Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1415
  Reference Plasmid   NZ_OR492670.1
  Reference Plasmid Size   385430
  Reference Plasmid GC Content   0.40
  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
M0116780 JKKIJAMP_00486 317815 3 Skin 0.19 protein_coding synonymous_variant LOW 99C>A Leu33Leu
M0116781 JKKIJAMP_00486 317818 3 Skin 0.19 protein_coding synonymous_variant LOW 96T>A Pro32Pro
M0116782 JKKIJAMP_00486 317823 3 Skin 0.19 protein_coding synonymous_variant LOW 91T>C Leu31Leu
M0116783 JKKIJAMP_00486 317839 3 Skin 0.19 protein_coding synonymous_variant LOW 75T>C Ala25Ala
M0116784 JKKIJAMP_00486 317851 3 Skin 0.19 protein_coding missense_variant MODERATE 63G>T Glu21Asp
M0116785 JKKIJAMP_00487 317930 3 Skin 0.19 protein_coding missense_variant MODERATE 448A>G Asn150Asp
M0116786 JKKIJAMP_00487 317931 3 Skin 0.19 protein_coding synonymous_variant LOW 447A>G Leu149Leu
M0116787 JKKIJAMP_00487 318024 4 Skin 0.25 protein_coding synonymous_variant LOW 354C>T Phe118Phe
M0116788 JKKIJAMP_00488 318404 3 Skin 0.19 protein_coding synonymous_variant LOW 207A>G Glu69Glu
M0116789 JKKIJAMP_00489 318891 3 Skin 0.19 protein_coding synonymous_variant LOW 1206C>G Ala402Ala
M0116790 JKKIJAMP_00489 318917 3 Skin 0.19 protein_coding missense_variant MODERATE 1180A>G Ser394Gly
M0116791 JKKIJAMP_00489 319184 4 Skin 0.25 protein_coding missense_variant MODERATE 913A>G Ile305Val
M0116792 JKKIJAMP_00489 319438 5 Skin 0.31 protein_coding missense_variant MODERATE 659A>C His220Pro
M0116793 JKKIJAMP_00489 319524 3 Skin 0.19 protein_coding synonymous_variant LOW 573A>G Gln191Gln
M0116794 JKKIJAMP_00489 319548 3 Skin 0.19 protein_coding synonymous_variant LOW 549C>T Thr183Thr
M0116795 JKKIJAMP_00489 319562 3 Skin 0.19 protein_coding missense_variant MODERATE 535A>T Ile179Phe
M0116796 JKKIJAMP_00489 319606 3 Skin 0.19 protein_coding missense_variant MODERATE 491G>A Gly164Asp
M0116797 JKKIJAMP_00489 319607 3 Skin 0.19 protein_coding missense_variant MODERATE 490G>A Gly164Ser
M0116798 JKKIJAMP_00489 319608 3 Skin 0.19 protein_coding synonymous_variant LOW 489G>A Leu163Leu
M0116799 JKKIJAMP_00489 319695 3 Skin 0.19 protein_coding synonymous_variant LOW 402A>C Pro134Pro
M0116800 JKKIJAMP_00489 319753 3 Skin 0.19 protein_coding missense_variant MODERATE 344G>A Arg115Gln
M0116801 JKKIJAMP_00489 319788 3 Skin 0.19 protein_coding synonymous_variant LOW 309A>C Thr103Thr
M0116802 JKKIJAMP_00489 319833 3 Skin 0.19 protein_coding synonymous_variant LOW 264T>C Gly88Gly
M0116803 JKKIJAMP_00489 319881 3 Skin 0.19 protein_coding synonymous_variant LOW 216T>C Arg72Arg
M0116804 JKKIJAMP_00489 319988 3 Skin 0.19 protein_coding missense_variant MODERATE 109A>G Asn37Asp
M0116805 JKKIJAMP_00489 320064 3 Skin 0.19 protein_coding synonymous_variant LOW 33A>G Leu11Leu
M0116806 JKKIJAMP_00490 320225 3 Skin 0.19 protein_coding synonymous_variant LOW 885A>T Pro295Pro
M0116807 JKKIJAMP_00490 320316 5 Skin 0.31 protein_coding missense_variant MODERATE 794G>A Gly265Glu
M0116808 JKKIJAMP_00490 320558 3 Skin 0.19 protein_coding synonymous_variant LOW 552G>A Leu184Leu
M0116809 JKKIJAMP_00490 320609 3 Skin 0.19 protein_coding synonymous_variant LOW 501G>T Gly167Gly
M0116810 JKKIJAMP_00490 320789 3 Skin 0.19 protein_coding synonymous_variant LOW 321C>T Leu107Leu
M0116811 JKKIJAMP_00490 320906 3 Skin 0.19 protein_coding synonymous_variant LOW 204C>T Ile68Ile
M0116812 JKKIJAMP_00490 320909 3 Skin 0.19 protein_coding synonymous_variant LOW 201T>G Gly67Gly
M0116813 JKKIJAMP_00490 320918 3 Skin 0.19 protein_coding synonymous_variant LOW 192T>C Thr64Thr
M0116814 JKKIJAMP_00490 320921 3 Skin 0.19 protein_coding synonymous_variant LOW 189T>C Thr63Thr
M0116815 JKKIJAMP_00484 321182 3 Skin 0.19 protein_coding upstream_gene_variant MODIFIER -4952T>C None
M0116816 JKKIJAMP_00484 321200 3 Skin 0.19 protein_coding upstream_gene_variant MODIFIER -4970A>G None
M0116817 JKKIJAMP_00484 321221 3 Skin 0.19 protein_coding upstream_gene_variant MODIFIER -4991A>G None
M0116818 JKKIJAMP_00485 321277 3 Skin 0.19 protein_coding upstream_gene_variant MODIFIER -4803A>G None
M0116819 JKKIJAMP_00492 321611 3 Skin 0.19 protein_coding synonymous_variant LOW 1080G>A Ser360Ser
M0116820 JKKIJAMP_00492 321623 3 Skin 0.19 protein_coding synonymous_variant LOW 1068T>C Ile356Ile
M0116821 JKKIJAMP_00492 321718 3 Skin 0.19 protein_coding missense_variant MODERATE 973G>A Ala325Thr
M0116822 JKKIJAMP_00492 321734 3 Skin 0.19 protein_coding synonymous_variant LOW 957T>C Asp319Asp
M0116823 JKKIJAMP_00492 321752 3 Skin 0.19 protein_coding synonymous_variant LOW 939T>C Leu313Leu
M0116824 JKKIJAMP_00492 321957 3 Skin 0.19 protein_coding missense_variant MODERATE 734T>G Val245Gly
M0116825 JKKIJAMP_00492 322028 4 Skin 0.25 protein_coding synonymous_variant LOW 663T>C Phe221Phe
M0116826 JKKIJAMP_00492 322094 3 Skin 0.19 protein_coding synonymous_variant LOW 597T>C Asp199Asp
M0116827 JKKIJAMP_00492 322169 3 Skin 0.19 protein_coding synonymous_variant LOW 522T>C Asn174Asn
M0116828 JKKIJAMP_00492 322205 3 Skin 0.19 protein_coding synonymous_variant LOW 486C>A Ala162Ala






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
JKKIJAMP_00235 Mercury (Hg) 88.7 5.5e-73 1 151 1.0000 1.0000 experiment
JKKIJAMP_00240 Mercury (Hg) 90.9 6.4e-56 1 121 1.0000 1.0000 experiment
JKKIJAMP_00241 Mercury (Hg) 93.4 2e-30 1 61 0.8971 0.7821 experiment
JKKIJAMP_00315 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Pyronin Y [class: Xanthene], Rhodamine 6G [class: Xanthene], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Acridine Orange [class: Acridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Sodium Deoxycholate (SDC) [class: Acid], Crystal Violet [class: Triarylmethane], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)] 99 1.1e-48 1 98 0.5665 0.8522 experiment
JKKIJAMP_00235 Mercury (Hg) 99.3 7.9e-81 1 151 1.0000 1.0000 prediction
JKKIJAMP_00240 Mercury (Hg) 99.2 4e-59 1 121 1.0000 1.0000 prediction
JKKIJAMP_00241 Mercury (Hg) 89.4 8.3e-30 1 66 0.9706 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
JKKIJAMP_00064 ARO:3003741 97.7 9.67e-181 6 261 0.9808 0.8707 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
JKKIJAMP_00078 ARO:3004623 99.3 1.59e-211 1 286 1.0000 1.0000 aminoglycoside antibiotic AAC(3) antibiotic inactivation
JKKIJAMP_00281 ARO:3002652 100 4.67e-186 1 259 1.0000 1.0000 aminoglycoside antibiotic APH(3') antibiotic inactivation
JKKIJAMP_00293 ARO:3000410 99.6 1.05e-198 24 302 0.9238 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
JKKIJAMP_00314 ARO:3000410 100 5.9e-145 1 204 1.0000 0.7312 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
JKKIJAMP_00315 ARO:3005010 99 2.43e-62 1 98 0.5665 0.8522 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
JKKIJAMP_00316 ARO:3002577 91.1 4.92e-110 1 163 0.8756 0.9185 aminoglycoside antibiotic AAC(6') antibiotic inactivation
JKKIJAMP_00317 ARO:3007370 79.9 1.92e-76 73 206 0.6505 1.0000 phosphonic acid antibiotic fosfomycin thiol transferase 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
JKKIJAMP_00457 PHI:8812 CopA (ABUW_2707) 73 9.3e-146 1 367 0.6637 0.9307 rodents nosocomial infection copper-translocating P-type ATPase unaffected pathogenicity
JKKIJAMP_00472 PHI:10532 mexF 70.7 8.8e-79 7 214 0.9412 0.8288 eudicots infection multidrug efflux RND transporter 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
JKKIJAMP_00215 QPG01653.1|GH23 100 2.27e-208 1 287 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
JKKIJAMP_00241 1.A.72.5.1 77 1.1e-24 1 61 0.8971 0.7821 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
JKKIJAMP_00342 2.A.6.2.40 76.7 6.2e-167 56 433 0.8164 0.9474 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
JKKIJAMP_00471 2.A.6.2.25 73.8 5.4e-284 2 672 0.9810 1.3400 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily