Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C963
  Reference Plasmid   NZ_CP085057.1
  Reference Plasmid Size   118805
  Reference Plasmid GC Content   0.52
  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
M0191081 ENLEJIFB_00009 13388 13 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3058C>T None
M0191082 ENLEJIFB_00009 13463 13 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3133T>C None
M0191083 ENLEJIFB_00017 14013 12 Gut 0.92 protein_coding missense_variant MODERATE 289C>A Leu97Met
M0191084 ENLEJIFB_00017 14015 13 Gut 1.00 protein_coding synonymous_variant LOW 291G>C Leu97Leu
M0191085 ENLEJIFB_00017 14025 13 Gut 1.00 protein_coding missense_variant MODERATE 301C>G Leu101Val
M0191086 ENLEJIFB_00017 14027 13 Gut 1.00 protein_coding synonymous_variant LOW 303G>A Leu101Leu
M0191087 ENLEJIFB_00017 14184 13 Gut 1.00 protein_coding missense_variant MODERATE 460A>T Arg154Trp
M0191088 ENLEJIFB_00017 14233 13 Gut 1.00 protein_coding missense_variant MODERATE 509A>C Gln170Pro
M0191089 ENLEJIFB_00018 14338 13 Gut 1.00 protein_coding synonymous_variant LOW 324G>A Arg108Arg
M0191090 ENLEJIFB_00018 14395 13 Gut 1.00 protein_coding synonymous_variant LOW 267G>T Gly89Gly
M0191091 ENLEJIFB_00019 14840 13 Gut 1.00 protein_coding synonymous_variant LOW 51G>A Gly17Gly
M0191092 ENLEJIFB_00019 14995 13 Gut 1.00 protein_coding missense_variant MODERATE 206G>T Gly69Val
M0191093 ENLEJIFB_00019 15003 13 Gut 1.00 protein_coding missense_variant MODERATE 214A>G Thr72Ala
M0191094 ENLEJIFB_00010 15522 13 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4933A>G None
M0191095 ENLEJIFB_00017 14062 3 Gut 0.23 protein_coding missense_variant MODERATE 338G>A Gly113Asp
M0191096 ENLEJIFB_00017 14063 3 Gut 0.23 protein_coding synonymous_variant LOW 339C>T Gly113Gly
M0191097 ENLEJIFB_00017 14086 3 Gut 0.23 protein_coding missense_variant MODERATE 362C>A Ala121Glu
M0191098 ENLEJIFB_00015 13136 3 Gut 0.23 protein_coding synonymous_variant LOW 180A>G Glu60Glu
M0191099 ENLEJIFB_00015 13178 3 Gut 0.23 protein_coding synonymous_variant LOW 138C>A Gly46Gly
M0191100 ENLEJIFB_00015 13190 3 Gut 0.23 protein_coding synonymous_variant LOW 126A>G Gly42Gly
M0191101 ENLEJIFB_00015 13214 3 Gut 0.23 protein_coding synonymous_variant LOW 102A>T Val34Val
M0191102 ENLEJIFB_00015 13219 3 Gut 0.23 protein_coding missense_variant MODERATE 97T>C Trp33Arg
M0191103 ENLEJIFB_00015 13238 3 Gut 0.23 protein_coding synonymous_variant LOW 78A>G Thr26Thr
M0191104 ENLEJIFB_00015 13256 3 Gut 0.23 protein_coding synonymous_variant LOW 60C>T Ala20Ala
M0191105 ENLEJIFB_00015 13273 3 Gut 0.23 protein_coding missense_variant MODERATE 43G>A Ala15Thr
M0191106 ENLEJIFB_00015 13280 3 Gut 0.23 protein_coding synonymous_variant LOW 36G>A Gln12Gln
M0191107 ENLEJIFB_00009 13319 5 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -2989T>C None
M0191108 ENLEJIFB_00009 13321 5 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -2991A>G None
M0191109 ENLEJIFB_00009 13322 5 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -2992G>A None
M0191110 ENLEJIFB_00009 13327 5 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -2997A>C None
M0191111 ENLEJIFB_00009 13328 5 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -2998G>A 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
ENLEJIFB_00026 VFG001827 ShET2 99.7 7.9e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
ENLEJIFB_00117 VFG048621 Aerobactin 99.7 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor IutA experiment
ENLEJIFB_00118 VFG000937 Aerobactin 97.9 1.3e-252 1 425 1.0 0.9551 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD experiment
ENLEJIFB_00119 VFG000938 Aerobactin 97.6 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC experiment
ENLEJIFB_00120 VFG000939 Aerobactin 96.2 1.7e-190 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB experiment
ENLEJIFB_00121 VFG000940 Aerobactin 94.9 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD experiment
ENLEJIFB_00026 VFG036084 Enterotoxin SenB/TieB 100 1.2e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB prediction
ENLEJIFB_00117 VFG033944 Aerobactin 100 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor precusor IutA prediction
ENLEJIFB_00118 VFG033958 Aerobactin 100 3.7e-256 1 425 1.0 1 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD prediction
ENLEJIFB_00119 VFG012522 Aerobactin 100 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC prediction
ENLEJIFB_00120 VFG033993 Aerobactin 99.7 3.2e-196 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB prediction
ENLEJIFB_00121 VFG012526 Aerobactin 100 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD prediction
ENLEJIFB_00126 VFG012590 Iron/manganese transport 100 3.8e-148 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitD prediction
ENLEJIFB_00127 VFG012585 Iron/manganese transport 100 1.4e-153 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitC prediction
ENLEJIFB_00128 VFG034214 Iron/manganese transport 100 5.5e-152 1 275 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter ATP-binding protein SitB prediction
ENLEJIFB_00129 VFG012575 Iron/manganese transport 99.7 2.2e-173 1 304 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter substrate-binding protein SitA 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
ENLEJIFB_00127 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87 9e-133 1 277 0.9719 0.9685 experiment
ENLEJIFB_00128 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 77.7 3.7e-115 2 266 0.9636 0.9707 experiment
ENLEJIFB_00129 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 75.8 1.5e-133 8 304 0.9770 0.9738 experiment
ENLEJIFB_00127 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87.8 3.4e-133 1 279 0.9789 0.9789 prediction
ENLEJIFB_00128 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 81.1 2.3e-118 2 266 0.9636 0.9707 prediction
ENLEJIFB_00129 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 76.4 5.2e-132 8 304 0.9770 0.9738 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
ENLEJIFB_00049 ARO:3001878 100 1.15e-202 1 291 1.0000 1.0000 cephalosporin CTX-M beta-lactamase antibiotic inactivation
ENLEJIFB_00053 ARO:3002581 98 1.4e-140 2 199 0.9950 0.9754 aminoglycoside antibiotic AAC(6') antibiotic inactivation
ENLEJIFB_00054 ARO:3001396 100 1.55e-142 1 197 1.0000 0.7138 cephalosporin OXA beta-lactamase antibiotic inactivation
ENLEJIFB_00059 ARO:3000165 99.7 7.17e-278 1 390 0.9774 0.9198 tetracycline antibiotic 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
ENLEJIFB_00023 PHI:10792 cjrA 100 5.6e-166 1 291 1.0000 1.0000 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
ENLEJIFB_00024 PHI:10793 cjrB 100 1.7e-137 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
ENLEJIFB_00025 PHI:10794 cjrC 100 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
ENLEJIFB_00026 PHI:10795 senB 100 4.2e-225 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
ENLEJIFB_00117 PHI:6563 iucA 99.7 0 1 732 1.0000 0.9986 rodents pneumonia aerobactin reduced virulence
ENLEJIFB_00118 PHI:3610 iucD 100 1.3e-256 1 425 1.0000 1.0000 birds colibacillosis aerobactin reduced virulence
ENLEJIFB_00119 PHI:124069 iucC (PAGR_g3925) 83.9 9.1e-301 1 577 0.9948 0.9983 monocots None aerobactin siderophores unaffected pathogenicity
ENLEJIFB_00120 PHI:124068 iucB (PAGR_g3926) 80 1.2e-158 1 315 1.0000 1.0000 monocots None aerobactin siderophores unaffected pathogenicity
ENLEJIFB_00121 PHI:124067 iucA (PAGR_g3927) 78.5 5.7e-271 1 573 0.9983 0.9598 monocots None aerobactin siderophores unaffected pathogenicity
ENLEJIFB_00127 PHI:10084 STM14_RS15355 87 1.5e-131 1 277 0.9719 0.9685 eudicots infection iron ABC transporter permease unaffected pathogenicity
ENLEJIFB_00128 PHI:10083 STM14_RS15350 77.7 6.1e-114 2 266 0.9636 0.9707 eudicots infection iron ABC transporter permease unaffected pathogenicity
ENLEJIFB_00129 PHI:10082 STM14_RS15345 75.8 2.5e-132 8 304 0.9770 0.9705 eudicots infection manganese/iron ABC transporter ATP-binding protein unaffected pathogenicity






        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





        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
ENLEJIFB_00024 2.C.1.1.3 100 3.7e-137 1 258 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.C Ion-gradient-driven energizers 2.C.1 The TonB-ExbB-ExbD/TolA-TolQ-TolR Outer Membrane Receptor Energizers and Stabilizers (TonB/TolA) Family
ENLEJIFB_00025 1.B.14.7.1 100 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
ENLEJIFB_00059 2.A.1.2.4 100 2.4e-223 1 399 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
ENLEJIFB_00060 2.A.7.3.67 100 1.8e-159 1 294 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
ENLEJIFB_00082 1.E.53.1.11 100 1.1e-21 1 49 1.0000 0.7206 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
ENLEJIFB_00127 3.A.1.15.7 87 3.4e-131 1 277 0.9719 0.9082 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
ENLEJIFB_00128 3.A.1.15.7 77.7 1.4e-113 2 266 0.9636 0.8689 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
ENLEJIFB_00129 3.A.1.15.7 75.8 5.5e-132 8 304 0.9770 0.9705 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily