Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2417
  Reference Plasmid   1111525849768046_bin.37__k141_202844
  Reference Plasmid Size   8122
  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
M0123881 GGKCGALI_00001 472 5 Oral 0.83 protein_coding upstream_gene_variant MODIFIER -1353G>A None
M0123882 GGKCGALI_00001 505 5 Oral 0.83 protein_coding upstream_gene_variant MODIFIER -1320A>G None
M0123883 GGKCGALI_00001 514 5 Oral 0.83 protein_coding upstream_gene_variant MODIFIER -1311A>T None
M0123884 GGKCGALI_00001 517 5 Oral 0.83 protein_coding upstream_gene_variant MODIFIER -1308T>C None
M0123885 GGKCGALI_00001 556 5 Oral 0.83 protein_coding upstream_gene_variant MODIFIER -1269C>A None
M0123886 GGKCGALI_00001 928 3 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -897A>G None
M0123887 GGKCGALI_00001 955 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -870A>G None
M0123888 GGKCGALI_00001 967 3 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -858T>C None
M0123889 GGKCGALI_00001 1043 3 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -782T>C None
M0123890 GGKCGALI_00001 1045 5 Oral 0.83 protein_coding upstream_gene_variant MODIFIER -780T>A None
M0123891 GGKCGALI_00001 1075 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -750C>T None
M0123892 GGKCGALI_00001 1081 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -744C>T None
M0123893 GGKCGALI_00001 1087 3 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -738A>G None
M0123894 GGKCGALI_00001 1090 3 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -735G>A None
M0123895 GGKCGALI_00001 1123 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -702C>A None
M0123896 GGKCGALI_00001 1132 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -693C>T None
M0123897 GGKCGALI_00001 1168 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -657A>G None
M0123898 GGKCGALI_00001 1201 5 Oral 0.83 protein_coding upstream_gene_variant MODIFIER -624T>C None
M0123899 GGKCGALI_00001 1282 5 Oral 0.83 protein_coding upstream_gene_variant MODIFIER -543C>T None
M0123900 GGKCGALI_00001 1294 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -531A>C None
M0123901 GGKCGALI_00001 1297 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -528A>T None
M0123902 GGKCGALI_00001 1300 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -525A>T None
M0123903 GGKCGALI_00001 1420 5 Oral 0.83 protein_coding upstream_gene_variant MODIFIER -405C>T None
M0123904 GGKCGALI_00001 1579 3 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -246C>T None
M0123905 GGKCGALI_00001 1681 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -144G>A None
M0123906 GGKCGALI_00001 2652 3 Oral 0.50 protein_coding synonymous_variant LOW 828C>T Phe276Phe
M0123907 GGKCGALI_00001 2758 5 Oral 0.83 protein_coding synonymous_variant LOW 934T>C Leu312Leu
M0123908 GGKCGALI_00001 2769 3 Oral 0.50 protein_coding synonymous_variant LOW 945A>G Lys315Lys
M0123909 GGKCGALI_00001 2823 4 Oral 0.67 protein_coding synonymous_variant LOW 999A>G Leu333Leu
M0123910 GGKCGALI_00001 2895 4 Oral 0.67 protein_coding synonymous_variant LOW 1071T>G Ser357Ser
M0123911 GGKCGALI_00001 2940 3 Oral 0.50 protein_coding synonymous_variant LOW 1116C>T Ala372Ala
M0123912 GGKCGALI_00001 2977 4 Oral 0.67 protein_coding missense_variant MODERATE 1153G>C Val385Leu
M0123913 GGKCGALI_00001 3057 4 Oral 0.67 protein_coding synonymous_variant LOW 1233G>T Ser411Ser
M0123914 GGKCGALI_00001 3072 3 Oral 0.50 protein_coding synonymous_variant LOW 1248C>T Ala416Ala
M0123915 GGKCGALI_00002 3975 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -28T>A None
M0123916 GGKCGALI_00002 4333 4 Oral 0.67 protein_coding missense_variant MODERATE 331A>G Thr111Ala
M0123917 GGKCGALI_00001 214 3 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -1611T>C None
M0123918 GGKCGALI_00001 637 3 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -1188A>T None
M0123919 GGKCGALI_00001 778 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -1047C>T None
M0123920 GGKCGALI_00001 1288 3 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -537G>A None
M0123921 GGKCGALI_00001 1598 3 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -227A>C None
M0123922 GGKCGALI_00001 1760 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -65G>C None
M0123923 GGKCGALI_00001 1884 3 Oral 0.50 protein_coding synonymous_variant LOW 60G>A Glu20Glu
M0123924 GGKCGALI_00001 2052 4 Oral 0.67 protein_coding synonymous_variant LOW 228G>A Thr76Thr
M0123925 GGKCGALI_00001 2072 3 Oral 0.50 protein_coding missense_variant MODERATE 248C>A Thr83Lys
M0123926 GGKCGALI_00001 2082 4 Oral 0.67 protein_coding synonymous_variant LOW 258C>T Leu86Leu
M0123927 GGKCGALI_00001 2124 4 Oral 0.67 protein_coding synonymous_variant LOW 300T>C Asp100Asp
M0123928 GGKCGALI_00001 2136 4 Oral 0.67 protein_coding synonymous_variant LOW 312T>A Pro104Pro
M0123929 GGKCGALI_00001 2145 4 Oral 0.67 protein_coding synonymous_variant LOW 321A>T Pro107Pro
M0123930 GGKCGALI_00001 2468 4 Oral 0.67 protein_coding missense_variant MODERATE 644A>G Lys215Arg
M0123931 GGKCGALI_00001 2781 3 Oral 0.50 protein_coding synonymous_variant LOW 957C>T Gly319Gly
M0123932 GGKCGALI_00001 1276 3 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -549A>G None
M0123933 GGKCGALI_00001 1593 3 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -232C>G None
M0123934 GGKCGALI_00001 2259 3 Oral 0.50 protein_coding synonymous_variant LOW 435T>G Ser145Ser
M0123935 GGKCGALI_00001 2286 3 Oral 0.50 protein_coding synonymous_variant LOW 462T>C Ala154Ala
M0123936 GGKCGALI_00001 2348 3 Oral 0.50 protein_coding missense_variant MODERATE 524C>T Thr175Met
M0123937 GGKCGALI_00001 2352 3 Oral 0.50 protein_coding synonymous_variant LOW 528T>C Leu176Leu
M0123938 GGKCGALI_00001 3123 3 Oral 0.50 protein_coding synonymous_variant LOW 1299A>T Ile433Ile
M0123939 GGKCGALI_00001 3186 3 Oral 0.50 protein_coding synonymous_variant LOW 1362T>A Val454Val
M0123940 GGKCGALI_00001 3246 3 Oral 0.50 protein_coding synonymous_variant LOW 1422A>G Val474Val
M0123941 GGKCGALI_00001 3285 3 Oral 0.50 protein_coding synonymous_variant LOW 1461A>T Thr487Thr
M0123942 GGKCGALI_00001 3288 3 Oral 0.50 protein_coding synonymous_variant LOW 1464C>T Ala488Ala
M0123943 GGKCGALI_00001 3384 3 Oral 0.50 protein_coding synonymous_variant LOW 1560C>T Arg520Arg
M0123944 GGKCGALI_00001 3438 3 Oral 0.50 protein_coding synonymous_variant LOW 1614T>A Ala538Ala
M0123945 GGKCGALI_00001 3459 3 Oral 0.50 protein_coding synonymous_variant LOW 1635T>C Asn545Asn
M0123946 GGKCGALI_00001 3525 3 Oral 0.50 protein_coding synonymous_variant LOW 1701G>T Ala567Ala
M0123947 GGKCGALI_00001 3536 3 Oral 0.50 protein_coding missense_variant MODERATE 1712G>A Arg571His
M0123948 GGKCGALI_00001 3555 3 Oral 0.50 protein_coding synonymous_variant LOW 1731C>T Leu577Leu
M0123949 GGKCGALI_00001 3588 3 Oral 0.50 protein_coding synonymous_variant LOW 1764T>C Asp588Asp
M0123950 GGKCGALI_00001 3672 3 Oral 0.50 protein_coding synonymous_variant LOW 1848T>A Pro616Pro
M0123951 GGKCGALI_00001 3699 3 Oral 0.50 protein_coding synonymous_variant LOW 1875C>T Phe625Phe
M0123952 GGKCGALI_00001 3774 3 Oral 0.50 protein_coding synonymous_variant LOW 1950T>C Asn650Asn
M0123953 GGKCGALI_00001 3882 3 Oral 0.50 protein_coding synonymous_variant LOW 2058G>A Gln686Gln
M0123954 GGKCGALI_00001 3894 3 Oral 0.50 protein_coding synonymous_variant LOW 2070T>C Val690Val
M0123955 GGKCGALI_00002 4113 3 Oral 0.50 protein_coding synonymous_variant LOW 111A>G Arg37Arg
M0123956 GGKCGALI_00002 4146 3 Oral 0.50 protein_coding synonymous_variant LOW 144G>A Gly48Gly
M0123957 GGKCGALI_00002 4470 3 Oral 0.50 protein_coding synonymous_variant LOW 468G>A Arg156Arg
M0123958 GGKCGALI_00002 4548 3 Oral 0.50 protein_coding synonymous_variant LOW 546T>C His182His
M0123959 GGKCGALI_00002 4596 3 Oral 0.50 protein_coding synonymous_variant LOW 594T>C Asn198Asn
M0123960 GGKCGALI_00002 4608 3 Oral 0.50 protein_coding missense_variant MODERATE 606T>G Asn202Lys
M0123961 GGKCGALI_00002 4714 3 Oral 0.50 protein_coding missense_variant MODERATE 712T>G Ser238Ala
M0123962 GGKCGALI_00002 4810 3 Oral 0.50 protein_coding missense_variant MODERATE 808G>A Ala270Thr
M0123963 GGKCGALI_00002 4952 3 Oral 0.50 protein_coding missense_variant MODERATE 950G>A Ser317Asn






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