Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C239
  Reference Plasmid   KU238092.1
  Reference Plasmid Size   61503
  Reference Plasmid GC Content   0.64
  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
M0071131 IBLOPMPH_00046 44816 9 Skin 0.26 protein_coding synonymous_variant LOW 1236T>C Tyr412Tyr
M0071132 IBLOPMPH_00046 44822 9 Skin 0.26 protein_coding synonymous_variant LOW 1242G>A Ala414Ala
M0071133 IBLOPMPH_00046 44825 9 Skin 0.26 protein_coding synonymous_variant LOW 1245A>G Ala415Ala
M0071134 IBLOPMPH_00046 44828 9 Skin 0.26 protein_coding synonymous_variant LOW 1248G>C Ala416Ala
M0071135 IBLOPMPH_00046 45191 7 Skin 0.20 protein_coding synonymous_variant LOW 1611G>A Thr537Thr
M0071136 IBLOPMPH_00048 45653 7 Skin 0.20 protein_coding missense_variant MODERATE 8A>G Asn3Ser
M0071137 IBLOPMPH_00049 45988 5 Skin 0.14 protein_coding missense_variant MODERATE 110G>A Gly37Glu
M0071138 IBLOPMPH_00046 44867 4 Skin 0.11 protein_coding synonymous_variant LOW 1287T>C Asp429Asp
M0071139 IBLOPMPH_00046 44870 4 Skin 0.11 protein_coding synonymous_variant LOW 1290G>A Ala430Ala
M0071140 IBLOPMPH_00046 44873 4 Skin 0.11 protein_coding synonymous_variant LOW 1293G>C Ala431Ala
M0071141 IBLOPMPH_00046 44877 4 Skin 0.11 protein_coding missense_variant MODERATE 1297G>A Asp433Asn
M0071142 IBLOPMPH_00046 44879 4 Skin 0.11 protein_coding synonymous_variant LOW 1299C>T Asp433Asp
M0071143 IBLOPMPH_00046 44888 4 Skin 0.11 protein_coding synonymous_variant LOW 1308A>G Ala436Ala
M0071144 IBLOPMPH_00046 44897 4 Skin 0.11 protein_coding synonymous_variant LOW 1317C>A Ala439Ala
M0071145 IBLOPMPH_00046 44912 4 Skin 0.11 protein_coding synonymous_variant LOW 1332T>C Asp444Asp
M0071146 IBLOPMPH_00046 44921 4 Skin 0.11 protein_coding synonymous_variant LOW 1341G>C Val447Val
M0071147 IBLOPMPH_00046 44924 4 Skin 0.11 protein_coding synonymous_variant LOW 1344G>C Ala448Ala






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
IBLOPMPH_00053 VFG045767 Lvh (Legionella vir homologs) type IVA secretion system 70.5 4.3e-124 1 315 0.9844 0.9813 Effector delivery system P-type conjugative transfer ATPase TrbB 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
IBLOPMPH_00043 Mercury (Hg) 100 1.7e-79 1 144 1.0000 1.0000 experiment
IBLOPMPH_00044 Mercury (Hg) 100 2.3e-63 1 116 1.0000 1.0000 experiment
IBLOPMPH_00045 Mercury (Hg) 100 2.7e-43 1 91 1.0000 1.0000 experiment
IBLOPMPH_00046 Mercury (Hg) 93.4 6.2e-295 1 561 1.0000 1.0000 experiment
IBLOPMPH_00047 Mercury (Hg) 100 1.9e-63 1 121 1.0000 1.0000 experiment
IBLOPMPH_00048 Mercury (Hg) 100 1.3e-41 1 78 1.0000 1.0000 experiment
IBLOPMPH_00043 Mercury (Hg) 100 3.9e-77 1 144 1.0000 1.0000 prediction
IBLOPMPH_00044 Mercury (Hg) 100 5.3e-61 1 116 1.0000 1.0000 prediction
IBLOPMPH_00045 Mercury (Hg) 100 6.3e-41 1 91 1.0000 1.0000 prediction
IBLOPMPH_00046 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 0 1 561 1.0000 1.0000 prediction
IBLOPMPH_00047 Mercury (Hg) 100 4.3e-61 1 121 1.0000 1.0000 prediction
IBLOPMPH_00048 Mercury (Hg) 100 3e-39 1 78 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
IBLOPMPH_00005 ARO:3000165 100 5.02e-296 1 415 0.9788 0.9788 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
IBLOPMPH_00008 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
IBLOPMPH_00013 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
IBLOPMPH_00014 ARO:3006173 99.7 9.17e-207 1 287 1.0000 1.0000 carbapenem GES beta-lactamase 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
IBLOPMPH_00015 PHI:9804 int 100 3.8e-14 1 37 0.1160 1.0000 rodents gastroenteritis integrase 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
IBLOPMPH_00065 QDL89612.1|GH23 100 7.37e-133 1 211 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
IBLOPMPH_00005 2.A.1.2.4 99.7 9.5e-223 26 424 0.9410 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
IBLOPMPH_00044 1.A.72.3.1 93.1 2.2e-57 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
IBLOPMPH_00045 1.A.72.3.1 94.5 2.2e-39 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
IBLOPMPH_00048 1.A.72.5.1 76 3e-29 1 75 0.9615 0.9615 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
IBLOPMPH_00053 3.A.7.4.1 99.7 3.4e-180 1 320 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IBLOPMPH_00056 3.A.7.4.1 99.4 0 1 852 1.0000 2.6625 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IBLOPMPH_00057 3.A.7.4.1 99.6 2.1e-148 1 260 1.0000 0.8125 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IBLOPMPH_00058 3.A.7.4.1 99.3 8.9e-167 1 299 1.0000 0.9344 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IBLOPMPH_00060 3.A.7.4.1 99.6 2.5e-264 1 473 1.0000 1.4781 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IBLOPMPH_00061 3.A.7.4.1 100 2.5e-130 1 254 1.0000 0.7938 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IBLOPMPH_00063 3.A.7.4.1 99.5 2.2e-283 1 572 1.0000 1.7875 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family