Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1401
  Reference Plasmid   NZ_OM046572.1
  Reference Plasmid Size   300837
  Reference Plasmid GC Content   0.38
  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
M0116775 IIMCOCMD_00078 93770 3 Skin 0.15 protein_coding missense_variant MODERATE 1465T>G Ser489Ala
M0116776 IIMCOCMD_00078 94529 3 Skin 0.15 protein_coding missense_variant MODERATE 706A>G Ile236Val






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
IIMCOCMD_00018 Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Sodium Deoxycholate (SDC) [class: Acid], Ethidium Bromide [class: Phenanthridine], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Rhodamine 123 [class: Xanthene], Synergise, Wex-cide-128. 74.7 0 1 1030 0.9981 0.9961 experiment
IIMCOCMD_00178 Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Sodium Deoxycholate (SDC) [class: Acid], Ethidium Bromide [class: Phenanthridine], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Rhodamine 123 [class: Xanthene], Synergize [class: QAC-Glutaraldehyde], Wex-cide-128 [class: Phenyl] 78 1.3e-208 1 464 0.9978 0.9978 experiment
IIMCOCMD_00179 Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Sodium Deoxycholate (SDC) [class: Acid], Ethidium Bromide [class: Phenanthridine], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Rhodamine 123 [class: Xanthene], Synergise, Wex-cide-128. 85.9 0 3 1037 0.9981 1.0000 experiment
IIMCOCMD_00180 Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Sodium Deoxycholate (SDC) [class: Acid], Ethidium Bromide [class: Phenanthridine], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Rhodamine 123 [class: Xanthene], Synergize [class: QAC-Glutaraldehyde], Wex-cide-128 [class: Phenyl] 82.8 2.2e-182 1 395 1.0000 0.9975 experiment
HIDAFFPD_00018 Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Sodium Deoxycholate (SDC) [class: Acid], Ethidium Bromide [class: Phenanthridine], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Rhodamine 123 [class: Xanthene], Synergise, Wex-cide-128. 74.7 0 1 1030 0.9981 0.9961 experiment
HIDAFFPD_00178 Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Sodium Deoxycholate (SDC) [class: Acid], Ethidium Bromide [class: Phenanthridine], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Rhodamine 123 [class: Xanthene], Synergize [class: QAC-Glutaraldehyde], Wex-cide-128 [class: Phenyl] 78 1.3e-208 1 464 0.9978 0.9978 experiment
HIDAFFPD_00179 Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Sodium Deoxycholate (SDC) [class: Acid], Ethidium Bromide [class: Phenanthridine], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Rhodamine 123 [class: Xanthene], Synergise, Wex-cide-128. 85.9 0 3 1037 0.9981 1.0000 experiment
HIDAFFPD_00180 Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Sodium Deoxycholate (SDC) [class: Acid], Ethidium Bromide [class: Phenanthridine], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Rhodamine 123 [class: Xanthene], Synergize [class: QAC-Glutaraldehyde], Wex-cide-128 [class: Phenyl] 82.8 2.2e-182 1 395 1.0000 0.9975 experiment
IIMCOCMD_00018 Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Sodium Deoxycholate (SDC) [class: Acid], Ethidium Bromide [class: Phenanthridine], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Rhodamine 123 [class: Xanthene], Synergise, Wex-cide-128. 75 0 1 1030 0.9971 0.9952 prediction
IIMCOCMD_00178 Acridine Orange [class: Acridine], Safranin O [class: Azin], Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate] 100 3.2e-258 1 465 1.0000 1.0000 prediction
IIMCOCMD_00179 Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Sodium Deoxycholate (SDC) [class: Acid], Ethidium Bromide [class: Phenanthridine], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Rhodamine 123 [class: Xanthene], Synergise, Wex-cide-128. 91 0 2 1037 0.9990 1.0000 prediction
IIMCOCMD_00180 Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Sodium Deoxycholate (SDC) [class: Acid], Ethidium Bromide [class: Phenanthridine], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Rhodamine 123 [class: Xanthene], Synergize [class: QAC-Glutaraldehyde], Wex-cide-128 [class: Phenyl] 85.1 3.2e-182 1 395 1.0000 1.0154 prediction
HIDAFFPD_00018 Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Sodium Deoxycholate (SDC) [class: Acid], Ethidium Bromide [class: Phenanthridine], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Rhodamine 123 [class: Xanthene], Synergise, Wex-cide-128. 75 0 1 1030 0.9971 0.9952 prediction
HIDAFFPD_00178 Acridine Orange [class: Acridine], Safranin O [class: Azin], Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate] 100 3.2e-258 1 465 1.0000 1.0000 prediction
HIDAFFPD_00179 Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Sodium Deoxycholate (SDC) [class: Acid], Ethidium Bromide [class: Phenanthridine], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Rhodamine 123 [class: Xanthene], Synergise, Wex-cide-128. 91 0 2 1037 0.9990 1.0000 prediction
HIDAFFPD_00180 Pyronin Y [class: Xanthene], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Sodium Deoxycholate (SDC) [class: Acid], Ethidium Bromide [class: Phenanthridine], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Rhodamine 123 [class: Xanthene], Synergize [class: QAC-Glutaraldehyde], Wex-cide-128 [class: Phenyl] 85.1 3.2e-182 1 395 1.0000 1.0154 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
IIMCOCMD_00018 ARO:3000775 74.7 0 1 1030 0.9981 0.9961 glycylcycline resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
IIMCOCMD_00019 ARO:3007669 97.8 0 1 504 1.0000 1.0000 macrolide antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
IIMCOCMD_00085 ARO:3004621 99 6.49e-211 1 286 1.0000 1.0000 aminoglycoside antibiotic AAC(3) antibiotic inactivation
IIMCOCMD_00091 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
IIMCOCMD_00092 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
IIMCOCMD_00102 ARO:3003109 100 0 1 491 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
IIMCOCMD_00103 ARO:3003741 100 1.87e-214 1 294 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
IIMCOCMD_00178 ARO:3003811 78 1.33e-261 1 464 0.9978 0.9978 glycylcycline resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
IIMCOCMD_00179 ARO:3000775 85.9 0 3 1037 0.9981 1.0000 glycylcycline resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
IIMCOCMD_00180 ARO:3000774 82.8 2.79e-228 1 395 1.0000 0.9975 glycylcycline resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
IIMCOCMD_00181 ARO:3000553 77.4 3.23e-129 1 239 0.9795 0.9676 glycylcycline resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
HIDAFFPD_00018 ARO:3000775 74.7 0 1 1030 0.9981 0.9961 glycylcycline resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
HIDAFFPD_00019 ARO:3007669 97.8 0 1 504 1.0000 1.0000 macrolide antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
HIDAFFPD_00085 ARO:3004621 99 6.49e-211 1 286 1.0000 1.0000 aminoglycoside antibiotic AAC(3) antibiotic inactivation
HIDAFFPD_00091 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
HIDAFFPD_00092 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
HIDAFFPD_00102 ARO:3003109 100 0 1 491 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
HIDAFFPD_00103 ARO:3003741 100 1.87e-214 1 294 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
HIDAFFPD_00178 ARO:3003811 78 1.33e-261 1 464 0.9978 0.9978 glycylcycline resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
HIDAFFPD_00179 ARO:3000775 85.9 0 3 1037 0.9981 1.0000 glycylcycline resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
HIDAFFPD_00180 ARO:3000774 82.8 2.79e-228 1 395 1.0000 0.9975 glycylcycline resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
HIDAFFPD_00181 ARO:3000553 77.4 3.23e-129 1 239 0.9795 0.9676 glycylcycline resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux






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
IIMCOCMD_00018 PHI:6384 adeB 74.9 0 1 1030 0.9971 1.0000 rodents pneumonia; bloodstream infection multidrug efflux protein unaffected pathogenicity
IIMCOCMD_00124 PHI:6782 kdpE 72.1 1.5e-89 6 234 0.9662 0.9580 rodents pneumonia potassium-dependent protein reduced virulence
IIMCOCMD_00178 PHI:6385 adeC 78.4 3.2e-208 1 464 0.9978 0.9893 rodents pneumonia; bloodstream infection multidrug efflux protein unaffected pathogenicity
IIMCOCMD_00179 PHI:6384 adeB 86.1 0 2 1037 0.9990 1.0000 rodents pneumonia; bloodstream infection multidrug efflux protein unaffected pathogenicity
IIMCOCMD_00180 PHI:6263 adeA 82.8 2.9e-181 1 395 1.0000 0.9975 moths nosocomial infection RND MDR efflux system reduced virulence
HIDAFFPD_00018 PHI:6384 adeB 74.9 0 1 1030 0.9971 1.0000 rodents pneumonia; bloodstream infection multidrug efflux protein unaffected pathogenicity
HIDAFFPD_00124 PHI:6782 kdpE 72.1 1.5e-89 6 234 0.9662 0.9580 rodents pneumonia potassium-dependent protein reduced virulence
HIDAFFPD_00178 PHI:6385 adeC 78.4 3.2e-208 1 464 0.9978 0.9893 rodents pneumonia; bloodstream infection multidrug efflux protein unaffected pathogenicity
HIDAFFPD_00179 PHI:6384 adeB 86.1 0 2 1037 0.9990 1.0000 rodents pneumonia; bloodstream infection multidrug efflux protein unaffected pathogenicity
HIDAFFPD_00180 PHI:6263 adeA 82.8 2.9e-181 1 395 1.0000 0.9975 moths nosocomial infection RND MDR efflux system 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
IIMCOCMD_00244 QXR12416.1|GH23 100 1.16e-204 1 284 1 1
HIDAFFPD_00244 QXR12416.1|GH23 100 1.16e-204 1 284 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
IIMCOCMD_00018 2.A.6.2.40 74.9 0 1 1030 0.9971 2.5840 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
IIMCOCMD_00178 2.A.6.2.40 78.4 7.2e-208 1 464 0.9978 1.1629 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
IIMCOCMD_00179 2.A.6.2.40 86.1 0 2 1037 0.9990 2.5965 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
IIMCOCMD_00180 2.A.6.2.40 82.8 6.4e-181 1 395 1.0000 0.9900 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
HIDAFFPD_00018 2.A.6.2.40 74.9 0 1 1030 0.9971 2.5840 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
HIDAFFPD_00178 2.A.6.2.40 78.4 7.2e-208 1 464 0.9978 1.1629 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
HIDAFFPD_00179 2.A.6.2.40 86.1 0 2 1037 0.9990 2.5965 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
HIDAFFPD_00180 2.A.6.2.40 82.8 6.4e-181 1 395 1.0000 0.9900 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily