Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C608
  Reference Plasmid   NZ_CP035871.1
  Reference Plasmid Size   95804
  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
M0169460 LDDAADJP_00001 5622 15 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -4564G>C None
M0169461 LDDAADJP_00001 5624 15 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -4566T>C None
M0169462 LDDAADJP_00001 5625 15 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -4567A>C None
M0169463 LDDAADJP_00001 5635 15 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -4577C>G None
M0169464 LDDAADJP_00001 5655 15 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -4597G>C None
M0169465 LDDAADJP_00001 5657 15 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -4599C>T None
M0169466 LDDAADJP_00001 5658 15 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -4600T>A None
M0169467 LDDAADJP_00001 5659 15 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -4601C>A None
M0169468 LDDAADJP_00001 5660 15 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -4602A>G None
M0169469 LDDAADJP_00001 5661 15 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -4603T>A None
M0169470 LDDAADJP_00016 13895 29 Gut 0.55 protein_coding missense_variant MODERATE 1058G>A Arg353His
M0169471 LDDAADJP_00033 31327 28 Gut 0.53 protein_coding synonymous_variant LOW 2232G>T Val744Val
M0169472 LDDAADJP_00033 31895 28 Gut 0.53 protein_coding missense_variant MODERATE 2800C>A Leu934Ile
M0169473 LDDAADJP_00033 32119 27 Gut 0.51 protein_coding missense_variant MODERATE 3024C>A His1008Gln
M0169474 LDDAADJP_00033 32190 27 Gut 0.51 protein_coding missense_variant MODERATE 3095T>A Val1032Glu
M0169475 LDDAADJP_00033 32299 27 Gut 0.51 protein_coding synonymous_variant LOW 3204G>A Glu1068Glu
M0169476 LDDAADJP_00034 33446 4 Gut 0.08 protein_coding synonymous_variant LOW 273A>G Gln91Gln
M0169477 LDDAADJP_00042 38778 15 Gut 0.28 protein_coding missense_variant MODERATE 125A>T Gln42Leu
M0169478 LDDAADJP_00081 76323 3 Gut 0.06 protein_coding missense_variant MODERATE 14T>C Phe5Ser
M0169479 LDDAADJP_00082 76910 4 Gut 0.08 protein_coding synonymous_variant LOW 12A>T Arg4Arg
M0169480 LDDAADJP_00052 50995 5 Gut 0.09 protein_coding missense_variant MODERATE 34A>G Thr12Ala






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






        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
LDDAADJP_00063 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
LDDAADJP_00107 ARO:3000166 99.3 3.06e-283 1 401 1.0000 1.0000 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
LDDAADJP_00108 ARO:3003479 100 1.46e-152 1 207 1.0000 0.9952 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic target alteration






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






        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
LDDAADJP_00024 SPE00673.1|GH23 100 1.33e-115 1 161 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
LDDAADJP_00003 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
LDDAADJP_00030 3.A.7.10.1 77.9 6.6e-124 1 271 0.9748 2.8021 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
LDDAADJP_00031 3.A.7.10.1 77.8 1.7e-175 1 379 0.9921 3.9479 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
LDDAADJP_00034 3.A.7.10.1 73.3 1.9e-40 1 116 1.0000 1.1979 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
LDDAADJP_00036 3.A.7.10.1 74.9 1.5e-138 1 324 1.0000 3.4063 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
LDDAADJP_00050 1.E.53.1.10 100 2e-18 8 50 0.8600 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
LDDAADJP_00059 3.A.7.10.1 76.1 1.1e-189 1 401 0.9218 4.1771 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
LDDAADJP_00061 3.A.7.10.1 79.6 0 1 724 0.9439 7.5417 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
LDDAADJP_00107 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)