Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C117
  Reference Plasmid   CP058028.1
  Reference Plasmid Size   81777
  Reference Plasmid GC Content   0.51
  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
M0144638 GHJFGPNE_00079 77133 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4000G>A None
M0144639 GHJFGPNE_00079 77182 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4049T>C None
M0144640 GHJFGPNE_00079 77195 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4062T>C None
M0144641 GHJFGPNE_00079 77234 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4101C>T None
M0144642 GHJFGPNE_00085 77568 3 Gut 0.60 protein_coding missense_variant MODERATE 656G>A Arg219Lys
M0144643 GHJFGPNE_00085 77639 3 Gut 0.60 protein_coding synonymous_variant LOW 585G>A Pro195Pro
M0144644 GHJFGPNE_00085 78116 3 Gut 0.60 protein_coding synonymous_variant LOW 108G>A Gly36Gly
M0144645 GHJFGPNE_00085 78119 3 Gut 0.60 protein_coding synonymous_variant LOW 105T>A Ser35Ser
M0144646 GHJFGPNE_00086 78418 3 Gut 0.60 protein_coding synonymous_variant LOW 1008G>A Ala336Ala
M0144647 GHJFGPNE_00086 78438 3 Gut 0.60 protein_coding synonymous_variant LOW 988C>T Leu330Leu
M0144648 GHJFGPNE_00086 78499 3 Gut 0.60 protein_coding synonymous_variant LOW 927T>C Ser309Ser
M0144649 GHJFGPNE_00086 79189 3 Gut 0.60 protein_coding synonymous_variant LOW 237C>T Asn79Asn
M0144650 GHJFGPNE_00086 79198 3 Gut 0.60 protein_coding synonymous_variant LOW 228G>A Arg76Arg
M0144651 GHJFGPNE_00080 79443 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4902C>T None
M0144652 GHJFGPNE_00080 79493 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4952G>A None
M0144653 GHJFGPNE_00080 79500 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4959C>A None
M0144654 GHJFGPNE_00080 79527 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4986A>G None
M0144655 GHJFGPNE_00081 79605 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4782T>C None
M0144656 GHJFGPNE_00081 79679 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4856A>C None
M0144657 GHJFGPNE_00081 79680 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4857G>T None
M0144658 GHJFGPNE_00081 79743 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4920A>G None
M0144659 GHJFGPNE_00087 79950 3 Gut 0.60 protein_coding missense_variant MODERATE 154G>A Ala52Thr
M0144660 GHJFGPNE_00088 80341 3 Gut 0.60 protein_coding synonymous_variant LOW 156A>G Lys52Lys
M0144661 GHJFGPNE_00088 80408 3 Gut 0.60 protein_coding missense_variant MODERATE 223C>T His75Tyr
M0144662 GHJFGPNE_00088 80416 3 Gut 0.60 protein_coding synonymous_variant LOW 231G>A Val77Val
M0144663 GHJFGPNE_00089 80617 3 Gut 0.60 protein_coding synonymous_variant LOW 184T>C Leu62Leu
M0144664 GHJFGPNE_00089 80664 3 Gut 0.60 protein_coding synonymous_variant LOW 231A>T Ala77Ala
M0144665 GHJFGPNE_00082 80736 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4738A>G 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
GHJFGPNE_00029 VFG034679 Ibes 71.9 5.2e-183 1 459 0.9957 0.9978 Invasion Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC experiment
GHJFGPNE_00029 VFG034652 Ibes 71.9 1e-182 1 459 0.9957 0.9978 Invasion Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC 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
GHJFGPNE_00026 Silver (Ag) 92.3 1.4e-70 1 143 1.0000 1.0000 experiment
GHJFGPNE_00027 Silver (Ag) 92.9 4.2e-255 1 491 1.0081 0.9960 experiment
GHJFGPNE_00028 Silver (Ag) 93.4 9.3e-117 1 226 1.0088 1.0000 experiment
GHJFGPNE_00029 Silver (Ag) 99.3 1.8e-255 1 461 1.0000 1.0000 experiment
GHJFGPNE_00030 Silver (Ag) 96.7 2e-46 28 117 0.7692 0.9375 experiment
GHJFGPNE_00031 Silver (Ag) 96.7 3.3e-240 1 430 1.0000 1.0000 experiment
GHJFGPNE_00032 Silver (Ag) 98.5 0 1 1048 1.0000 1.0000 experiment
GHJFGPNE_00034 Silver (Ag) 94 0 1 815 1.0012 0.9903 experiment
GHJFGPNE_00026 Silver (Ag) 100 8e-75 1 143 1.0000 1.0000 prediction
GHJFGPNE_00027 Silver (Ag) 100 1.4e-275 1 491 1.0000 1.0000 prediction
GHJFGPNE_00028 Silver (Ag) 100 1e-124 1 226 1.0000 1.0000 prediction
GHJFGPNE_00029 Silver (Ag) 100 2.8e-254 1 461 1.0000 1.0000 prediction
GHJFGPNE_00030 Silver (Ag) 99.1 2.7e-60 1 117 1.0000 1.0000 prediction
GHJFGPNE_00031 Silver (Ag) 100 4.2e-244 1 430 1.0000 1.0000 prediction
GHJFGPNE_00032 Silver (Ag) 100 0 1 1048 1.0000 1.0000 prediction
GHJFGPNE_00034 Silver (Ag) 100 0 1 815 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
GHJFGPNE_00012 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
GHJFGPNE_00013 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
GHJFGPNE_00021 ARO:3003479 100 1.46e-152 1 207 1.0000 0.9952 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic target alteration
GHJFGPNE_00022 ARO:3000166 99.3 3.06e-283 1 401 1.0000 1.0000 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
GHJFGPNE_00009 PHI:8004 fecI 99.4 6.4e-93 1 173 1.0000 1.0000 even-toed ungulates bovine mastitis RNA polymerase sigma factor reduced virulence
GHJFGPNE_00010 PHI:8005 fecR 99.4 4.3e-180 1 317 1.0000 1.0000 even-toed ungulates bovine mastitis Fec operon regulator reduced virulence
GHJFGPNE_00011 PHI:8006 fecA 99.4 0 1 774 1.0000 1.0000 even-toed ungulates bovine mastitis ferric citrate outer membrane transporter 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
GHJFGPNE_00076 AXQ86427.1|GH23 100 7.04e-124 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
GHJFGPNE_00011 1.B.14.1.20 99.4 0 1 774 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
GHJFGPNE_00017 2.A.27.1.4 100 5.3e-215 1 401 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.27 The Glutamate:Na+ Symporter (ESS) Family
GHJFGPNE_00022 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)
GHJFGPNE_00029 1.B.17.3.4 99.3 6.6e-254 1 461 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.17 The Outer Membrane Factor (OMF) Family
GHJFGPNE_00032 2.A.6.1.3 98.5 0 1 1048 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
GHJFGPNE_00034 3.A.3.5.4 94 0 1 815 1.0000 0.9879 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
GHJFGPNE_00041 1.E.53.1.11 98.5 1.1e-32 1 68 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family