Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3295
  Reference Plasmid   MGYG000298047__MGYG000298047_31
  Reference Plasmid Size   12869
  Reference Plasmid GC Content   0.59
  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
M0134078 LDIFKEMB_00001 534 3 Oral 1.00 protein_coding synonymous_variant LOW 480A>G Leu160Leu
M0134079 LDIFKEMB_00001 561 3 Oral 1.00 protein_coding synonymous_variant LOW 453C>T Arg151Arg
M0134080 LDIFKEMB_00001 582 3 Oral 1.00 protein_coding synonymous_variant LOW 432C>T Gly144Gly
M0134081 LDIFKEMB_00001 585 3 Oral 1.00 protein_coding synonymous_variant LOW 429G>C Ala143Ala
M0134082 LDIFKEMB_00001 597 3 Oral 1.00 protein_coding synonymous_variant LOW 417G>T Val139Val
M0134083 LDIFKEMB_00001 600 3 Oral 1.00 protein_coding synonymous_variant LOW 414T>G Val138Val
M0134084 LDIFKEMB_00001 612 3 Oral 1.00 protein_coding synonymous_variant LOW 402T>C Gly134Gly
M0134085 LDIFKEMB_00001 630 3 Oral 1.00 protein_coding synonymous_variant LOW 384G>A Glu128Glu
M0134086 LDIFKEMB_00001 633 3 Oral 1.00 protein_coding synonymous_variant LOW 381A>G Glu127Glu
M0134087 LDIFKEMB_00001 638 3 Oral 1.00 protein_coding synonymous_variant LOW 376C>T Leu126Leu
M0134088 LDIFKEMB_00001 639 3 Oral 1.00 protein_coding synonymous_variant LOW 375C>T Arg125Arg
M0134089 LDIFKEMB_00001 654 3 Oral 1.00 protein_coding synonymous_variant LOW 360A>G Ala120Ala
M0134090 LDIFKEMB_00001 690 3 Oral 1.00 protein_coding synonymous_variant LOW 324C>T Ile108Ile
M0134091 LDIFKEMB_00001 729 3 Oral 1.00 protein_coding synonymous_variant LOW 285T>C Arg95Arg
M0134092 LDIFKEMB_00001 780 3 Oral 1.00 protein_coding synonymous_variant LOW 234A>G Val78Val
M0134093 LDIFKEMB_00001 933 3 Oral 1.00 protein_coding synonymous_variant LOW 81T>C Arg27Arg
M0134094 LDIFKEMB_00001 942 3 Oral 1.00 protein_coding synonymous_variant LOW 72T>C Val24Val
M0134095 LDIFKEMB_00002 1436 3 Oral 1.00 protein_coding synonymous_variant LOW 2289T>C Ser763Ser
M0134096 LDIFKEMB_00002 1466 3 Oral 1.00 protein_coding synonymous_variant LOW 2259T>C Ser753Ser
M0134097 LDIFKEMB_00002 1493 3 Oral 1.00 protein_coding synonymous_variant LOW 2232A>G Ala744Ala
M0134098 LDIFKEMB_00002 1496 3 Oral 1.00 protein_coding synonymous_variant LOW 2229T>C Ser743Ser
M0134099 LDIFKEMB_00002 1538 3 Oral 1.00 protein_coding synonymous_variant LOW 2187C>A Ala729Ala
M0134100 LDIFKEMB_00002 1569 3 Oral 1.00 protein_coding missense_variant MODERATE 2156T>C Val719Ala
M0134101 LDIFKEMB_00002 1611 3 Oral 1.00 protein_coding missense_variant MODERATE 2114C>T Ala705Val
M0134102 LDIFKEMB_00002 2555 3 Oral 1.00 protein_coding synonymous_variant LOW 1170G>T Ser390Ser
M0134103 LDIFKEMB_00002 2612 3 Oral 1.00 protein_coding synonymous_variant LOW 1113C>G Leu371Leu
M0134104 LDIFKEMB_00002 2694 3 Oral 1.00 protein_coding missense_variant MODERATE 1031C>A Thr344Asn
M0134105 LDIFKEMB_00002 2698 3 Oral 1.00 protein_coding missense_variant MODERATE 1027A>G Thr343Ala
M0134106 LDIFKEMB_00002 3304 3 Oral 1.00 protein_coding missense_variant MODERATE 421A>G Met141Val
M0134107 LDIFKEMB_00002 3419 3 Oral 1.00 protein_coding synonymous_variant LOW 306T>C Asp102Asp
M0134108 LDIFKEMB_00002 3431 3 Oral 1.00 protein_coding synonymous_variant LOW 294G>C Thr98Thr
M0134109 LDIFKEMB_00002 3554 3 Oral 1.00 protein_coding synonymous_variant LOW 171G>A Ala57Ala
M0134110 LDIFKEMB_00001 3897 3 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -2884T>C None
M0134111 LDIFKEMB_00003 3967 3 Oral 1.00 protein_coding synonymous_variant LOW 1557T>G Leu519Leu
M0134112 LDIFKEMB_00003 4105 3 Oral 1.00 protein_coding synonymous_variant LOW 1419T>C Asn473Asn
M0134113 LDIFKEMB_00004 6246 3 Oral 1.00 protein_coding synonymous_variant LOW 1446G>A Glu482Glu
M0134114 LDIFKEMB_00004 6267 3 Oral 1.00 protein_coding missense_variant MODERATE 1425G>A Met475Ile
M0134115 LDIFKEMB_00004 6366 3 Oral 1.00 protein_coding synonymous_variant LOW 1326T>C Arg442Arg
M0134116 LDIFKEMB_00004 6486 3 Oral 1.00 protein_coding synonymous_variant LOW 1206T>C Ala402Ala
M0134117 LDIFKEMB_00004 6708 3 Oral 1.00 protein_coding synonymous_variant LOW 984T>C Ile328Ile
M0134118 LDIFKEMB_00004 6783 3 Oral 1.00 protein_coding synonymous_variant LOW 909T>C Ile303Ile
M0134119 LDIFKEMB_00004 6894 3 Oral 1.00 protein_coding synonymous_variant LOW 798C>T Asn266Asn
M0134120 LDIFKEMB_00004 6907 3 Oral 1.00 protein_coding missense_variant MODERATE 785T>C Ile262Thr
M0134121 LDIFKEMB_00005 8209 3 Oral 1.00 protein_coding synonymous_variant LOW 1764G>T Val588Val
M0134122 LDIFKEMB_00005 8215 3 Oral 1.00 protein_coding synonymous_variant LOW 1758G>T Val586Val
M0134123 LDIFKEMB_00005 8763 3 Oral 1.00 protein_coding missense_variant MODERATE 1210T>C Ser404Pro
M0134124 LDIFKEMB_00005 9094 3 Oral 1.00 protein_coding synonymous_variant LOW 879A>G Leu293Leu
M0134125 LDIFKEMB_00005 9326 3 Oral 1.00 protein_coding missense_variant MODERATE 647C>T Ala216Val






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






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





        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