Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C521
  Reference Plasmid   NZ_CP025687.1
  Reference Plasmid Size   185046
  Reference Plasmid GC Content   0.36
  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
M0167613 JGLINNHK_00162 148269 3 Gut 0.25 protein_coding synonymous_variant LOW 300T>C His100His
M0167614 JGLINNHK_00162 148287 3 Gut 0.25 protein_coding synonymous_variant LOW 282T>C Ala94Ala
M0167615 JGLINNHK_00163 148801 4 Gut 0.33 protein_coding synonymous_variant LOW 426T>C Val142Val
M0167616 JGLINNHK_00164 150068 5 Gut 0.42 protein_coding synonymous_variant LOW 1446A>G Gly482Gly
M0167617 JGLINNHK_00164 150347 3 Gut 0.25 protein_coding synonymous_variant LOW 1167A>G Leu389Leu
M0167618 JGLINNHK_00164 150548 4 Gut 0.33 protein_coding synonymous_variant LOW 966G>A Gly322Gly
M0167619 JGLINNHK_00164 150876 3 Gut 0.25 protein_coding missense_variant MODERATE 638G>A Gly213Glu
M0167620 JGLINNHK_00161 151589 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -4124A>T None
M0167621 JGLINNHK_00165 151921 3 Gut 0.25 protein_coding synonymous_variant LOW 135G>A Ala45Ala
M0167622 JGLINNHK_00165 152464 3 Gut 0.25 protein_coding synonymous_variant LOW 678T>C Phe226Phe
M0167623 JGLINNHK_00165 153910 6 Gut 0.50 protein_coding synonymous_variant LOW 2124T>C Asp708Asp
M0167624 JGLINNHK_00166 154294 6 Gut 0.50 protein_coding missense_variant MODERATE 133A>G Asn45Asp






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
JGLINNHK_00161 VFG002197 BopD 85.1 1.1e-163 1 336 0.9912 1 Biofilm sugar-binding transcriptional regulator, LacI family experiment
JGLINNHK_00098 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.3 0 1 696 1.0 1 Adherence minor pilin subunit prediction
JGLINNHK_00099 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 98.8 4.9e-38 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
JGLINNHK_00100 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 97.6 3.5e-129 1 253 1.0 1.008 Adherence cell wall-associated LPXTG-like protein prediction
JGLINNHK_00101 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 100 1.3e-139 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
JGLINNHK_00102 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 98.5 0 1 658 1.0 1 Adherence PilA prediction
JGLINNHK_00103 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 98.7 8.8e-124 1 223 1.0 1 Adherence putative housekeeping sortase prediction
JGLINNHK_00161 VFG045671 BopD 89.3 1.4e-168 1 337 0.9941 0.9941 Biofilm sugar-binding transcriptional regulator, LacI family 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






        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
JGLINNHK_00033 PHI:5205 HMPREF0351_10118 (WxL locusC) 71.8 1.2e-168 1 389 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
JGLINNHK_00053 PHI:5205 HMPREF0351_10118 (WxL locusC) 89.3 3.7e-205 1 394 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
JGLINNHK_00109 PHI:5205 HMPREF0351_10118 (WxL locusC) 74.2 1.9e-172 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
JGLINNHK_00135 PHI:5205 HMPREF0351_10118 (WxL locusC) 74.7 9.9e-174 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
JGLINNHK_00149 PHI:5205 HMPREF0351_10118 (WxL locusC) 79.3 9.9e-182 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
JGLINNHK_00169 PHI:5205 HMPREF0351_10118 (WxL locusC) 78.8 8.1e-184 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
JGLINNHK_00194 PHI:5205 HMPREF0351_10118 (WxL locusC) 71.8 1.2e-168 1 389 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis 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
JGLINNHK_00007 QAA20997.1|GH32 100 0 1 486 1 1
JGLINNHK_00015 QTO59404.1|GH1 100 0 17 484 0.9669 1
JGLINNHK_00087 QZY25062.1|GH73 100 1.44e-273 1 401 1 1
JGLINNHK_00164 QAA21135.1|GH65 100 0 1 764 1 1
JGLINNHK_00170 CCO10203.2|GH1 87.6 1.34e-245 1 388 0.9949 0.9949
JGLINNHK_00179 QAA21148.1|GH4 100 0 1 436 1 1
JGLINNHK_00183 QAA21152.1|GH36 100 0 1 727 1 1
JGLINNHK_00184 QQJ93880.1|GH13_31 100 1.79e-306 1 406 1 1
JGLINNHK_00185 AOM14759.1|GH13_18 100 0 1 486 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
JGLINNHK_00181 3.A.1.1.28 74.1 2.8e-125 1 290 1.0000 0.7692 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
JGLINNHK_00182 3.A.1.1.28 75.3 5.4e-118 5 276 0.9855 0.7294 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily