Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2290
  Reference Plasmid   1111525849759006_bin.31__k141_214076
  Reference Plasmid Size   13345
  Reference Plasmid GC Content   0.64
  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
M0033799 GJCADEND_00007 9092 23 Skin 0.37 protein_coding synonymous_variant LOW 741G>C Arg247Arg
M0033800 GJCADEND_00007 9099 23 Skin 0.37 protein_coding missense_variant MODERATE 734G>C Ser245Thr
M0033801 GJCADEND_00007 9257 32 Skin 0.51 protein_coding synonymous_variant LOW 576G>A Lys192Lys
M0033802 GJCADEND_00007 9263 32 Skin 0.51 protein_coding synonymous_variant LOW 570G>A Glu190Glu
M0033803 GJCADEND_00007 9268 32 Skin 0.51 protein_coding missense_variant MODERATE 565A>G Thr189Ala
M0033804 GJCADEND_00007 9272 32 Skin 0.51 protein_coding synonymous_variant LOW 561C>T Val187Val
M0033805 GJCADEND_00007 9273 32 Skin 0.51 protein_coding missense_variant MODERATE 560T>C Val187Ala
M0033806 GJCADEND_00007 9274 32 Skin 0.51 protein_coding missense_variant MODERATE 559G>A Val187Ile
M0033807 GJCADEND_00007 9296 33 Skin 0.52 protein_coding synonymous_variant LOW 537A>G Leu179Leu
M0033808 GJCADEND_00007 9591 23 Skin 0.37 protein_coding missense_variant MODERATE 242T>C Val81Ala
M0033809 GJCADEND_00007 9617 22 Skin 0.35 protein_coding synonymous_variant LOW 216A>G Gln72Gln
M0033810 GJCADEND_00008 9944 23 Skin 0.37 protein_coding missense_variant MODERATE 44T>C Val15Ala
M0033811 GJCADEND_00008 9982 22 Skin 0.35 protein_coding synonymous_variant LOW 6A>C Pro2Pro
M0033812 GJCADEND_00003 10128 10 Skin 0.16 protein_coding upstream_gene_variant MODIFIER -4202T>C None
M0033813 GJCADEND_00003 10164 9 Skin 0.14 protein_coding upstream_gene_variant MODIFIER -4238A>C None
M0033814 GJCADEND_00003 10168 8 Skin 0.13 protein_coding upstream_gene_variant MODIFIER -4242T>C None
M0033815 GJCADEND_00003 10169 8 Skin 0.13 protein_coding upstream_gene_variant MODIFIER -4243T>G None
M0033816 GJCADEND_00003 10218 6 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4292C>G None
M0033817 GJCADEND_00003 10231 7 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -4305C>T None
M0033818 GJCADEND_00001 587 19 Skin 0.30 protein_coding downstream_gene_variant MODIFIER *101A>G None
M0033819 GJCADEND_00001 715 6 Skin 0.10 protein_coding synonymous_variant LOW 945A>G Arg315Arg
M0033820 GJCADEND_00001 827 19 Skin 0.30 protein_coding missense_variant MODERATE 833T>C Leu278Pro
M0033821 GJCADEND_00001 828 19 Skin 0.30 protein_coding missense_variant MODERATE 832C>G Leu278Val
M0033822 GJCADEND_00001 1180 13 Skin 0.21 protein_coding synonymous_variant LOW 480G>A Ala160Ala
M0033823 GJCADEND_00001 1186 13 Skin 0.21 protein_coding synonymous_variant LOW 474G>T Leu158Leu
M0033824 GJCADEND_00003 2419 9 Skin 0.14 protein_coding synonymous_variant LOW 3508T>C Leu1170Leu
M0033825 GJCADEND_00003 2603 9 Skin 0.14 protein_coding synonymous_variant LOW 3324C>T Gly1108Gly
M0033826 GJCADEND_00003 2771 15 Skin 0.24 protein_coding synonymous_variant LOW 3156C>T Ile1052Ile
M0033827 GJCADEND_00003 3037 7 Skin 0.11 protein_coding synonymous_variant LOW 2890T>C Leu964Leu
M0033828 GJCADEND_00003 3336 39 Skin 0.62 protein_coding missense_variant MODERATE 2591T>C Val864Ala
M0033829 GJCADEND_00003 4726 35 Skin 0.56 protein_coding synonymous_variant LOW 1201T>C Leu401Leu
M0033830 GJCADEND_00004 6102 11 Skin 0.17 protein_coding synonymous_variant LOW 708A>G Arg236Arg
M0033831 GJCADEND_00004 6144 8 Skin 0.13 protein_coding synonymous_variant LOW 666T>C Arg222Arg
M0033832 GJCADEND_00004 6207 8 Skin 0.13 protein_coding missense_variant MODERATE 603G>C Glu201Asp
M0033833 GJCADEND_00004 6210 8 Skin 0.13 protein_coding synonymous_variant LOW 600G>C Leu200Leu
M0033834 GJCADEND_00004 6225 8 Skin 0.13 protein_coding synonymous_variant LOW 585G>A Leu195Leu
M0033835 GJCADEND_00004 6234 8 Skin 0.13 protein_coding synonymous_variant LOW 576C>T Tyr192Tyr
M0033836 GJCADEND_00004 6255 8 Skin 0.13 protein_coding synonymous_variant LOW 555C>G Ser185Ser
M0033837 GJCADEND_00004 6300 13 Skin 0.21 protein_coding synonymous_variant LOW 510G>A Pro170Pro
M0033838 GJCADEND_00004 6312 13 Skin 0.21 protein_coding synonymous_variant LOW 498G>A Leu166Leu
M0033839 GJCADEND_00005 7181 39 Skin 0.62 protein_coding synonymous_variant LOW 966G>A Gln322Gln
M0033840 GJCADEND_00005 7280 14 Skin 0.22 protein_coding synonymous_variant LOW 867A>G Gln289Gln
M0033841 GJCADEND_00005 7291 14 Skin 0.22 protein_coding missense_variant MODERATE 856G>A Gly286Ser
M0033842 GJCADEND_00005 7358 10 Skin 0.16 protein_coding synonymous_variant LOW 789C>A Arg263Arg
M0033843 GJCADEND_00005 7622 13 Skin 0.21 protein_coding synonymous_variant LOW 525A>G Pro175Pro
M0033844 GJCADEND_00005 7643 13 Skin 0.21 protein_coding synonymous_variant LOW 504C>T Cys168Cys
M0033845 GJCADEND_00005 8084 40 Skin 0.63 protein_coding synonymous_variant LOW 63A>G Gln21Gln
M0033846 GJCADEND_00006 8563 6 Skin 0.10 protein_coding synonymous_variant LOW 69G>A Ser23Ser
M0033847 GJCADEND_00007 9784 17 Skin 0.27 protein_coding synonymous_variant LOW 49C>T Leu17Leu
M0033848 GJCADEND_00007 9803 17 Skin 0.27 protein_coding synonymous_variant LOW 30C>G Ala10Ala
M0033849 GJCADEND_00004 6669 14 Skin 0.22 protein_coding synonymous_variant LOW 141C>G Ala47Ala
M0033850 GJCADEND_00004 6681 14 Skin 0.22 protein_coding synonymous_variant LOW 129A>G Arg43Arg
M0033851 GJCADEND_00005 7490 36 Skin 0.57 protein_coding synonymous_variant LOW 657A>C Arg219Arg
M0033852 GJCADEND_00005 7505 36 Skin 0.57 protein_coding synonymous_variant LOW 642T>C Asp214Asp
M0033853 GJCADEND_00006 8383 14 Skin 0.22 protein_coding synonymous_variant LOW 249G>A Pro83Pro
M0033854 GJCADEND_00007 8930 17 Skin 0.27 protein_coding synonymous_variant LOW 903A>C Arg301Arg
M0033855 GJCADEND_00007 8933 17 Skin 0.27 protein_coding synonymous_variant LOW 900C>G Gly300Gly
M0033856 GJCADEND_00007 8936 17 Skin 0.27 protein_coding synonymous_variant LOW 897C>T Val299Val
M0033857 GJCADEND_00007 8980 12 Skin 0.19 protein_coding synonymous_variant LOW 853T>C Leu285Leu
M0033858 GJCADEND_00007 8981 12 Skin 0.19 protein_coding synonymous_variant LOW 852T>G Leu284Leu
M0033859 GJCADEND_00007 9148 24 Skin 0.38 protein_coding synonymous_variant LOW 685T>C Leu229Leu
M0033860 GJCADEND_00007 9178 25 Skin 0.40 protein_coding missense_variant MODERATE 655G>A Val219Met
M0033861 GJCADEND_00007 9182 25 Skin 0.40 protein_coding synonymous_variant LOW 651G>A Gly217Gly
M0033862 GJCADEND_00004 6486 13 Skin 0.21 protein_coding synonymous_variant LOW 324C>T Gly108Gly
M0033863 GJCADEND_00004 6498 12 Skin 0.19 protein_coding synonymous_variant LOW 312G>T Ala104Ala
M0033864 GJCADEND_00004 6558 13 Skin 0.21 protein_coding synonymous_variant LOW 252A>G Glu84Glu
M0033865 GJCADEND_00004 6747 14 Skin 0.22 protein_coding missense_variant MODERATE 63G>C Glu21Asp
M0033866 GJCADEND_00004 6753 14 Skin 0.22 protein_coding synonymous_variant LOW 57G>A Ala19Ala
M0033867 GJCADEND_00005 7895 19 Skin 0.30 protein_coding synonymous_variant LOW 252C>T Ala84Ala
M0033868 GJCADEND_00005 7900 19 Skin 0.30 protein_coding synonymous_variant LOW 247T>C Leu83Leu
M0033869 GJCADEND_00005 7901 19 Skin 0.30 protein_coding synonymous_variant LOW 246A>T Pro82Pro
M0033870 GJCADEND_00005 7934 19 Skin 0.30 protein_coding synonymous_variant LOW 213T>G Gly71Gly
M0033871 GJCADEND_00005 8008 13 Skin 0.21 protein_coding synonymous_variant LOW 139C>T Leu47Leu
M0033872 GJCADEND_00005 8009 13 Skin 0.21 protein_coding synonymous_variant LOW 138C>T Asn46Asn
M0033873 GJCADEND_00007 9463 31 Skin 0.49 protein_coding missense_variant MODERATE 370G>A Ala124Thr
M0033874 GJCADEND_00007 9512 24 Skin 0.38 protein_coding synonymous_variant LOW 321A>G Gln107Gln
M0033875 GJCADEND_00001 562 17 Skin 0.27 protein_coding downstream_gene_variant MODIFIER *126C>T None
M0033876 GJCADEND_00001 1584 10 Skin 0.16 protein_coding missense_variant MODERATE 76C>A Pro26Thr
M0033877 GJCADEND_00001 1593 10 Skin 0.16 protein_coding missense_variant MODERATE 67T>C Ser23Pro
M0033878 GJCADEND_00001 1594 10 Skin 0.16 protein_coding synonymous_variant LOW 66G>A Val22Val
M0033879 GJCADEND_00001 1609 10 Skin 0.16 protein_coding synonymous_variant LOW 51C>T Thr17Thr
M0033880 GJCADEND_00001 1618 10 Skin 0.16 protein_coding synonymous_variant LOW 42G>A Leu14Leu
M0033881 GJCADEND_00001 1630 10 Skin 0.16 protein_coding synonymous_variant LOW 30T>C Thr10Thr
M0033882 GJCADEND_00001 1645 10 Skin 0.16 protein_coding synonymous_variant LOW 15C>T Pro5Pro
M0033883 GJCADEND_00002 1758 20 Skin 0.32 protein_coding synonymous_variant LOW 630A>G Ala210Ala
M0033884 GJCADEND_00002 1872 11 Skin 0.17 protein_coding synonymous_variant LOW 516G>C Ala172Ala
M0033885 GJCADEND_00002 2337 16 Skin 0.25 protein_coding synonymous_variant LOW 51C>T Gly17Gly
M0033886 GJCADEND_00003 2900 10 Skin 0.16 protein_coding synonymous_variant LOW 3027C>T Ala1009Ala
M0033887 GJCADEND_00003 2912 9 Skin 0.14 protein_coding synonymous_variant LOW 3015C>A Val1005Val
M0033888 GJCADEND_00003 3377 13 Skin 0.21 protein_coding synonymous_variant LOW 2550A>T Arg850Arg
M0033889 GJCADEND_00003 4538 12 Skin 0.19 protein_coding synonymous_variant LOW 1389T>C Ala463Ala
M0033890 GJCADEND_00003 4568 13 Skin 0.21 protein_coding synonymous_variant LOW 1359C>G Ala453Ala
M0033891 GJCADEND_00003 4888 20 Skin 0.32 protein_coding synonymous_variant LOW 1039T>C Leu347Leu
M0033892 GJCADEND_00003 4895 20 Skin 0.32 protein_coding synonymous_variant LOW 1032A>G Pro344Pro
M0033893 GJCADEND_00003 4910 19 Skin 0.30 protein_coding synonymous_variant LOW 1017A>G Arg339Arg
M0033894 GJCADEND_00003 4957 14 Skin 0.22 protein_coding missense_variant MODERATE 970G>A Val324Met
M0033895 GJCADEND_00003 4973 14 Skin 0.22 protein_coding synonymous_variant LOW 954C>T Arg318Arg
M0033896 GJCADEND_00003 5003 14 Skin 0.22 protein_coding synonymous_variant LOW 924G>C Val308Val
M0033897 GJCADEND_00003 5453 14 Skin 0.22 protein_coding synonymous_variant LOW 474T>C Asn158Asn
M0033898 GJCADEND_00003 5492 13 Skin 0.21 protein_coding synonymous_variant LOW 435T>C Thr145Thr
M0033899 GJCADEND_00003 5579 29 Skin 0.46 protein_coding synonymous_variant LOW 348A>C Thr116Thr
M0033900 GJCADEND_00003 5668 27 Skin 0.43 protein_coding stop_gained HIGH 259C>T Gln87*
M0033901 GJCADEND_00003 5780 26 Skin 0.41 protein_coding synonymous_variant LOW 147T>C Thr49Thr
M0033902 GJCADEND_00003 5786 26 Skin 0.41 protein_coding synonymous_variant LOW 141G>C Ser47Ser
M0033903 GJCADEND_00003 5813 25 Skin 0.40 protein_coding synonymous_variant LOW 114A>G Ala38Ala
M0033904 GJCADEND_00003 5842 25 Skin 0.40 protein_coding missense_variant MODERATE 85A>G Met29Val
M0033905 GJCADEND_00005 6853 12 Skin 0.19 protein_coding missense_variant MODERATE 1294A>G Thr432Ala
M0033906 GJCADEND_00005 7021 11 Skin 0.17 protein_coding synonymous_variant LOW 1126C>T Leu376Leu
M0033907 GJCADEND_00005 7025 11 Skin 0.17 protein_coding synonymous_variant LOW 1122C>T Arg374Arg
M0033908 GJCADEND_00005 7712 14 Skin 0.22 protein_coding synonymous_variant LOW 435C>T Gly145Gly
M0033909 GJCADEND_00005 7730 14 Skin 0.22 protein_coding synonymous_variant LOW 417C>G Thr139Thr
M0033910 GJCADEND_00005 7792 13 Skin 0.21 protein_coding synonymous_variant LOW 355T>C Leu119Leu
M0033911 GJCADEND_00006 8416 12 Skin 0.19 protein_coding synonymous_variant LOW 216A>C Ala72Ala
M0033912 GJCADEND_00006 8425 11 Skin 0.17 protein_coding missense_variant MODERATE 207C>G Asp69Glu
M0033913 GJCADEND_00006 8516 12 Skin 0.19 protein_coding missense_variant MODERATE 116A>C Asp39Ala
M0033914 GJCADEND_00007 8715 16 Skin 0.25 protein_coding missense_variant MODERATE 1118T>A Leu373Gln
M0033915 GJCADEND_00007 8771 14 Skin 0.22 protein_coding synonymous_variant LOW 1062C>T Arg354Arg
M0033916 GJCADEND_00007 9455 3 Skin 0.05 protein_coding synonymous_variant LOW 378C>T Ile126Ile
M0033917 GJCADEND_00003 3188 16 Skin 0.25 protein_coding synonymous_variant LOW 2739A>G Gln913Gln
M0033918 GJCADEND_00003 3218 12 Skin 0.19 protein_coding synonymous_variant LOW 2709T>C Arg903Arg
M0033919 GJCADEND_00003 3233 12 Skin 0.19 protein_coding synonymous_variant LOW 2694A>G Glu898Glu
M0033920 GJCADEND_00003 5411 13 Skin 0.21 protein_coding synonymous_variant LOW 516C>T Thr172Thr
M0033921 GJCADEND_00003 5426 13 Skin 0.21 protein_coding synonymous_variant LOW 501A>G Lys167Lys
M0033922 GJCADEND_00004 6399 11 Skin 0.17 protein_coding synonymous_variant LOW 411A>G Glu137Glu
M0033923 GJCADEND_00004 6402 9 Skin 0.14 protein_coding synonymous_variant LOW 408C>T Asn136Asn
M0033924 GJCADEND_00005 8102 10 Skin 0.16 protein_coding synonymous_variant LOW 45C>T Arg15Arg
M0033925 GJCADEND_00005 12378 7 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -4232G>A None
M0033926 GJCADEND_00001 129 7 Skin 0.11 protein_coding downstream_gene_variant MODIFIER *559T>C None
M0033927 GJCADEND_00002 2106 11 Skin 0.17 protein_coding synonymous_variant LOW 282T>C Ala94Ala
M0033928 GJCADEND_00007 8791 3 Skin 0.05 protein_coding missense_variant MODERATE 1042A>C Thr348Pro
M0033929 GJCADEND_00001 916 7 Skin 0.11 protein_coding synonymous_variant LOW 744T>C Ser248Ser
M0033930 GJCADEND_00002 1902 9 Skin 0.14 protein_coding synonymous_variant LOW 486C>T Ala162Ala
M0033931 GJCADEND_00005 6884 12 Skin 0.19 protein_coding synonymous_variant LOW 1263T>C Gly421Gly
M0033932 GJCADEND_00005 6905 13 Skin 0.21 protein_coding synonymous_variant LOW 1242G>A Gln414Gln
M0033933 GJCADEND_00005 6923 13 Skin 0.21 protein_coding synonymous_variant LOW 1224G>A Glu408Glu
M0033934 GJCADEND_00008 9910 22 Skin 0.35 protein_coding synonymous_variant LOW 78T>C Phe26Phe
M0033935 GJCADEND_00003 3293 11 Skin 0.17 protein_coding synonymous_variant LOW 2634G>C Ala878Ala
M0033936 GJCADEND_00003 3310 10 Skin 0.16 protein_coding synonymous_variant LOW 2617C>T Leu873Leu
M0033937 GJCADEND_00001 1297 8 Skin 0.13 protein_coding synonymous_variant LOW 363T>C Arg121Arg
M0033938 GJCADEND_00003 10295 3 Skin 0.05 protein_coding upstream_gene_variant MODIFIER -4369A>G None
M0033939 GJCADEND_00002 2054 6 Skin 0.10 protein_coding missense_variant MODERATE 334G>A Gly112Ser
M0033940 GJCADEND_00001 991 4 Skin 0.06 protein_coding synonymous_variant LOW 669G>A Glu223Glu






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
GJCADEND_00004 VFG041026 HSI-2 77.2 9.4e-130 1 285 0.9727 0.9862 Effector delivery system type IVB secretion system protein IcmH/DotU experiment
GJCADEND_00005 VFG041025 HSI-2 79.5 2.6e-208 1 443 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssK experiment
GJCADEND_00006 VFG041024 HSI-2 71.8 8.9e-58 1 149 0.9312 0.8869 Effector delivery system type VI secretion system lipoprotein TssJ experiment
GJCADEND_00004 VFG041026 HSI-2 77.2 7e-129 1 285 0.9727 0.9862 Effector delivery system type IVB secretion system protein IcmH/DotU prediction
GJCADEND_00005 VFG051572 HSI-2 80.4 2.4e-213 1 443 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssK prediction
GJCADEND_00006 VFG051560 HSI-2 72.5 1.8e-57 1 149 0.9312 0.8869 Effector delivery system type VI secretion system lipoprotein TssJ 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






        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