Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1666
  Reference Plasmid   1111525849486260_bin.28__k141_77669
  Reference Plasmid Size   29883
  Reference Plasmid GC Content   0.37
  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
M0141099 EMAMCCFE_00022 22597 4 Vaginal 0.40 protein_coding synonymous_variant LOW 24T>C Arg8Arg
M0141100 EMAMCCFE_00001 135 3 Vaginal 0.30 protein_coding downstream_gene_variant MODIFIER *1247T>C None
M0141101 EMAMCCFE_00001 723 3 Vaginal 0.30 protein_coding downstream_gene_variant MODIFIER *659A>G None
M0141102 EMAMCCFE_00001 1502 3 Vaginal 0.30 protein_coding missense_variant MODERATE 1602A>C Arg534Ser
M0141103 EMAMCCFE_00001 1634 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1470C>T Gly490Gly
M0141104 EMAMCCFE_00001 1853 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1251G>C Arg417Arg
M0141105 EMAMCCFE_00001 1906 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1198T>C Leu400Leu
M0141106 EMAMCCFE_00001 1910 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1194C>T His398His
M0141107 EMAMCCFE_00001 1916 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1188T>C Phe396Phe
M0141108 EMAMCCFE_00001 1919 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1185C>T Phe395Phe
M0141109 EMAMCCFE_00001 1928 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1176G>A Glu392Glu
M0141110 EMAMCCFE_00001 1934 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1170A>G Gln390Gln
M0141111 EMAMCCFE_00001 1940 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1164T>A Thr388Thr
M0141112 EMAMCCFE_00001 2027 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1077T>C Asp359Asp
M0141113 EMAMCCFE_00001 2033 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1071A>G Lys357Lys
M0141114 EMAMCCFE_00001 2036 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1068T>C Ile356Ile
M0141115 EMAMCCFE_00001 2048 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1056C>T Val352Val
M0141116 EMAMCCFE_00001 2049 3 Vaginal 0.30 protein_coding missense_variant MODERATE 1055T>C Val352Ala
M0141117 EMAMCCFE_00001 2078 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1026C>T Asp342Asp
M0141118 EMAMCCFE_00001 2120 3 Vaginal 0.30 protein_coding synonymous_variant LOW 984C>T Phe328Phe
M0141119 EMAMCCFE_00001 2135 3 Vaginal 0.30 protein_coding synonymous_variant LOW 969T>C Tyr323Tyr
M0141120 EMAMCCFE_00001 2141 3 Vaginal 0.30 protein_coding synonymous_variant LOW 963C>T Ala321Ala
M0141121 EMAMCCFE_00001 2147 3 Vaginal 0.30 protein_coding synonymous_variant LOW 957A>G Glu319Glu
M0141122 EMAMCCFE_00001 2153 3 Vaginal 0.30 protein_coding synonymous_variant LOW 951A>G Leu317Leu
M0141123 EMAMCCFE_00001 2183 3 Vaginal 0.30 protein_coding synonymous_variant LOW 921C>T Asn307Asn
M0141124 EMAMCCFE_00001 2819 4 Vaginal 0.40 protein_coding synonymous_variant LOW 285A>C Val95Val
M0141125 EMAMCCFE_00001 2870 4 Vaginal 0.40 protein_coding synonymous_variant LOW 234T>C Arg78Arg
M0141126 EMAMCCFE_00001 2984 3 Vaginal 0.30 protein_coding synonymous_variant LOW 120C>T His40His
M0141127 EMAMCCFE_00002 3333 4 Vaginal 0.40 protein_coding missense_variant MODERATE 1436C>T Thr479Ile
M0141128 EMAMCCFE_00002 3370 4 Vaginal 0.40 protein_coding missense_variant MODERATE 1399A>G Lys467Glu
M0141129 EMAMCCFE_00002 3373 4 Vaginal 0.40 protein_coding missense_variant MODERATE 1396C>A Gln466Lys
M0141130 EMAMCCFE_00002 3410 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1359C>T Asn453Asn
M0141131 EMAMCCFE_00002 3534 4 Vaginal 0.40 protein_coding missense_variant MODERATE 1235C>T Ala412Val
M0141132 EMAMCCFE_00002 3597 4 Vaginal 0.40 protein_coding missense_variant MODERATE 1172T>C Ile391Thr
M0141133 EMAMCCFE_00002 3722 4 Vaginal 0.40 protein_coding synonymous_variant LOW 1047A>G Gln349Gln
M0141134 EMAMCCFE_00002 3728 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1041G>A Lys347Lys
M0141135 EMAMCCFE_00002 3729 3 Vaginal 0.30 protein_coding missense_variant MODERATE 1040A>G Lys347Arg
M0141136 EMAMCCFE_00002 3746 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1023A>G Leu341Leu
M0141137 EMAMCCFE_00002 3752 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1017T>C Ala339Ala
M0141138 EMAMCCFE_00002 3818 4 Vaginal 0.40 protein_coding synonymous_variant LOW 951A>G Val317Val
M0141139 EMAMCCFE_00002 3839 4 Vaginal 0.40 protein_coding synonymous_variant LOW 930T>G Thr310Thr
M0141140 EMAMCCFE_00002 3845 4 Vaginal 0.40 protein_coding synonymous_variant LOW 924T>C Asp308Asp
M0141141 EMAMCCFE_00002 3851 4 Vaginal 0.40 protein_coding synonymous_variant LOW 918A>G Lys306Lys
M0141142 EMAMCCFE_00002 3854 4 Vaginal 0.40 protein_coding synonymous_variant LOW 915G>A Lys305Lys
M0141143 EMAMCCFE_00002 3871 4 Vaginal 0.40 protein_coding missense_variant MODERATE 898G>A Glu300Lys
M0141144 EMAMCCFE_00002 3881 4 Vaginal 0.40 protein_coding synonymous_variant LOW 888A>G Gln296Gln
M0141145 EMAMCCFE_00002 3890 4 Vaginal 0.40 protein_coding synonymous_variant LOW 879C>T Asn293Asn
M0141146 EMAMCCFE_00002 3926 4 Vaginal 0.40 protein_coding synonymous_variant LOW 843G>A Val281Val
M0141147 EMAMCCFE_00002 3940 4 Vaginal 0.40 protein_coding synonymous_variant LOW 829T>C Leu277Leu
M0141148 EMAMCCFE_00002 3947 4 Vaginal 0.40 protein_coding synonymous_variant LOW 822C>T Arg274Arg
M0141149 EMAMCCFE_00002 3971 4 Vaginal 0.40 protein_coding synonymous_variant LOW 798G>A Leu266Leu
M0141150 EMAMCCFE_00002 3973 4 Vaginal 0.40 protein_coding synonymous_variant LOW 796T>C Leu266Leu
M0141151 EMAMCCFE_00002 3974 4 Vaginal 0.40 protein_coding synonymous_variant LOW 795C>T Asn265Asn
M0141152 EMAMCCFE_00002 3977 4 Vaginal 0.40 protein_coding synonymous_variant LOW 792T>C Val264Val
M0141153 EMAMCCFE_00002 3980 4 Vaginal 0.40 protein_coding synonymous_variant LOW 789C>T Ser263Ser
M0141154 EMAMCCFE_00002 4100 3 Vaginal 0.30 protein_coding synonymous_variant LOW 669C>T Ile223Ile
M0141155 EMAMCCFE_00002 4112 3 Vaginal 0.30 protein_coding missense_variant MODERATE 657A>G Ile219Met
M0141156 EMAMCCFE_00002 4114 3 Vaginal 0.30 protein_coding missense_variant MODERATE 655A>G Ile219Val
M0141157 EMAMCCFE_00002 4151 3 Vaginal 0.30 protein_coding synonymous_variant LOW 618G>A Ala206Ala
M0141158 EMAMCCFE_00002 4765 3 Vaginal 0.30 protein_coding missense_variant MODERATE 4C>G Pro2Ala
M0141159 EMAMCCFE_00003 5254 3 Vaginal 0.30 protein_coding missense_variant MODERATE 56A>C Asp19Ala
M0141160 EMAMCCFE_00004 5478 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1008A>C Ala336Ala
M0141161 EMAMCCFE_00004 6203 3 Vaginal 0.30 protein_coding missense_variant MODERATE 283G>A Glu95Lys
M0141162 EMAMCCFE_00004 6427 3 Vaginal 0.30 protein_coding missense_variant MODERATE 59C>T Ser20Leu
M0141163 EMAMCCFE_00005 6814 3 Vaginal 0.30 protein_coding missense_variant MODERATE 751G>A Glu251Lys
M0141164 EMAMCCFE_00006 8315 3 Vaginal 0.30 protein_coding missense_variant MODERATE 31G>C Gly11Arg
M0141165 EMAMCCFE_00007 8822 5 Vaginal 0.50 protein_coding missense_variant MODERATE 1079T>C Ile360Thr
M0141166 EMAMCCFE_00007 9541 3 Vaginal 0.30 protein_coding synonymous_variant LOW 360T>C Tyr120Tyr
M0141167 EMAMCCFE_00023 22712 3 Vaginal 0.30 protein_coding synonymous_variant LOW 900T>C Asn300Asn






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
EMAMCCFE_00001 QPP18338.1|CBM34|GH13_20 100 0 1 573 1 1
EMAMCCFE_00002 QWS36353.1|GH13_31 100 0 1 553 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