 PCLCBLIG_00072 70060 3 Skin 0.09 protein_coding synonymous_variant LOW 429C>T Gly143Gly
M0104733 PCLCBLIG_00072 70114 3 Skin 0.09 protein_coding synonymous_variant LOW 375G>A Leu125Leu
M0104734 PCLCBLIG_00072 70190 3 Skin 0.09 protein_coding stop_gained HIGH 299G>A Trp100*
M0104735 PCLCBLIG_00072 70225 3 Skin 0.09 protein_coding synonymous_variant LOW 264C>T Phe88Phe
M0104736 PCLCBLIG_00072 70295 3 Skin 0.09 protein_coding missense_variant MODERATE 194C>T Pro65Leu
M0104737 PCLCBLIG_00072 70383 3 Skin 0.09 protein_coding stop_gained HIGH 106C>T Gln36*
M0104738 PCLCBLIG_00072 70408 3 Skin 0.09 protein_coding synonymous_variant LOW 81G>A Glu27Glu
M0104739 PCLCBLIG_00073 70665 3 Skin 0.09 protein_coding synonymous_variant LOW 33G>A Ala11Ala
M0104740 PCLCBLIG_00073 70668 3 Skin 0.09 protein_coding synonymous_variant LOW 36G>A Lys12Lys
M0104741 PCLCBLIG_00073 70695 3 Skin 0.09 protein_coding synonymous_variant LOW 63A>T Ser21Ser
M0104742 PCLCBLIG_00084 81317 4 Skin 0.12 protein_coding synonymous_variant LOW 705G>A Gly235Gly
M0104743 PCLCBLIG_00084 81491 3 Skin 0.09 protein_coding synonymous_variant LOW 531C>T Val177Val
M0104744 PCLCBLIG_00084 81662 3 Skin 0.09 protein_coding synonymous_variant LOW 360C>T Tyr120Tyr
M0104745 PCLCBLIG_00084 81716 3 Skin 0.09 protein_coding synonymous_variant LOW 306A>T Ser102Ser
M0104746 PCLCBLIG_00084 81722 3 Skin 0.09 protein_coding synonymous_variant LOW 300T>G Val100Val
M0104747 PCLCBLIG_00084 81784 3 Skin 0.09 protein_coding synonymous_variant LOW 238C>T Leu80Leu
M0104748 PCLCBLIG_00084 81794 3 Skin 0.09 protein_coding synonymous_variant LOW 228C>G Ser76Ser
M0104749 PCLCBLIG_00084 81941 3 Skin 0.09 protein_coding synonymous_variant LOW 81C>G Leu27Leu
M0104750 PCLCBLIG_00080 82035 3 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -3727C>A None
M0104751 PCLCBLIG_00080 82097 3 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -3789A>T None
M0104752 PCLCBLIG_00080 82149 3 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -3841C>A None
M0104753 PCLCBLIG_00080 82150 3 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -3842G>A None
M0104754 PCLCBLIG_00085 82501 3 Skin 0.09 protein_coding synonymous_variant LOW 345C>T Ile115Ile
M0104755 PCLCBLIG_00080 82899 3 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -4591A>T 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
PCLCBLIG_00090 Arsenic (As) 70.8 1.2e-87 24 237 0.9114 0.9310 experiment
PCLCBLIG_00090 Arsenic (As) 75.1 2.5e-97 6 237 0.9831 0.9708 prediction
PCLCBLIG_00091 Arsenic (As) 98.3 7.9e-185 1 346 1.0000 1.0000 prediction
PCLCBLIG_00141 Cadmium (Cd), Zinc (Zn) 82.7 4.6e-109 1 226 1.0000 0.9869 prediction
PCLCBLIG_00144 Copper (Cu) 100 0 1 791 1.0000 1.0000 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
PCLCBLIG_00103 PHI:3165 hopA1 73.8 7.8e-64 10 158 0.9030 0.9693 eudicots leaf spot (celery); leaf spot (eggplant); leaf spot (sweet pepper); wilt rot (muskmelon); stem rot (muskmelon); stem rot (chrysanthemum); leaf spot (soybean) effector (plant avirulence determinant) effector (plant avirulence determinant)
PCLCBLIG_00137 PHI:10396 copB (ABUW_3320) 70.7 9.5e-124 1 306 1.0000 1.0000 moths nosocomial infection autotransporter domain-containing protein reduced virulence
PCLCBLIG_00138 PHI:10393 cueO (ABUW_3321) 78.4 2.2e-272 1 556 1.0000 0.8709 moths nosocomial infection copper resistance protein A reduced virulence
PCLCBLIG_00141 PHI:10397 cusR (ABUW_3323) 95.1 2.5e-121 1 226 1.0000 0.9956 moths nosocomial infection DNA-binding response regulator reduced virulence
PCLCBLIG_00142 PHI:10394 cusS (ABUW_3324) 75.5 3.3e-200 1 457 0.9807 0.9978 moths nosocomial infection sensor kinase reduced virulence
PCLCBLIG_00149 PHI:10398 copC (ABUW_3326) 78.6 2.3e-52 1 126 1.0000 1.0000 moths nosocomial infection copper resistance protein reduced virulence
PCLCBLIG_00150 PHI:10395 copD (ABUW_3327) 74.4 9.4e-121 1 293 1.0000 1.0000 moths nosocomial infection copper resistance D reduced virulence
PCLCBLIG_00152 PHI:8812 CopA (ABUW_2707) 75.4 0 1 822 0.9964 0.9988 rodents nosocomial infection copper-translocating P-type ATPase 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





        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
PCLCBLIG_00001 2.A.14.1.1 72.6 4.6e-225 5 554 0.9928 0.9946 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.14 The Lactate Permease (LctP) Family
PCLCBLIG_00150 9.B.62.1.6 74.4 2.1e-120 1 293 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.62 The Copper Resistance (CopD) Family