Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C910
  Reference Plasmid   NZ_CP076548.1
  Reference Plasmid Size   221626
  Reference Plasmid GC Content   0.57
  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
M0188476 BIBPBKJD_00181 180079 11 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -4306A>T None
M0188477 BIBPBKJD_00181 180081 11 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -4308A>T None
M0188478 BIBPBKJD_00181 180082 11 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -4309A>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
BIBPBKJD_00112 VFG048543 Sal 100 0 1 727 1.0 0.9719 Nutritional/Metabolic factor salmochelin receptor IroN 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
BIBPBKJD_00156 Triclosan [class: Phenolic compounds] 93.1 6.5e-138 1 262 1.0000 1.0000 experiment
BIBPBKJD_00183 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
BIBPBKJD_00156 Triclosan [class: Phenolic compounds] 100 3.5e-145 1 262 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
BIBPBKJD_00052 ARO:3004127 80.2 8.69e-156 1 248 1.0000 1.0000 fluoroquinolone antibiotic MipA-interacting Protein reduced permeability to antibiotic
BIBPBKJD_00156 ARO:3004045 93.1 1.12e-174 1 262 1.0000 1.0000 disinfecting agents and antiseptics antibiotic resistant fabI antibiotic target alteration
BIBPBKJD_00182 ARO:3002602 100 5.68e-187 1 259 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
BIBPBKJD_00183 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






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
BIBPBKJD_00010 PHI:10387 SEN1538 93.3 2.9e-24 1 60 0.9836 1.0000 rodents salmonellosis conserved hypothetical protein reduced virulence
BIBPBKJD_00013 PHI:11382 katN 82.6 4.2e-137 1 287 0.9729 0.9829 moths salmonellosis catalase reduced virulence
BIBPBKJD_00104 PHI:11380 katE 80.9 0 1 752 1.0000 1.0000 moths salmonellosis catalase reduced virulence
BIBPBKJD_00108 PHI:10587 kduD 73.9 3.5e-108 1 253 1.0000 1.0000 monocots soft rot 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase unaffected pathogenicity
BIBPBKJD_00128 PHI:9321 trpB 91.4 4.6e-211 3 397 0.9950 0.9975 eudicots fire blight tryptophan synthase beta chain reduced virulence
BIBPBKJD_00181 PHI:9804 int 100 3.5e-14 1 37 0.1250 1.0000 rodents gastroenteritis integrase reduced virulence
BIBPBKJD_00200 PHI:7657 pspA 92.3 1.8e-100 1 222 1.0000 1.0000 rodents salmonellosis phage-shock protein reduced virulence
BIBPBKJD_00201 PHI:7658 pspB 81.1 1.3e-29 1 74 1.0000 1.0000 rodents salmonellosis phage-shock protein reduced virulence
BIBPBKJD_00203 PHI:7660 pspD 76.4 2.8e-26 1 72 1.0000 1.0000 rodents salmonellosis phage-shock protein reduced virulence
BIBPBKJD_00208 PHI:4563 TyrR 70.2 9.1e-212 1 510 0.9942 0.9829 rodents plague regulator of aromatic amino acid metabolism reduced virulence
BIBPBKJD_00216 PHI:9508 ovrB (Z0346) 85 1.9e-145 1 294 1.0000 1.0000 rodents hemorrhagic colitis; hemolytic uremic syndrome LysR-type 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
BIBPBKJD_00038 QIR52611.1|GT9 100 8.71e-277 1 378 1 1
BIBPBKJD_00059 ATN97300.1|GH18 100 9.30999999999999e-310 1 417 1 1
BIBPBKJD_00102 ATX24986.1|GH4 100 0 1 448 1 1
BIBPBKJD_00103 VDZ83556.1|GH4 75.8 2.06e-133 1 252 1 0.7213
BIBPBKJD_00196 QKT76252.1|GH0 100 0 1 769 1 1
BIBPBKJD_00207 QJO14411.1|GH4 100 0 1 437 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
BIBPBKJD_00027 2.A.76.1.5 73.6 1.3e-82 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
BIBPBKJD_00034 2.A.1.17.3 77.8 8.7e-162 1 392 0.9949 0.9975 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
BIBPBKJD_00052 1.B.93.1.2 81 6.5e-123 1 248 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.93 The MipA-interacting Protein (MipA) Family
BIBPBKJD_00061 2.A.1.1.115 93.5 1.6e-239 1 459 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
BIBPBKJD_00067 2.A.1.1.92 84.4 3.2e-208 1 449 0.9934 0.9934 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
BIBPBKJD_00084 3.A.1.19.4 75.6 1.4e-172 4 392 0.9923 1.7880 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
BIBPBKJD_00098 4.A.3.2.7 100 6.8e-53 1 106 1.0000 0.9217 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.3 The PTS Lactose-N,N'-Diacetylchitobiose-β-glucoside (Lac) Family
BIBPBKJD_00099 4.A.3.2.7 100 8e-252 1 452 1.0000 3.9304 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.3 The PTS Lactose-N,N'-Diacetylchitobiose-β-glucoside (Lac) Family
BIBPBKJD_00100 4.A.3.2.7 98.3 3.9e-54 1 115 1.0000 1.0000 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.3 The PTS Lactose-N,N'-Diacetylchitobiose-β-glucoside (Lac) Family
BIBPBKJD_00106 2.A.23.1.8 91.3 8.8e-230 1 462 0.9978 0.9978 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.23 The Dicarboxylate/Amino Acid:Cation (Na+ or H+) Symporter (DAACS) Family
BIBPBKJD_00113 9.B.357.1.1 93.2 3.6e-91 1 177 0.9888 0.9568 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.357 The Bacterial Envelope Biogenesis (BEB) Family
BIBPBKJD_00116 1.B.39.1.6 80.2 1.4e-97 1 212 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.39 The Bacterial Porin, OmpW (OmpW) Family
BIBPBKJD_00118 1.B.14.1.9 77.1 0 1 761 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
BIBPBKJD_00124 2.A.1.14.3 74.5 5.8e-183 3 434 0.9908 0.9577 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
BIBPBKJD_00159 3.A.1.5.5 92.5 2.2e-140 1 267 0.9926 0.9963 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
BIBPBKJD_00160 3.A.1.5.5 91.8 1e-184 1 330 1.0000 1.2313 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
BIBPBKJD_00161 3.A.1.5.5 92.6 4.2e-153 1 296 1.0000 1.1045 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
BIBPBKJD_00192 3.A.1.5.5 90 1.3e-163 1 321 1.0000 1.1978 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
BIBPBKJD_00193 3.A.1.5.5 85.8 2.2e-280 1 547 1.0000 2.0485 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
BIBPBKJD_00200 9.B.100.1.1 92.3 4.1e-100 1 222 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.100 The Phage Shock Protein (Psp) Family
BIBPBKJD_00213 3.A.1.5.1 87 1.4e-284 1 538 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