Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1664
  Reference Plasmid   1111525849486260_bin.28__k141_17820
  Reference Plasmid Size   41563
  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
M0141009 NPFFIEGC_00042 40677 7 Vaginal 0.70 protein_coding synonymous_variant LOW 54C>T Val18Val
M0141010 NPFFIEGC_00011 11303 5 Vaginal 0.50 protein_coding missense_variant MODERATE 29T>C Leu10Ser
M0141011 NPFFIEGC_00011 11698 3 Vaginal 0.30 protein_coding missense_variant MODERATE 424C>T Leu142Phe
M0141012 NPFFIEGC_00012 12552 4 Vaginal 0.40 protein_coding synonymous_variant LOW 756G>A Glu252Glu
M0141013 NPFFIEGC_00012 12603 3 Vaginal 0.30 protein_coding synonymous_variant LOW 705C>T Ser235Ser
M0141014 NPFFIEGC_00006 13351 5 Vaginal 0.50 protein_coding upstream_gene_variant MODIFIER -4892T>C None
M0141015 NPFFIEGC_00013 13679 4 Vaginal 0.40 protein_coding synonymous_variant LOW 1752C>T Gly584Gly
M0141016 NPFFIEGC_00013 13880 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1551T>C Phe517Phe
M0141017 NPFFIEGC_00013 13927 3 Vaginal 0.30 protein_coding missense_variant MODERATE 1504G>A Glu502Lys
M0141018 NPFFIEGC_00013 14305 3 Vaginal 0.30 protein_coding missense_variant MODERATE 1126C>A Gln376Lys
M0141019 NPFFIEGC_00013 14561 3 Vaginal 0.30 protein_coding synonymous_variant LOW 870T>C Ile290Ile
M0141020 NPFFIEGC_00013 14564 3 Vaginal 0.30 protein_coding synonymous_variant LOW 867A>G Glu289Glu
M0141021 NPFFIEGC_00013 14582 3 Vaginal 0.30 protein_coding synonymous_variant LOW 849A>T Thr283Thr
M0141022 NPFFIEGC_00013 14591 3 Vaginal 0.30 protein_coding synonymous_variant LOW 840G>A Ala280Ala
M0141023 NPFFIEGC_00013 14592 3 Vaginal 0.30 protein_coding missense_variant MODERATE 839C>T Ala280Val
M0141024 NPFFIEGC_00013 14620 3 Vaginal 0.30 protein_coding synonymous_variant LOW 811T>C Leu271Leu
M0141025 NPFFIEGC_00013 14654 3 Vaginal 0.30 protein_coding synonymous_variant LOW 777C>A Ala259Ala
M0141026 NPFFIEGC_00013 14666 3 Vaginal 0.30 protein_coding synonymous_variant LOW 765C>T Gly255Gly
M0141027 NPFFIEGC_00013 14702 3 Vaginal 0.30 protein_coding synonymous_variant LOW 729G>A Lys243Lys
M0141028 NPFFIEGC_00013 14707 3 Vaginal 0.30 protein_coding missense_variant MODERATE 724G>A Ala242Thr
M0141029 NPFFIEGC_00013 14714 3 Vaginal 0.30 protein_coding synonymous_variant LOW 717A>G Ser239Ser
M0141030 NPFFIEGC_00013 14717 3 Vaginal 0.30 protein_coding synonymous_variant LOW 714C>T Ile238Ile
M0141031 NPFFIEGC_00013 14726 3 Vaginal 0.30 protein_coding synonymous_variant LOW 705T>C Cys235Cys
M0141032 NPFFIEGC_00013 14729 3 Vaginal 0.30 protein_coding synonymous_variant LOW 702A>G Arg234Arg
M0141033 NPFFIEGC_00013 14786 3 Vaginal 0.30 protein_coding synonymous_variant LOW 645G>A Leu215Leu
M0141034 NPFFIEGC_00013 14804 3 Vaginal 0.30 protein_coding synonymous_variant LOW 627A>G Thr209Thr
M0141035 NPFFIEGC_00013 14922 3 Vaginal 0.30 protein_coding missense_variant MODERATE 509G>A Gly170Asp
M0141036 NPFFIEGC_00014 15555 4 Vaginal 0.40 protein_coding synonymous_variant LOW 816G>T Gly272Gly
M0141037 NPFFIEGC_00014 15802 3 Vaginal 0.30 protein_coding missense_variant MODERATE 569A>G Glu190Gly
M0141038 NPFFIEGC_00014 16302 4 Vaginal 0.40 protein_coding synonymous_variant LOW 69T>C Phe23Phe
M0141039 NPFFIEGC_00014 16305 4 Vaginal 0.40 protein_coding synonymous_variant LOW 66C>T Gly22Gly
M0141040 NPFFIEGC_00014 16317 4 Vaginal 0.40 protein_coding synonymous_variant LOW 54C>T Ile18Ile
M0141041 NPFFIEGC_00014 16320 4 Vaginal 0.40 protein_coding synonymous_variant LOW 51G>A Glu17Glu
M0141042 NPFFIEGC_00014 16322 4 Vaginal 0.40 protein_coding missense_variant MODERATE 49G>A Glu17Lys
M0141043 NPFFIEGC_00014 16326 4 Vaginal 0.40 protein_coding synonymous_variant LOW 45T>C Gly15Gly
M0141044 NPFFIEGC_00014 16329 4 Vaginal 0.40 protein_coding synonymous_variant LOW 42T>C Asn14Asn
M0141045 NPFFIEGC_00014 16332 4 Vaginal 0.40 protein_coding synonymous_variant LOW 39T>C Asn13Asn
M0141046 NPFFIEGC_00014 16335 4 Vaginal 0.40 protein_coding synonymous_variant LOW 36A>G Leu12Leu
M0141047 NPFFIEGC_00014 16337 4 Vaginal 0.40 protein_coding synonymous_variant LOW 34C>T Leu12Leu
M0141048 NPFFIEGC_00014 16338 4 Vaginal 0.40 protein_coding synonymous_variant LOW 33C>T Thr11Thr
M0141049 NPFFIEGC_00012 16396 4 Vaginal 0.40 protein_coding upstream_gene_variant MODIFIER -3089A>T None
M0141050 NPFFIEGC_00015 16527 5 Vaginal 0.50 protein_coding missense_variant MODERATE 43C>A Pro15Thr
M0141051 NPFFIEGC_00015 16597 5 Vaginal 0.50 protein_coding missense_variant MODERATE 113T>C Phe38Ser
M0141052 NPFFIEGC_00015 16686 4 Vaginal 0.40 protein_coding missense_variant MODERATE 202A>G Asn68Asp
M0141053 NPFFIEGC_00027 28893 6 Vaginal 0.60 protein_coding missense_variant MODERATE 2021A>G Asp674Gly
M0141054 NPFFIEGC_00027 28897 6 Vaginal 0.60 protein_coding missense_variant MODERATE 2017G>A Glu673Lys
M0141055 NPFFIEGC_00027 29226 4 Vaginal 0.40 protein_coding missense_variant MODERATE 1688G>A Gly563Glu
M0141056 NPFFIEGC_00027 29245 4 Vaginal 0.40 protein_coding missense_variant MODERATE 1669G>A Glu557Lys
M0141057 NPFFIEGC_00027 29254 4 Vaginal 0.40 protein_coding missense_variant MODERATE 1660A>C Thr554Pro
M0141058 NPFFIEGC_00027 29260 4 Vaginal 0.40 protein_coding missense_variant MODERATE 1654G>T Asp552Tyr
M0141059 NPFFIEGC_00027 29267 4 Vaginal 0.40 protein_coding synonymous_variant LOW 1647A>G Val549Val
M0141060 NPFFIEGC_00027 29272 4 Vaginal 0.40 protein_coding missense_variant MODERATE 1642A>G Lys548Glu
M0141061 NPFFIEGC_00027 29301 4 Vaginal 0.40 protein_coding missense_variant MODERATE 1613C>A Thr538Lys
M0141062 NPFFIEGC_00029 31974 3 Vaginal 0.30 protein_coding missense_variant MODERATE 152G>A Cys51Tyr
M0141063 NPFFIEGC_00032 33192 3 Vaginal 0.30 protein_coding missense_variant MODERATE 541A>G Ile181Val
M0141064 NPFFIEGC_00035 35916 6 Vaginal 0.60 protein_coding stop_lost&splice_region_variant HIGH 283T>C Ter95Glnext*?
M0141065 NPFFIEGC_00037 36991 3 Vaginal 0.30 protein_coding synonymous_variant LOW 15A>G Arg5Arg
M0141066 NPFFIEGC_00017 18589 3 Vaginal 0.30 protein_coding synonymous_variant LOW 165G>A Gln55Gln
M0141067 NPFFIEGC_00018 19920 3 Vaginal 0.30 protein_coding synonymous_variant LOW 507C>T Ala169Ala
M0141068 NPFFIEGC_00018 19926 3 Vaginal 0.30 protein_coding synonymous_variant LOW 513T>A Ser171Ser
M0141069 NPFFIEGC_00018 19932 3 Vaginal 0.30 protein_coding synonymous_variant LOW 519G>C Gly173Gly
M0141070 NPFFIEGC_00018 19935 3 Vaginal 0.30 protein_coding synonymous_variant LOW 522C>T Ile174Ile
M0141071 NPFFIEGC_00018 19971 3 Vaginal 0.30 protein_coding synonymous_variant LOW 558T>C Leu186Leu
M0141072 NPFFIEGC_00018 19986 3 Vaginal 0.30 protein_coding synonymous_variant LOW 573C>T Ile191Ile
M0141073 NPFFIEGC_00018 19998 3 Vaginal 0.30 protein_coding synonymous_variant LOW 585T>C Gly195Gly
M0141074 NPFFIEGC_00018 20001 3 Vaginal 0.30 protein_coding synonymous_variant LOW 588A>C Gly196Gly
M0141075 NPFFIEGC_00018 20002 3 Vaginal 0.30 protein_coding synonymous_variant LOW 589T>C Leu197Leu
M0141076 NPFFIEGC_00018 20004 3 Vaginal 0.30 protein_coding missense_variant MODERATE 591A>T Leu197Phe
M0141077 NPFFIEGC_00018 20016 3 Vaginal 0.30 protein_coding synonymous_variant LOW 603C>T Asn201Asn
M0141078 NPFFIEGC_00018 20022 3 Vaginal 0.30 protein_coding synonymous_variant LOW 609T>C Gly203Gly
M0141079 NPFFIEGC_00018 20028 3 Vaginal 0.30 protein_coding synonymous_variant LOW 615T>C Ala205Ala
M0141080 NPFFIEGC_00018 20034 3 Vaginal 0.30 protein_coding synonymous_variant LOW 621T>C Val207Val
M0141081 NPFFIEGC_00018 20046 3 Vaginal 0.30 protein_coding synonymous_variant LOW 633T>C Ile211Ile
M0141082 NPFFIEGC_00018 20100 3 Vaginal 0.30 protein_coding synonymous_variant LOW 687T>C Gly229Gly
M0141083 NPFFIEGC_00018 20208 3 Vaginal 0.30 protein_coding synonymous_variant LOW 795A>G Lys265Lys
M0141084 NPFFIEGC_00018 20238 3 Vaginal 0.30 protein_coding synonymous_variant LOW 825C>T Cys275Cys
M0141085 NPFFIEGC_00018 20247 3 Vaginal 0.30 protein_coding synonymous_variant LOW 834T>A Leu278Leu
M0141086 NPFFIEGC_00018 20250 3 Vaginal 0.30 protein_coding synonymous_variant LOW 837A>T Pro279Pro
M0141087 NPFFIEGC_00018 20268 3 Vaginal 0.30 protein_coding synonymous_variant LOW 855C>T Phe285Phe
M0141088 NPFFIEGC_00018 20280 3 Vaginal 0.30 protein_coding synonymous_variant LOW 867G>A Lys289Lys
M0141089 NPFFIEGC_00019 20339 3 Vaginal 0.30 protein_coding synonymous_variant LOW 33T>C Thr11Thr
M0141090 NPFFIEGC_00019 20345 3 Vaginal 0.30 protein_coding synonymous_variant LOW 39T>C Thr13Thr
M0141091 NPFFIEGC_00019 20366 3 Vaginal 0.30 protein_coding synonymous_variant LOW 60G>A Glu20Glu
M0141092 NPFFIEGC_00019 20387 3 Vaginal 0.30 protein_coding synonymous_variant LOW 81C>T Asn27Asn
M0141093 NPFFIEGC_00019 20390 3 Vaginal 0.30 protein_coding synonymous_variant LOW 84C>T Ile28Ile
M0141094 NPFFIEGC_00019 20394 3 Vaginal 0.30 protein_coding synonymous_variant LOW 88T>C Leu30Leu
M0141095 NPFFIEGC_00016 22937 3 Vaginal 0.30 protein_coding upstream_gene_variant MODIFIER -4879T>C None
M0141096 NPFFIEGC_00023 23987 3 Vaginal 0.30 protein_coding missense_variant MODERATE 883G>T Val295Leu
M0141097 NPFFIEGC_00027 29162 3 Vaginal 0.30 protein_coding synonymous_variant LOW 1752G>A Pro584Pro






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