Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C707
  Reference Plasmid   NZ_CP049937.1
  Reference Plasmid Size   127295
  Reference Plasmid GC Content   0.52
  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
M0173094 IGMNFIPA_00128 122162 4 Gut 0.44 protein_coding upstream_gene_variant MODIFIER -4614T>C None
M0173095 IGMNFIPA_00130 123120 4 Gut 0.44 protein_coding upstream_gene_variant MODIFIER -4354G>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
IGMNFIPA_00062 VFG001445 TraJ 98 6.2e-113 1 200 0.8772 0.995 Invasion unknown protein experiment
IGMNFIPA_00095 VFG000940 Aerobactin 94.9 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD experiment
IGMNFIPA_00096 VFG000939 Aerobactin 96.2 1.7e-190 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB experiment
IGMNFIPA_00097 VFG000938 Aerobactin 97.6 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC experiment
IGMNFIPA_00098 VFG000937 Aerobactin 97.9 1.3e-252 1 425 1.0 0.9551 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD experiment
IGMNFIPA_00099 VFG048621 Aerobactin 99.6 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor IutA experiment
IGMNFIPA_00062 VFG001445 TraJ 98 4.6e-112 1 200 0.8772 0.995 Invasion unknown protein prediction
IGMNFIPA_00087 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
IGMNFIPA_00088 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
IGMNFIPA_00089 VFG012585 Iron/manganese transport 99.6 3e-153 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitC prediction
IGMNFIPA_00090 VFG012590 Iron/manganese transport 100 3.8e-148 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitD prediction
IGMNFIPA_00095 VFG012526 Aerobactin 100 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD prediction
IGMNFIPA_00096 VFG033993 Aerobactin 99.7 3.2e-196 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB prediction
IGMNFIPA_00097 VFG012522 Aerobactin 100 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC prediction
IGMNFIPA_00098 VFG033958 Aerobactin 100 3.7e-256 1 425 1.0 1 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD prediction
IGMNFIPA_00099 VFG033944 Aerobactin 99.9 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor precusor IutA 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
IGMNFIPA_00087 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 75.8 1.1e-133 8 304 0.9770 0.9738 experiment
IGMNFIPA_00088 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 77.7 3.7e-115 2 266 0.9636 0.9707 experiment
IGMNFIPA_00089 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87 6.9e-133 1 277 0.9719 0.9685 experiment
IGMNFIPA_00087 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 76.4 4e-132 8 304 0.9770 0.9738 prediction
IGMNFIPA_00088 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 81.1 2.3e-118 2 266 0.9636 0.9707 prediction
IGMNFIPA_00089 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87.8 2.6e-133 1 279 0.9789 0.9789 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
IGMNFIPA_00001 ARO:3004623 100 4.76e-213 1 286 1.0000 1.0000 aminoglycoside antibiotic AAC(3) antibiotic inactivation
IGMNFIPA_00009 ARO:3002860 99.4 5.26e-112 26 182 0.8626 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
IGMNFIPA_00014 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
IGMNFIPA_00016 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
IGMNFIPA_00017 ARO:3002639 99.2 2.43e-188 1 252 1.0000 0.9438 aminoglycoside antibiotic APH(3'') antibiotic inactivation
IGMNFIPA_00018 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
IGMNFIPA_00020 ARO:3000165 99.5 4.14e-277 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
IGMNFIPA_00010 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
IGMNFIPA_00087 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
IGMNFIPA_00088 PHI:10083 STM14_RS15350 77.7 6.1e-114 2 266 0.9636 0.9707 eudicots infection iron ABC transporter permease unaffected pathogenicity
IGMNFIPA_00089 PHI:10084 STM14_RS15355 87 1.2e-131 1 277 0.9719 0.9685 eudicots infection iron ABC transporter permease unaffected pathogenicity
IGMNFIPA_00095 PHI:124067 iucA (PAGR_g3927) 78.5 5.7e-271 1 573 0.9983 0.9598 monocots None aerobactin siderophores unaffected pathogenicity
IGMNFIPA_00096 PHI:124068 iucB (PAGR_g3926) 80 1.2e-158 1 315 1.0000 1.0000 monocots None aerobactin siderophores unaffected pathogenicity
IGMNFIPA_00097 PHI:124069 iucC (PAGR_g3925) 83.9 9.1e-301 1 577 0.9948 0.9983 monocots None aerobactin siderophores unaffected pathogenicity
IGMNFIPA_00098 PHI:3610 iucD 100 1.3e-256 1 425 1.0000 1.0000 birds colibacillosis aerobactin reduced virulence
IGMNFIPA_00099 PHI:6563 iucA 99.6 0 1 732 1.0000 0.9986 rodents pneumonia aerobactin reduced virulence
IGMNFIPA_00110 PHI:6531 HlyF 99.7 2.8e-215 1 369 1.0000 1.0000 birds colibacillosis hemolysin 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
IGMNFIPA_00064 ALD27964.1|GH23 100 2.87e-123 1 169 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
IGMNFIPA_00020 2.A.1.2.4 99.7 1.2e-222 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)
IGMNFIPA_00087 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
IGMNFIPA_00088 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
IGMNFIPA_00089 3.A.1.15.7 87 2.6e-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
IGMNFIPA_00111 9.B.50.1.1 72.9 1.9e-143 1 317 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.50 The Outer Membrane Beta-barrel Endoprotease, Omptin (Omptin) Family