Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C900
  Reference Plasmid   NZ_CP075633.1
  Reference Plasmid Size   120601
  Reference Plasmid GC Content   0.49
  Reference Plasmid Mobility Type   conjugative





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
M0188226 ILKPPFLA_00035 36783 3 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -4173C>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
ILKPPFLA_00012 VFG001827 ShET2 99.5 3e-224 1 391 1.0 1 Exotoxin enterotoxin experiment
ILKPPFLA_00043 VFG000842 Hemolysin 98.2 1.3e-99 1 171 1.0 1 Exotoxin Hemolysin C experiment
ILKPPFLA_00044 VFG000840 Hemolysin 98.5 0 1 998 1.0 1 Exotoxin Hemolysin A experiment
ILKPPFLA_00045 VFG000841 Hemolysin 99.7 0 1 705 1.0 0.9986 Exotoxin Hemolysin B experiment
ILKPPFLA_00046 VFG000843 Hemolysin 99.2 1e-266 1 479 1.0 1 Exotoxin Hemolysin D experiment
ILKPPFLA_00061 VFG048621 Aerobactin 99.7 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor IutA experiment
ILKPPFLA_00062 VFG000937 Aerobactin 97.9 1.3e-252 1 425 1.0 0.9551 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD experiment
ILKPPFLA_00063 VFG000938 Aerobactin 97.6 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC experiment
ILKPPFLA_00064 VFG000939 Aerobactin 96.2 1.7e-190 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB experiment
ILKPPFLA_00065 VFG000940 Aerobactin 94.9 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD experiment
ILKPPFLA_00105 VFG001445 TraJ 98.5 1.2e-113 1 200 0.8772 0.995 Invasion unknown protein experiment
ILKPPFLA_00012 VFG001827 ShET2 99.5 2.2e-223 1 391 1.0 1 Exotoxin enterotoxin prediction
ILKPPFLA_00018 VFG043983 Colicin S4 86.6 9.7e-248 1 498 1.0 0.998 Exotoxin colicin S4 prediction
ILKPPFLA_00041 VFG042367 Sab 79.1 0 1 1444 1.0 1.0091 Effector delivery system autotransporter adhesin Sab prediction
ILKPPFLA_00043 VFG000842 Hemolysin 98.2 9.8e-99 1 171 1.0 1 Exotoxin Hemolysin C prediction
ILKPPFLA_00044 VFG033890 Hemolysin 98.6 0 1 998 1.0 1 Exotoxin Hemolysin A prediction
ILKPPFLA_00045 VFG033882 Hemolysin 99.9 0 1 705 1.0 0.9986 Exotoxin Hemolysin B prediction
ILKPPFLA_00046 VFG000843 Hemolysin 99.2 7.6e-266 1 479 1.0 1 Exotoxin Hemolysin D prediction
ILKPPFLA_00061 VFG033944 Aerobactin 100 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor precusor IutA prediction
ILKPPFLA_00062 VFG033958 Aerobactin 100 3.7e-256 1 425 1.0 1 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD prediction
ILKPPFLA_00063 VFG012522 Aerobactin 100 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC prediction
ILKPPFLA_00064 VFG033993 Aerobactin 99.7 3.2e-196 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB prediction
ILKPPFLA_00065 VFG012526 Aerobactin 100 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD prediction
ILKPPFLA_00071 VFG012590 Iron/manganese transport 100 3.8e-148 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitD prediction
ILKPPFLA_00072 VFG012585 Iron/manganese transport 100 1.4e-153 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitC prediction
ILKPPFLA_00073 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
ILKPPFLA_00074 VFG012575 Iron/manganese transport 100 7.4e-174 1 304 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter substrate-binding protein SitA prediction
ILKPPFLA_00105 VFG001445 TraJ 98.5 9.3e-113 1 200 0.8772 0.995 Invasion unknown protein 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
ILKPPFLA_00072 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87 9e-133 1 277 0.9719 0.9685 experiment
ILKPPFLA_00073 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 77.7 3.7e-115 2 266 0.9636 0.9707 experiment
ILKPPFLA_00074 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 75.8 1.1e-133 8 304 0.9770 0.9738 experiment
ILKPPFLA_00072 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87.8 3.4e-133 1 279 0.9789 0.9789 prediction
ILKPPFLA_00073 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 81.1 2.3e-118 2 266 0.9636 0.9707 prediction
ILKPPFLA_00074 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 76.4 4e-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






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
ILKPPFLA_00010 PHI:10793 cjrB 98.4 9.1e-136 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
ILKPPFLA_00011 PHI:10794 cjrC 98.8 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
ILKPPFLA_00012 PHI:10795 senB 99.2 2.3e-223 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
ILKPPFLA_00047 PHI:6737 L7052 80.6 3.9e-36 1 93 0.7623 0.9894 nematodes urinary tract infection transcriptional regulator increased virulence (hypervirulence)
ILKPPFLA_00061 PHI:6563 iucA 99.7 0 1 732 1.0000 0.9986 rodents pneumonia aerobactin reduced virulence
ILKPPFLA_00062 PHI:3610 iucD 100 1.3e-256 1 425 1.0000 1.0000 birds colibacillosis aerobactin reduced virulence
ILKPPFLA_00063 PHI:124069 iucC (PAGR_g3925) 83.9 9.1e-301 1 577 0.9948 0.9983 monocots None aerobactin siderophores unaffected pathogenicity
ILKPPFLA_00064 PHI:124068 iucB (PAGR_g3926) 80 1.2e-158 1 315 1.0000 1.0000 monocots None aerobactin siderophores unaffected pathogenicity
ILKPPFLA_00065 PHI:124067 iucA (PAGR_g3927) 78.5 5.7e-271 1 573 0.9983 0.9598 monocots None aerobactin siderophores unaffected pathogenicity
ILKPPFLA_00072 PHI:10084 STM14_RS15355 87 1.5e-131 1 277 0.9719 0.9685 eudicots infection iron ABC transporter permease unaffected pathogenicity
ILKPPFLA_00073 PHI:10083 STM14_RS15350 77.7 6.1e-114 2 266 0.9636 0.9707 eudicots infection iron ABC transporter permease unaffected pathogenicity
ILKPPFLA_00074 PHI:10082 STM14_RS15345 75.8 1.9e-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
ILKPPFLA_00103 QBZ35910.1|GH23 100 1.8e-124 1 169 1 0.845





        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
ILKPPFLA_00010 2.C.1.1.3 98.4 2e-135 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
ILKPPFLA_00011 1.B.14.7.1 98.8 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
ILKPPFLA_00018 1.C.1.3.4 86.6 7.7e-248 1 498 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
ILKPPFLA_00025 2.A.8.1.9 71.8 6.7e-152 1 418 0.9905 0.9952 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.8 The Gluconate:H+ Symporter (GntP) Family
ILKPPFLA_00044 1.C.11.1.6 98.7 0 1 998 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.11 The Pore-forming RTX Toxin (RTX-toxin) Family
ILKPPFLA_00045 3.A.1.109.1 73.4 3.4e-302 10 705 0.9872 0.9844 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
ILKPPFLA_00072 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
ILKPPFLA_00073 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
ILKPPFLA_00074 3.A.1.15.7 75.8 4.2e-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
ILKPPFLA_00123 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