Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C895
  Reference Plasmid   NZ_CP073927.1
  Reference Plasmid Size   118380
  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
M0188185 GHNOPLNO_00047 41340 5 Gut 0.83 protein_coding synonymous_variant LOW 375G>A Gln125Gln
M0188186 GHNOPLNO_00047 41376 5 Gut 0.83 protein_coding synonymous_variant LOW 339G>A Lys113Lys






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
GHNOPLNO_00120 VFG048621 Aerobactin 99.7 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor IutA experiment
GHNOPLNO_00121 VFG000937 Aerobactin 97.9 1.3e-252 1 425 1.0 0.9551 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD experiment
GHNOPLNO_00122 VFG000938 Aerobactin 97.6 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC experiment
GHNOPLNO_00123 VFG000939 Aerobactin 96.2 1.7e-190 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB experiment
GHNOPLNO_00124 VFG000940 Aerobactin 94.9 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD experiment
GHNOPLNO_00120 VFG033944 Aerobactin 100 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor precusor IutA prediction
GHNOPLNO_00121 VFG033958 Aerobactin 100 3.7e-256 1 425 1.0 1 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD prediction
GHNOPLNO_00122 VFG012522 Aerobactin 100 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC prediction
GHNOPLNO_00123 VFG033993 Aerobactin 99.7 3.2e-196 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB prediction
GHNOPLNO_00124 VFG012526 Aerobactin 100 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD prediction
GHNOPLNO_00129 VFG012590 Iron/manganese transport 100 3.8e-148 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitD prediction
GHNOPLNO_00130 VFG012585 Iron/manganese transport 100 1.4e-153 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitC prediction
GHNOPLNO_00131 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
GHNOPLNO_00132 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
GHNOPLNO_00130 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87 9e-133 1 277 0.9719 0.9685 experiment
GHNOPLNO_00131 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 77.7 3.7e-115 2 266 0.9636 0.9707 experiment
GHNOPLNO_00132 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 75.8 1.5e-133 8 304 0.9770 0.9738 experiment
GHNOPLNO_00130 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87.8 3.4e-133 1 279 0.9789 0.9789 prediction
GHNOPLNO_00131 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 81.1 2.3e-118 2 266 0.9636 0.9707 prediction
GHNOPLNO_00132 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
GHNOPLNO_00045 ARO:3000166 99.3 3.06e-283 1 401 1.0000 1.0000 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
GHNOPLNO_00046 ARO:3003479 100 1.46e-152 1 207 1.0000 0.9952 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic target alteration
GHNOPLNO_00055 ARO:3003839 100 4.74e-272 1 412 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
GHNOPLNO_00056 ARO:3000316 100 1e-217 1 301 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
GHNOPLNO_00059 ARO:3002860 99.4 1.04e-111 43 199 0.7889 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
GHNOPLNO_00065 ARO:3001878 100 1.15e-202 1 291 1.0000 1.0000 cephalosporin CTX-M beta-lactamase antibiotic inactivation
GHNOPLNO_00072 ARO:3004621 99 6.49e-211 1 286 1.0000 1.0000 aminoglycoside antibiotic AAC(3) antibiotic inactivation
GHNOPLNO_00075 ARO:3001396 100 1.55e-142 1 197 1.0000 0.7138 cephalosporin OXA beta-lactamase antibiotic inactivation
GHNOPLNO_00076 ARO:3002581 98 1.4e-140 2 199 0.9950 0.9754 aminoglycoside antibiotic AAC(6') antibiotic inactivation






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
GHNOPLNO_00060 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
GHNOPLNO_00120 PHI:6563 iucA 99.7 0 1 732 1.0000 0.9986 rodents pneumonia aerobactin reduced virulence
GHNOPLNO_00121 PHI:3610 iucD 100 1.3e-256 1 425 1.0000 1.0000 birds colibacillosis aerobactin reduced virulence
GHNOPLNO_00122 PHI:124069 iucC (PAGR_g3925) 83.9 9.1e-301 1 577 0.9948 0.9983 monocots None aerobactin siderophores unaffected pathogenicity
GHNOPLNO_00123 PHI:124068 iucB (PAGR_g3926) 80 1.2e-158 1 315 1.0000 1.0000 monocots None aerobactin siderophores unaffected pathogenicity
GHNOPLNO_00124 PHI:124067 iucA (PAGR_g3927) 78.5 5.7e-271 1 573 0.9983 0.9598 monocots None aerobactin siderophores unaffected pathogenicity
GHNOPLNO_00130 PHI:10084 STM14_RS15355 87 1.5e-131 1 277 0.9719 0.9685 eudicots infection iron ABC transporter permease unaffected pathogenicity
GHNOPLNO_00131 PHI:10083 STM14_RS15350 77.7 6.1e-114 2 266 0.9636 0.9707 eudicots infection iron ABC transporter permease unaffected pathogenicity
GHNOPLNO_00132 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
GHNOPLNO_00034 2.A.108.2.10 100 5e-101 3 175 0.9886 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
GHNOPLNO_00035 2.A.108.2.10 99.8 0 1 628 1.0000 3.6301 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
GHNOPLNO_00045 2.A.1.2.68 99.8 6.4e-221 1 401 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
GHNOPLNO_00086 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
GHNOPLNO_00130 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
GHNOPLNO_00131 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
GHNOPLNO_00132 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