Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C846
  Reference Plasmid   NZ_CP069921.1
  Reference Plasmid Size   9515
  Reference Plasmid GC Content   0.56
  Reference Plasmid Mobility Type   non-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
M0184606 NLGBEDAF_00001 80 14 Gut 0.56 protein_coding upstream_gene_variant MODIFIER -48G>C None
M0184607 NLGBEDAF_00002 1605 15 Gut 0.60 protein_coding synonymous_variant LOW 105C>T Gly35Gly
M0184608 NLGBEDAF_00005 4539 4 Gut 0.16 protein_coding missense_variant MODERATE 22G>C Val8Leu
M0184609 NLGBEDAF_00006 6884 3 Gut 0.12 protein_coding missense_variant MODERATE 46G>A Ala16Thr
M0184610 NLGBEDAF_00007 7211 4 Gut 0.16 protein_coding synonymous_variant LOW 759A>G Pro253Pro
M0184611 NLGBEDAF_00007 7379 3 Gut 0.12 protein_coding synonymous_variant LOW 591T>G Val197Val
M0184612 NLGBEDAF_00002 1497 3 Gut 0.12 protein_coding synonymous_variant LOW 213G>A Ser71Ser
M0184613 NLGBEDAF_00003 2406 4 Gut 0.16 protein_coding synonymous_variant LOW 261T>C Gly87Gly
M0184614 NLGBEDAF_00006 6362 3 Gut 0.12 protein_coding missense_variant MODERATE 568A>G Thr190Ala
M0184615 NLGBEDAF_00006 6630 4 Gut 0.16 protein_coding synonymous_variant LOW 300T>C Asn100Asn






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







        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
NLGBEDAF_00002 Nickel (Ni), Cobalt (Co) 100 3.7e-146 1 255 1.0000 1.0000 experiment
NLGBEDAF_00003 Nickel (Ni), Cobalt (Co) 99.7 4e-174 1 318 1.0000 1.0000 experiment
NLGBEDAF_00002 Nickel (Ni), Cobalt (Co) 100 8.5e-144 1 255 1.0000 1.0000 prediction
NLGBEDAF_00003 Nickel (Ni), Cobalt (Co) 100 2.4e-172 1 318 1.0000 0.9695 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
NLGBEDAF_00002 PHI:8010 fecE 100 6.2e-145 1 255 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport ATP-binding protein reduced virulence
NLGBEDAF_00003 PHI:8009 fecD 99.7 6.7e-173 1 318 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport system permease protein reduced virulence
NLGBEDAF_00004 PHI:8008 fecC 100 1.8e-181 1 332 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport system permease protein reduced virulence
NLGBEDAF_00005 PHI:8007 fecB 99.3 2.4e-164 1 300 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate-binding periplasmic protein reduced virulence
NLGBEDAF_00006 PHI:8006 fecA 99.6 0 1 774 1.0000 1.0000 even-toed ungulates bovine mastitis ferric citrate outer membrane transporter reduced virulence
NLGBEDAF_00007 PHI:8005 fecR 100 5.1e-181 1 317 1.0000 1.0000 even-toed ungulates bovine mastitis Fec operon regulator reduced virulence
NLGBEDAF_00008 PHI:8004 fecI 100 1.3e-93 1 173 1.0000 1.0000 even-toed ungulates bovine mastitis RNA polymerase sigma factor 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





        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
NLGBEDAF_00002 3.A.1.14.1 100 1.4e-144 1 255 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
NLGBEDAF_00003 3.A.1.14.1 99.7 1.5e-172 1 318 1.0000 1.2471 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
NLGBEDAF_00004 3.A.1.14.1 100 4.1e-181 1 332 1.0000 1.3020 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
NLGBEDAF_00005 3.A.1.14.1 99.3 5.4e-164 1 300 1.0000 1.1765 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
NLGBEDAF_00006 1.B.14.1.20 99.6 0 1 774 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family