Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1316
  Reference Plasmid   NZ_CP155542.1
  Reference Plasmid Size   32420
  Reference Plasmid GC Content   0.30
  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
M0115960 PDPMKEMA_00001 424 7 Skin 0.08 protein_coding missense_variant MODERATE 421A>C Thr141Pro
M0115961 PDPMKEMA_00002 503 6 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -349T>A None
M0115962 PDPMKEMA_00002 504 6 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -348T>A None
M0115963 PDPMKEMA_00002 1274 8 Skin 0.09 protein_coding synonymous_variant LOW 423T>C Arg141Arg
M0115964 PDPMKEMA_00005 3757 10 Skin 0.11 protein_coding synonymous_variant LOW 1185A>G Ala395Ala
M0115965 PDPMKEMA_00008 6383 9 Skin 0.10 protein_coding missense_variant MODERATE 268G>A Gly90Ser
M0115966 PDPMKEMA_00003 6674 10 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -4536T>A None
M0115967 PDPMKEMA_00003 6675 10 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -4537T>A None
M0115968 PDPMKEMA_00034 32331 7 Skin 0.08 protein_coding missense_variant MODERATE 724C>G Gln242Glu
M0115969 PDPMKEMA_00032 30160 3 Skin 0.03 protein_coding missense_variant MODERATE 277C>A Leu93Ile
M0115970 PDPMKEMA_00020 16893 4 Skin 0.04 protein_coding missense_variant MODERATE 1139T>C Met380Thr
M0115971 PDPMKEMA_00003 2219 9 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -81C>T None
M0115972 PDPMKEMA_00003 2220 11 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -82T>G None
M0115973 PDPMKEMA_00003 2222 9 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -84C>T None
M0115974 PDPMKEMA_00005 4225 3 Skin 0.03 protein_coding synonymous_variant LOW 1653C>T Asp551Asp
M0115975 PDPMKEMA_00023 19457 3 Skin 0.03 protein_coding synonymous_variant LOW 132C>T Pro44Pro
M0115976 PDPMKEMA_00001 306 3 Skin 0.03 protein_coding synonymous_variant LOW 303T>C Asp101Asp
M0115977 PDPMKEMA_00032 30356 3 Skin 0.03 protein_coding synonymous_variant LOW 81C>T Tyr27Tyr
M0115978 PDPMKEMA_00032 30366 3 Skin 0.03 protein_coding missense_variant MODERATE 71G>A Gly24Asp
M0115979 PDPMKEMA_00009 8563 5 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -50C>G None
M0115980 PDPMKEMA_00012 10925 6 Skin 0.07 protein_coding synonymous_variant LOW 318G>A Glu106Glu
M0115981 PDPMKEMA_00012 10991 7 Skin 0.08 protein_coding missense_variant MODERATE 252T>G Asp84Glu
M0115982 PDPMKEMA_00012 11102 8 Skin 0.09 protein_coding synonymous_variant LOW 141C>T Ile47Ile
M0115983 PDPMKEMA_00009 11245 5 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -2732T>C None
M0115984 PDPMKEMA_00009 11254 7 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -2741T>G None
M0115985 PDPMKEMA_00013 11303 3 Skin 0.03 protein_coding synonymous_variant LOW 576T>A Ile192Ile
M0115986 PDPMKEMA_00013 11354 3 Skin 0.03 protein_coding synonymous_variant LOW 525T>C Ser175Ser
M0115987 PDPMKEMA_00013 11504 8 Skin 0.09 protein_coding synonymous_variant LOW 375C>T Ile125Ile
M0115988 PDPMKEMA_00013 11531 7 Skin 0.08 protein_coding synonymous_variant LOW 348A>G Thr116Thr
M0115989 PDPMKEMA_00020 17577 5 Skin 0.06 protein_coding missense_variant MODERATE 455C>T Ala152Val
M0115990 PDPMKEMA_00013 11464 3 Skin 0.03 protein_coding missense_variant MODERATE 415A>G Asn139Asp
M0115991 PDPMKEMA_00013 11627 4 Skin 0.04 protein_coding synonymous_variant LOW 252A>G Val84Val
M0115992 PDPMKEMA_00013 11734 3 Skin 0.03 protein_coding missense_variant MODERATE 145G>A Ala49Thr
M0115993 PDPMKEMA_00013 11741 4 Skin 0.04 protein_coding synonymous_variant LOW 138T>A Gly46Gly
M0115994 PDPMKEMA_00013 11777 3 Skin 0.03 protein_coding synonymous_variant LOW 102A>G Lys34Lys
M0115995 PDPMKEMA_00013 11780 4 Skin 0.04 protein_coding synonymous_variant LOW 99G>A Arg33Arg
M0115996 PDPMKEMA_00013 11781 3 Skin 0.03 protein_coding missense_variant MODERATE 98G>A Arg33Lys
M0115997 PDPMKEMA_00013 11793 3 Skin 0.03 protein_coding missense_variant MODERATE 86G>A Arg29Lys
M0115998 PDPMKEMA_00013 11810 3 Skin 0.03 protein_coding synonymous_variant LOW 69A>G Leu23Leu
M0115999 PDPMKEMA_00013 11816 4 Skin 0.04 protein_coding synonymous_variant LOW 63A>G Val21Val
M0116000 PDPMKEMA_00013 11846 3 Skin 0.03 protein_coding synonymous_variant LOW 33T>G Leu11Leu
M0116001 PDPMKEMA_00009 11910 3 Skin 0.03 protein_coding upstream_gene_variant MODIFIER -3397C>T None
M0116002 PDPMKEMA_00009 11915 3 Skin 0.03 protein_coding upstream_gene_variant MODIFIER -3402T>C None
M0116003 PDPMKEMA_00015 18081 6 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -4979C>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
PDPMKEMA_00013 Cadmium (Cd), Zinc (Zn) 94.1 1.7e-101 1 205 1.0000 1.0000 experiment
PDPMKEMA_00020 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Crystal Violet [class: Triarylmethane], Pyronin Y [class: Xanthene], Quinaldine red [class: Quinolines], Rhodamine 6G [class: Xanthene], Safranin O [class: Azin], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Alexidine [class: Biguanides], Amicarbalide [class: Diamidine], Pentamidine [class: Diamidine], Hexamidine [class: Diamidine], Propamidine [class: Diamidine], Diamidinodiphenylamine [class: Diamidine], Dibrompropamidine [class: Diamidine], 1a-62/JC-1-127 [class: Guanylhydrazones], 1i-39/JC-1-134 [class: Guanylhydrazones], Stilbamidine [class: Diamidine], Phenamidine [class: Diamidine], Diminazene [class: Diamidine] 100 3.2e-274 1 514 1.0000 1.0000 experiment
PDPMKEMA_00021 Chlorhexidine [class: Biguanides], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Pentamidine [class: Diamidine], Propamidine [class: Diamidine], Diaminodiphenylamine [class: Diamidine] 99.5 4.7e-106 1 188 1.0000 1.0000 experiment
CELKIDOE_00013 Cadmium (Cd), Zinc (Zn) 94.1 1.7e-101 1 205 1.0000 1.0000 experiment
CELKIDOE_00020 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Crystal Violet [class: Triarylmethane], Pyronin Y [class: Xanthene], Quinaldine red [class: Quinolines], Rhodamine 6G [class: Xanthene], Safranin O [class: Azin], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Alexidine [class: Biguanides], Amicarbalide [class: Diamidine], Pentamidine [class: Diamidine], Hexamidine [class: Diamidine], Propamidine [class: Diamidine], Diamidinodiphenylamine [class: Diamidine], Dibrompropamidine [class: Diamidine], 1a-62/JC-1-127 [class: Guanylhydrazones], 1i-39/JC-1-134 [class: Guanylhydrazones], Stilbamidine [class: Diamidine], Phenamidine [class: Diamidine], Diminazene [class: Diamidine] 100 3.2e-274 1 514 1.0000 1.0000 experiment
CELKIDOE_00021 Chlorhexidine [class: Biguanides], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Pentamidine [class: Diamidine], Propamidine [class: Diamidine], Diaminodiphenylamine [class: Diamidine] 99.5 4.7e-106 1 188 1.0000 1.0000 experiment
PDPMKEMA_00005 Copper (Cu), Silver (Ag) 75.6 0 1 795 1.0000 1.0013 prediction
PDPMKEMA_00006 Copper (Cu) 100 1.6e-33 1 69 1.0000 1.0000 prediction
PDPMKEMA_00013 Cadmium (Cd), Zinc (Zn) 100 1.3e-102 1 205 1.0000 1.0000 prediction
PDPMKEMA_00020 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Crystal Violet [class: Triarylmethane], Pyronin Y [class: Xanthene], Quinaldine red [class: Quinolines], Rhodamine 6G [class: Xanthene], Safranin O [class: Azin], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Alexidine [class: Biguanides], Amicarbalide [class: Diamidine], Pentamidine [class: Diamidine], Hexamidine [class: Diamidine], Propamidine [class: Diamidine], Diamidinodiphenylamine [class: Diamidine], Dibrompropamidine [class: Diamidine], 1a-62/JC-1-127 [class: Guanylhydrazones], 1i-39/JC-1-134 [class: Guanylhydrazones], Stilbamidine [class: Diamidine], Phenamidine [class: Diamidine], Diminazene [class: Diamidine] 100 7.4e-272 1 514 1.0000 1.0000 prediction
PDPMKEMA_00021 Chlorhexidine [class: Biguanides], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Pentamidine [class: Diamidine], Propamidine [class: Diamidine], Diaminodiphenylamine [class: Diamidine] 100 5.7e-105 1 188 1.0000 0.9947 prediction
CELKIDOE_00005 Copper (Cu), Silver (Ag) 75.6 0 1 795 1.0000 1.0013 prediction
CELKIDOE_00006 Copper (Cu) 100 1.6e-33 1 69 1.0000 1.0000 prediction
CELKIDOE_00013 Cadmium (Cd), Zinc (Zn) 100 1.3e-102 1 205 1.0000 1.0000 prediction
CELKIDOE_00020 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Crystal Violet [class: Triarylmethane], Pyronin Y [class: Xanthene], Quinaldine red [class: Quinolines], Rhodamine 6G [class: Xanthene], Safranin O [class: Azin], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Alexidine [class: Biguanides], Amicarbalide [class: Diamidine], Pentamidine [class: Diamidine], Hexamidine [class: Diamidine], Propamidine [class: Diamidine], Diamidinodiphenylamine [class: Diamidine], Dibrompropamidine [class: Diamidine], 1a-62/JC-1-127 [class: Guanylhydrazones], 1i-39/JC-1-134 [class: Guanylhydrazones], Stilbamidine [class: Diamidine], Phenamidine [class: Diamidine], Diminazene [class: Diamidine] 100 7.4e-272 1 514 1.0000 1.0000 prediction
CELKIDOE_00021 Chlorhexidine [class: Biguanides], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Pentamidine [class: Diamidine], Propamidine [class: Diamidine], Diaminodiphenylamine [class: Diamidine] 100 5.7e-105 1 188 1.0000 0.9947 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
PDPMKEMA_00020 ARO:3003046 99.8 0 1 514 1.0000 1.0000 fluoroquinolone antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
PDPMKEMA_00025 ARO:3003111 99.6 0 1 492 1.0000 1.0000 lincosamide antibiotic lsa-type ABC-F protein antibiotic target protection
PDPMKEMA_00026 ARO:3003441 100 1.68e-256 1 349 1.0000 1.0000 lincosamide antibiotic Cfr 23S ribosomal RNA methyltransferase antibiotic target alteration
PDPMKEMA_00031 ARO:3000319 98.7 1.82e-228 1 299 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
PDPMKEMA_00032 ARO:3000251 95.7 2.0997789948253e-320 1 488 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
CELKIDOE_00020 ARO:3003046 99.8 0 1 514 1.0000 1.0000 fluoroquinolone antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
CELKIDOE_00025 ARO:3003111 99.6 0 1 492 1.0000 1.0000 lincosamide antibiotic lsa-type ABC-F protein antibiotic target protection
CELKIDOE_00026 ARO:3003441 100 1.68e-256 1 349 1.0000 1.0000 lincosamide antibiotic Cfr 23S ribosomal RNA methyltransferase antibiotic target alteration
CELKIDOE_00031 ARO:3000319 98.7 1.82e-228 1 299 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
CELKIDOE_00032 ARO:3000251 95.7 2.0997789948253e-320 1 488 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection






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





        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
PDPMKEMA_00005 3.A.3.5.19 73.6 0 4 795 0.9962 0.9888 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
PDPMKEMA_00013 2.A.77.1.1 93.7 1.4e-99 1 205 1.0000 0.9809 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.77 The Cadmium Resistance (CadD) Family
PDPMKEMA_00020 2.A.1.3.4 100 1.2e-272 1 514 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
PDPMKEMA_00032 3.A.1.121.1 98.8 5.7e-272 1 488 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
CELKIDOE_00005 3.A.3.5.19 73.6 0 4 795 0.9962 0.9888 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
CELKIDOE_00013 2.A.77.1.1 93.7 1.4e-99 1 205 1.0000 0.9809 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.77 The Cadmium Resistance (CadD) Family
CELKIDOE_00020 2.A.1.3.4 100 1.2e-272 1 514 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
CELKIDOE_00032 3.A.1.121.1 98.8 5.7e-272 1 488 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily