Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1540
  Reference Plasmid   1111525849479042_bin.22__k141_102845
  Reference Plasmid Size   253329
  Reference Plasmid GC Content   0.55
  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
M0006367 FCJFCOMK_00110 127518 6 Skin 0.01 protein_coding missense_variant MODERATE 23A>C Lys8Thr
M0006368 FCJFCOMK_00131 152826 9 Skin 0.02 protein_coding missense_variant MODERATE 1180C>A Arg394Ser






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
FCJFCOMK_00063 Tellurium (Te), Proflavin [class: Acridine] 80.7 2.6e-91 5 196 0.9697 0.9746 experiment
FCJFCOMK_00112 Acriflavine [class: Acridine], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Hoechst 33342 [class: Bisbenzimide], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Methyl Viologen [class: Paraquat], Ethidium Bromide [class: Phenanthridine], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)] 76.3 1.4e-197 1 497 1.0000 0.9960 experiment
FCJFCOMK_00116 Methyl Viologen [class: Paraquat] 75.5 3.2e-119 1 273 0.9964 0.9317 experiment
FCJFCOMK_00143 Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Sodium Deoxycholate (SDC) [class: Acid], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Triclosan [class: Phenolic compounds], Methyl Viologen [class: Paraquat], Hydrogen Peroxide (H2O2) [class: Peroxides] 84.4 7.7e-49 1 122 1.0000 1.0167 experiment
FCJFCOMK_00144 Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Sodium Deoxycholate (SDC) [class: Acid], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Triclosan [class: Phenolic compounds], Methyl Viologen [class: Paraquat], Hydrogen Peroxide (H2O2) [class: Peroxides] 85.3 1.8e-49 1 109 1.0000 1.0000 experiment
FCJFCOMK_00179 Cyclohexane [class: Cycloalkane], Diphenyl Ether [class: Phenyl], n-hexane [class: Alkane] 92.1 5.5e-66 1 126 0.9921 0.9921 experiment
FCJFCOMK_00180 Cyclohexane [class: Cycloalkane], Diphenyl Ether [class: Phenyl], n-hexane [class: Alkane] 88.1 3.6e-70 20 162 0.8773 0.9931 experiment
FCJFCOMK_00063 Tellurium (Te), Proflavin [class: Acridine] 87 1.1e-98 5 197 0.9747 0.9797 prediction
FCJFCOMK_00112 Acriflavine [class: Acridine], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Hoechst 33342 [class: Bisbenzimide], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Methyl Viologen [class: Paraquat], Ethidium Bromide [class: Phenanthridine], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)] 90.7 1.8e-235 1 494 0.9940 0.9940 prediction
FCJFCOMK_00116 Methyl Viologen [class: Paraquat] 78.8 1.7e-121 1 274 1.0000 0.9352 prediction
FCJFCOMK_00143 Spermidine [class: Polyamines] 100 4.5e-58 1 122 1.0000 1.0000 prediction
FCJFCOMK_00144 Sodium Deoxycholate (SDC) [class: Acid], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Spermidine [class: Polyamines] 100 1.7e-53 1 109 1.0000 1.0000 prediction
FCJFCOMK_00179 Cyclohexane [class: Cycloalkane], Diphenyl Ether [class: Phenyl], n-hexane [class: Alkane] 100 1.8e-70 1 127 1.0000 0.9845 prediction
FCJFCOMK_00180 Cyclohexane [class: Cycloalkane], Diphenyl Ether [class: Phenyl], n-hexane [class: Alkane] 100 8e-87 1 163 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
FCJFCOMK_00143 ARO:3004580 84.4 1.94e-63 1 122 1.0000 1.0167 macrolide antibiotic small multidrug resistance (SMR) antibiotic efflux pump antibiotic efflux
FCJFCOMK_00144 ARO:3004583 85.3 2.81e-64 1 109 1.0000 1.0000 macrolide antibiotic small multidrug resistance (SMR) antibiotic efflux pump antibiotic efflux
FCJFCOMK_00179 ARO:3000263 92.1 1.35e-84 1 126 0.9921 0.9921 fluoroquinolone antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
FCJFCOMK_00180 ARO:3003378 88.7 1.92e-88 21 162 0.8712 0.9861 fluoroquinolone antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic target alteration






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
FCJFCOMK_00002 PHI:10113 STM14_RS07770 (ttrA) 70.6 0 1 1023 1.0000 1.0000 eudicots infection tetrathionate reductase subunit A reduced virulence
FCJFCOMK_00053 PHI:6982 trg 81.5 2.1e-222 5 535 0.9550 0.9815 primates salmonellosis methyl-accepting chemotaxis protein reduced virulence
FCJFCOMK_00060 PHI:10993 mdoD 85.5 2.1e-299 1 550 0.9982 0.9982 rodents infection glucans biosynthesis protein D unaffected pathogenicity
FCJFCOMK_00076 PHI:7225 ydcR 83.8 2.1e-231 1 469 0.9958 0.9873 rodents salmonellosis putative transcriptional regulator reduced virulence
FCJFCOMK_00106 PHI:10519 narV 81.4 3.7e-109 1 226 1.0000 1.0000 rodents urinary tract infection respiratory nitrate reductase 2 gamma chain reduced virulence
FCJFCOMK_00107 PHI:10518 narW 77.9 1.2e-102 1 231 1.0000 1.0000 rodents urinary tract infection probable nitrate reductase molybdenum cofactor assembly chaperone reduced virulence
FCJFCOMK_00108 PHI:10517 narY 90.7 1.6e-296 1 514 1.0000 1.0000 rodents urinary tract infection respiratory nitrate reductase 2 beta chain reduced virulence
FCJFCOMK_00109 PHI:10516 narZ 89.2 0 1 1246 1.0000 1.0000 rodents urinary tract infection respiratory nitrate reductase 2 alpha chain reduced virulence
FCJFCOMK_00110 PHI:123381 narU 84.3 1.1e-224 1 459 0.9935 0.9935 rodents salmonellosis nitrate/nitrite transporter unaffected pathogenicity
FCJFCOMK_00117 PHI:10997 fdnG 93.8 6.7e-107 1 195 1.0000 0.9833 rodents infection formate dehydrogenase, nitrate-inducible, major subunit unaffected pathogenicity
FCJFCOMK_00118 PHI:10997 fdnG 89.4 0 1 803 1.0000 0.9833 rodents infection formate dehydrogenase, nitrate-inducible, major subunit unaffected pathogenicity
FCJFCOMK_00143 PHI:8966 mdtJ 84.4 1.3e-47 1 122 1.0000 1.0000 rodents pneumonia multidrug transporter subunit reduced virulence
FCJFCOMK_00144 PHI:8967 mdtI 86.2 1.4e-48 1 109 1.0000 1.0000 rodents pneumonia multidrug resistance protein reduced virulence
FCJFCOMK_00179 PHI:5369 MarA 92.9 9.2e-65 1 126 0.9921 0.9921 rodents bacteremia transcriptional regulator 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
FCJFCOMK_00070 QIU88825.1|CBM5|GH18 99.7 0 1 727 1 0.9973
FCJFCOMK_00171 QIU88917.1|GH5_48 99.7 2.73e-309 1 395 1 1
FCJFCOMK_00198 QMR38355.1|GH88 96.9 8.92e-291 1 388 1 1
FCJFCOMK_00217 QIU88954.1|GH5_13 99.4 2.22e-280 1 362 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
FCJFCOMK_00006 2.A.76.1.5 77.4 9.3e-86 1 212 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.76 The Resistance to Homoserine/Threonine (RhtB) Family
FCJFCOMK_00007 9.B.121.4.1 70.5 0 1 878 1.0000 0.9989 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.121 The AsmA (AsmA) Family
FCJFCOMK_00033 1.E.53.1.6 72 1.9e-13 1 50 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
FCJFCOMK_00077 3.A.1.11.9 90.3 5.5e-214 1 381 1.0000 1.1306 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
FCJFCOMK_00078 3.A.1.11.9 84.1 9.7e-162 1 333 0.9881 0.9881 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
FCJFCOMK_00079 3.A.1.11.9 87.9 1.9e-151 3 313 0.9936 0.9288 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
FCJFCOMK_00080 3.A.1.11.9 92 9.8e-133 1 261 0.9739 0.7745 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
FCJFCOMK_00090 2.A.7.21.2 82.6 9.5e-61 1 149 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
FCJFCOMK_00095 1.B.14.9.5 78.9 0 1 703 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
FCJFCOMK_00100 2.A.3.1.8 92.5 2e-256 1 480 0.9938 0.9658 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.3 The Amino Acid-Polyamine-Organocation (APC) Family
FCJFCOMK_00109 5.A.3.1.2 89.2 0 1 1246 1.0000 1.0000 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
FCJFCOMK_00110 2.A.1.8.10 83.3 5.5e-224 1 462 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
FCJFCOMK_00112 2.A.1.3.14 75.9 5.4e-193 1 494 0.9940 0.9980 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
FCJFCOMK_00116 2.A.7.17.2 77.7 2.6e-120 1 274 1.0000 0.9352 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
FCJFCOMK_00118 5.A.3.2.1 89.4 0 1 803 1.0000 0.7911 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
FCJFCOMK_00142 2.A.86.1.4 76.4 1e-134 1 343 1.0000 0.9971 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.86 The Autoinducer-2 Exporter (AI-2E) Family (Formerly the PerM Family, TC #9.B.22)
FCJFCOMK_00143 2.A.7.1.9 82.9 1.6e-42 3 113 0.9098 0.9174 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
FCJFCOMK_00144 2.A.7.1.9 84.4 9.8e-47 1 109 1.0000 0.9008 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
FCJFCOMK_00151 2.A.1.36.1 87.7 1.7e-203 1 416 0.9905 0.9976 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
FCJFCOMK_00155 2.A.49.5.4 78.2 5.5e-178 13 429 0.9675 0.9976 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.49 The Chloride Carrier/Channel (ClC) Family
FCJFCOMK_00157 5.A.3.3.1 84 0 1 808 0.9988 1.0012 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
FCJFCOMK_00162 2.A.7.26.1 83.2 1.3e-46 1 107 0.9907 0.9907 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
FCJFCOMK_00165 2.A.1.6.9 82.2 1.4e-190 29 444 0.9083 0.9649 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
FCJFCOMK_00176 2.A.1.2.55 71.9 1.8e-159 1 388 0.9798 0.9823 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
FCJFCOMK_00177 2.A.7.3.2 80.1 4.6e-131 1 297 0.9933 0.9933 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
FCJFCOMK_00181 2.A.95.1.1 89.1 1.1e-102 1 221 0.9955 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.95 The 6 TMS Neutral Amino Acid Transporter (NAAT) Family
FCJFCOMK_00182 2.A.1.2.15 83.1 6.7e-178 1 396 0.9950 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
FCJFCOMK_00205 1.A.46.2.6 77.9 5e-136 6 313 0.9840 0.9595 1 Channels/Pores 1.A α-Type Channels 1.A.46 The Anion Channel-forming Bestrophin (Bestrophin) Family