Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1383
  Reference Plasmid   NZ_MN961670.1
  Reference Plasmid Size   636818
  Reference Plasmid GC Content   0.56
  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
M0116675 NAFPHALK_00243 242093 6 Skin 0.14 protein_coding missense_variant MODERATE 1103T>C Ile368Thr
M0116676 NAFPHALK_00243 243238 3 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -43T>C None
M0116677 NAFPHALK_00246 244914 8 Skin 0.19 protein_coding synonymous_variant LOW 111C>T Pro37Pro
M0116678 NAFPHALK_00246 245457 3 Skin 0.07 protein_coding synonymous_variant LOW 654C>T Pro218Pro
M0116679 NAFPHALK_00243 245667 4 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -2472G>C None
M0116680 NAFPHALK_00235 238410 4 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -4668G>A None
M0116681 NAFPHALK_00243 242019 3 Skin 0.07 protein_coding missense_variant MODERATE 1177A>G Thr393Ala
M0116682 NAFPHALK_00243 242021 3 Skin 0.07 protein_coding missense_variant MODERATE 1175T>A Phe392Tyr
M0116683 NAFPHALK_00320 319644 5 Skin 0.12 protein_coding missense_variant MODERATE 137G>A Ser46Asn
M0116684 NAFPHALK_00243 241032 3 Skin 0.07 protein_coding missense_variant MODERATE 2164G>C Ala722Pro
M0116685 NAFPHALK_00243 241591 3 Skin 0.07 protein_coding synonymous_variant LOW 1605G>A Glu535Glu
M0116686 NAFPHALK_00244 243674 5 Skin 0.12 protein_coding synonymous_variant LOW 354A>G Leu118Leu






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
NAFPHALK_00294 VFG037028 KatA 72 8.8e-210 6 475 0.9792 0.9325 Stress survival catalase experiment
NAFPHALK_00735 VFG010906 CsrA 72.4 7.8e-18 1 58 0.9355 0.9062 Regulation carbon storage regulator CsrA experiment
NAFPHALK_00294 VFG037030 KatA 72.2 5e-209 6 475 0.9792 0.9325 Stress survival catalase prediction
NAFPHALK_00735 VFG045727 CsrA 74.1 2.6e-17 1 58 0.9355 0.9062 Regulation carbon storage regulator CsrA prediction







        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
NAFPHALK_00139 Tellurium (Te) 71.1 6.5e-79 1 190 0.9948 0.9896 experiment
NAFPHALK_00140 Tellurium (Te) 71.7 3.3e-78 1 191 0.9948 1.0000 experiment
NAFPHALK_00156 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)] 100 1.1e-60 1 115 1.0000 1.0000 experiment
NAFPHALK_00164 Chromium (Cr) 99.8 1.5e-229 1 416 1.0000 1.0000 experiment
NAFPHALK_00165 Chromium (Cr) 76.1 3.3e-81 1 188 0.9447 0.9543 experiment
NAFPHALK_00180 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)] 100 1.1e-60 1 115 1.0000 1.0000 experiment
NAFPHALK_00237 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)] 100 1.1e-60 1 115 1.0000 1.0000 experiment
NAFPHALK_00408 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)] 100 1.1e-60 1 115 1.0000 1.0000 experiment
NAFPHALK_00139 Tellurium (Te) 72.6 1.2e-78 1 190 0.9948 0.9896 prediction
NAFPHALK_00140 Tellurium (Te) 72.3 3.3e-76 1 191 0.9948 1.0000 prediction
NAFPHALK_00163 Chromium (Cr), Methyl Viologen [class: Paraquat], Menadione [class: Naphthoquinone] 100 2.9e-178 1 314 1.0000 1.0000 prediction
NAFPHALK_00164 Chromium (Cr) 99.8 3.4e-227 1 416 1.0000 1.0000 prediction
NAFPHALK_00165 Chromium (Cr) 100 5.5e-114 1 199 1.0000 1.0000 prediction
NAFPHALK_00166 Chromium (Cr) 72.1 6.2e-54 1 136 0.9128 0.9067 prediction
NAFPHALK_00208 Manganese (Mn), Iron (Fe), Cobalt (Co), Zinc (Zn), Nickel (Ni), Copper (Cu), Cadmium (Cd), Gallium (Ga) 100 0 1 807 1.0000 1.0000 prediction
NAFPHALK_00228 Mercury (Hg) 96.7 9.7e-42 1 91 1.0000 1.0000 prediction
NAFPHALK_00322 Mercury (Hg) 96.7 9.7e-42 1 91 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
NAFPHALK_00154 ARO:3002596 100 1.67e-144 1 193 1.0000 1.0000 aminoglycoside antibiotic AAC(6') antibiotic inactivation
NAFPHALK_00155 ARO:3001405 100 1.87e-192 14 279 0.9534 1.0000 cephalosporin OXA beta-lactamase antibiotic inactivation
NAFPHALK_00156 ARO:3005010 100 2.01e-78 1 115 1.0000 1.0000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
NAFPHALK_00157 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
NAFPHALK_00169 ARO:3003109 100 0 1 491 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
NAFPHALK_00170 ARO:3003741 100 1.87e-214 1 294 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
NAFPHALK_00176 ARO:3002848 100 4.06e-115 1 150 1.0000 1.0000 rifamycin antibiotic rifampin ADP-ribosyltransferase (Arr) antibiotic inactivation
NAFPHALK_00178 ARO:3002601 99.6 1.33e-186 1 259 1.0000 0.9848 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
NAFPHALK_00180 ARO:3005010 100 2.01e-78 1 115 1.0000 1.0000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
NAFPHALK_00181 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
NAFPHALK_00193 ARO:3002864 98.7 1.44e-54 1 78 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
NAFPHALK_00194 ARO:3002577 99.5 2.91e-136 1 184 1.0000 1.0000 aminoglycoside antibiotic AAC(6') antibiotic inactivation
NAFPHALK_00195 ARO:3002272 100 1.91e-193 1 266 1.0000 1.0000 carbapenem VIM beta-lactamase antibiotic inactivation
NAFPHALK_00236 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
NAFPHALK_00237 ARO:3005010 100 2.01e-78 1 115 1.0000 1.0000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
NAFPHALK_00238 ARO:3005334 100 1.4e-135 1 177 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
NAFPHALK_00245 ARO:3002639 100 3.6e-203 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
NAFPHALK_00246 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
NAFPHALK_00391 ARO:3002705 89.9 1.9e-251 1 404 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
NAFPHALK_00394 ARO:3002272 100 1.91e-193 1 266 1.0000 1.0000 carbapenem VIM beta-lactamase antibiotic inactivation
NAFPHALK_00395 ARO:3002577 99.5 2.91e-136 1 184 1.0000 1.0000 aminoglycoside antibiotic AAC(6') antibiotic inactivation
NAFPHALK_00396 ARO:3002864 98.7 1.44e-54 1 78 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
NAFPHALK_00405 ARO:3002803 100 9.75e-87 1 218 1.0000 1.0000 fluoroquinolone antibiotic quinolone resistance protein (qnr) antibiotic target protection
NAFPHALK_00407 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
NAFPHALK_00408 ARO:3005010 100 2.01e-78 1 115 1.0000 1.0000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
NAFPHALK_00409 ARO:3002577 100 7.15e-137 1 184 1.0000 1.0000 aminoglycoside antibiotic AAC(6') antibiotic inactivation
NAFPHALK_00411 ARO:3005492 100 5.71e-185 1 246 1.0000 1.0000 carbapenem IMP beta-lactamase 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
NAFPHALK_00153 PHI:9804 int 97.3 1.2e-13 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
NAFPHALK_00175 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
NAFPHALK_00192 PHI:9804 int 97.3 1.2e-13 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
NAFPHALK_00294 PHI:10648 katA 74.9 1.3e-220 3 475 0.9854 0.9834 rodents opportunistic infection catalase unaffected pathogenicity
NAFPHALK_00397 PHI:9804 int 97.3 1.2e-13 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
NAFPHALK_00412 PHI:9804 int 97.3 1.2e-13 1 37 0.1098 1.0000 rodents gastroenteritis integrase 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
NAFPHALK_00444 QDQ70376.1|GH23 100 1.2e-164 1 227 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
NAFPHALK_00164 2.A.51.1.3 99.8 5.6e-228 1 416 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.51 The Chromate Ion Transporter (CHR) Family
NAFPHALK_00204 2.A.53.3.1 75.3 7.5e-203 1 493 0.9960 0.9919 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.53 The Sulfate Permease (SulP) Family
NAFPHALK_00242 2.A.53.3.1 74.5 1e-204 1 494 0.9980 0.9939 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.53 The Sulfate Permease (SulP) Family
NAFPHALK_00391 2.A.1.2.110 91.3 1.8e-199 1 404 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)