Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2060
  Reference Plasmid   1111525849737367_bin.26__k141_90484
  Reference Plasmid Size   67754
  Reference Plasmid GC Content   0.55
  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
M0023651 IFJFGEKM_00001 713 10 Skin 0.09 protein_coding synonymous_variant LOW 228C>A Arg76Arg
M0023652 IFJFGEKM_00003 2611 11 Skin 0.10 protein_coding synonymous_variant LOW 1308C>T Gly436Gly
M0023653 IFJFGEKM_00004 3313 14 Skin 0.13 protein_coding missense_variant MODERATE 475C>T Arg159Cys
M0023654 IFJFGEKM_00004 3486 18 Skin 0.16 protein_coding synonymous_variant LOW 648A>C Pro216Pro
M0023655 IFJFGEKM_00004 3810 15 Skin 0.14 protein_coding synonymous_variant LOW 972A>G Thr324Thr
M0023656 IFJFGEKM_00001 5004 13 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -4064A>G None
M0023657 IFJFGEKM_00008 5360 4 Skin 0.04 protein_coding synonymous_variant LOW 144A>T Ala48Ala
M0023658 IFJFGEKM_00008 5372 4 Skin 0.04 protein_coding synonymous_variant LOW 156G>A Pro52Pro
M0023659 IFJFGEKM_00008 5486 8 Skin 0.07 protein_coding synonymous_variant LOW 270T>C Ser90Ser
M0023660 IFJFGEKM_00009 7709 7 Skin 0.06 protein_coding synonymous_variant LOW 1276C>T Leu426Leu
M0023661 IFJFGEKM_00009 7889 6 Skin 0.05 protein_coding synonymous_variant LOW 1456C>T Leu486Leu
M0023662 IFJFGEKM_00010 9662 9 Skin 0.08 protein_coding missense_variant MODERATE 284T>C Val95Ala
M0023663 IFJFGEKM_00010 10488 5 Skin 0.05 protein_coding synonymous_variant LOW 1110T>C Ala370Ala
M0023664 IFJFGEKM_00010 10491 5 Skin 0.05 protein_coding synonymous_variant LOW 1113T>C Tyr371Tyr
M0023665 IFJFGEKM_00010 10509 5 Skin 0.05 protein_coding synonymous_variant LOW 1131A>G Gln377Gln
M0023666 IFJFGEKM_00010 10549 14 Skin 0.13 protein_coding missense_variant MODERATE 1171A>T Ile391Leu
M0023667 IFJFGEKM_00010 10739 3 Skin 0.03 protein_coding missense_variant MODERATE 1361T>C Val454Ala
M0023668 IFJFGEKM_00010 11580 9 Skin 0.08 protein_coding synonymous_variant LOW 2202A>G Ala734Ala
M0023669 IFJFGEKM_00063 67097 8 Skin 0.07 protein_coding missense_variant MODERATE 400A>G Thr134Ala
M0023670 IFJFGEKM_00063 67121 8 Skin 0.07 protein_coding synonymous_variant LOW 376C>T Leu126Leu
M0023671 IFJFGEKM_00063 67139 8 Skin 0.07 protein_coding missense_variant MODERATE 358G>A Val120Ile
M0023672 IFJFGEKM_00063 67142 8 Skin 0.07 protein_coding missense_variant MODERATE 355G>C Gly119Arg
M0023673 IFJFGEKM_00063 67161 8 Skin 0.07 protein_coding synonymous_variant LOW 336G>A Gln112Gln
M0023674 IFJFGEKM_00063 67175 8 Skin 0.07 protein_coding missense_variant MODERATE 322A>C Ser108Arg
M0023675 IFJFGEKM_00063 67190 8 Skin 0.07 protein_coding missense_variant MODERATE 307T>C Trp103Arg
M0023676 IFJFGEKM_00063 67196 8 Skin 0.07 protein_coding missense_variant MODERATE 301G>T Gly101Trp
M0023677 IFJFGEKM_00063 67202 8 Skin 0.07 protein_coding missense_variant MODERATE 295A>G Asn99Asp
M0023678 IFJFGEKM_00063 67221 8 Skin 0.07 protein_coding synonymous_variant LOW 276G>A Gln92Gln
M0023679 IFJFGEKM_00063 67256 8 Skin 0.07 protein_coding missense_variant MODERATE 241T>C Tyr81His
M0023680 IFJFGEKM_00063 67259 8 Skin 0.07 protein_coding missense_variant MODERATE 238C>G Arg80Gly
M0023681 IFJFGEKM_00063 67262 8 Skin 0.07 protein_coding missense_variant MODERATE 235G>C Gly79Arg
M0023682 IFJFGEKM_00063 67299 8 Skin 0.07 protein_coding synonymous_variant LOW 198G>T Pro66Pro
M0023683 IFJFGEKM_00063 67331 8 Skin 0.07 protein_coding missense_variant MODERATE 166C>G Arg56Gly
M0023684 IFJFGEKM_00063 67349 8 Skin 0.07 protein_coding missense_variant MODERATE 148A>G Ser50Gly
M0023685 IFJFGEKM_00063 67367 8 Skin 0.07 protein_coding missense_variant MODERATE 130A>G Ile44Val
M0023686 IFJFGEKM_00063 67368 8 Skin 0.07 protein_coding synonymous_variant LOW 129A>G Gln43Gln
M0023687 IFJFGEKM_00063 67388 8 Skin 0.07 protein_coding missense_variant MODERATE 109G>C Glu37Gln
M0023688 IFJFGEKM_00063 67400 8 Skin 0.07 protein_coding missense_variant MODERATE 97A>G Ile33Val
M0023689 IFJFGEKM_00063 67406 8 Skin 0.07 protein_coding missense_variant MODERATE 91C>T Arg31Trp
M0023690 IFJFGEKM_00063 67439 8 Skin 0.07 protein_coding missense_variant MODERATE 58A>G Ser20Gly
M0023691 IFJFGEKM_00063 67463 8 Skin 0.07 protein_coding missense_variant MODERATE 34G>A Ala12Thr
M0023692 IFJFGEKM_00063 67478 8 Skin 0.07 protein_coding missense_variant MODERATE 19G>A Val7Ile
M0023693 IFJFGEKM_00058 67511 8 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -4560A>G None
M0023694 IFJFGEKM_00058 67517 8 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -4566A>G None
M0023695 IFJFGEKM_00054 59897 20 Skin 0.18 protein_coding missense_variant MODERATE 236A>C Asn79Thr
M0023696 IFJFGEKM_00001 614 5 Skin 0.05 protein_coding synonymous_variant LOW 327T>C Arg109Arg
M0023697 IFJFGEKM_00003 1777 12 Skin 0.11 protein_coding synonymous_variant LOW 474A>G Leu158Leu
M0023698 IFJFGEKM_00003 2482 14 Skin 0.13 protein_coding synonymous_variant LOW 1179A>C Val393Val
M0023699 IFJFGEKM_00003 2656 7 Skin 0.06 protein_coding synonymous_variant LOW 1353A>G Thr451Thr
M0023700 IFJFGEKM_00004 2893 11 Skin 0.10 protein_coding missense_variant MODERATE 55T>C Phe19Leu
M0023701 IFJFGEKM_00004 2973 5 Skin 0.05 protein_coding synonymous_variant LOW 135G>A Lys45Lys
M0023702 IFJFGEKM_00031 36214 15 Skin 0.14 protein_coding missense_variant MODERATE 53C>A Pro18His
M0023703 IFJFGEKM_00031 36903 14 Skin 0.13 protein_coding missense_variant MODERATE 742C>G Pro248Ala
M0023704 IFJFGEKM_00031 37307 15 Skin 0.14 protein_coding synonymous_variant LOW 1146T>C Arg382Arg
M0023705 IFJFGEKM_00001 5050 13 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -4110C>T None
M0023706 IFJFGEKM_00001 5053 13 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -4113T>C None
M0023707 IFJFGEKM_00001 5101 11 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4161T>C None
M0023708 IFJFGEKM_00008 5321 4 Skin 0.04 protein_coding synonymous_variant LOW 105G>A Leu35Leu
M0023709 IFJFGEKM_00008 5915 8 Skin 0.07 protein_coding synonymous_variant LOW 699A>G Leu233Leu
M0023710 IFJFGEKM_00008 5925 8 Skin 0.07 protein_coding missense_variant MODERATE 709G>A Val237Ile
M0023711 IFJFGEKM_00008 5973 7 Skin 0.06 protein_coding missense_variant MODERATE 757C>G Pro253Ala
M0023712 IFJFGEKM_00035 42261 9 Skin 0.08 protein_coding missense_variant MODERATE 149T>A Val50Glu
M0023713 IFJFGEKM_00006 4173 7 Skin 0.06 protein_coding synonymous_variant LOW 147A>G Gly49Gly
M0023714 IFJFGEKM_00008 5285 3 Skin 0.03 protein_coding synonymous_variant LOW 69G>T Pro23Pro
M0023715 IFJFGEKM_00010 11199 6 Skin 0.05 protein_coding synonymous_variant LOW 1821G>A Gly607Gly
M0023716 IFJFGEKM_00010 11223 8 Skin 0.07 protein_coding synonymous_variant LOW 1845A>G Ala615Ala
M0023717 IFJFGEKM_00010 11382 7 Skin 0.06 protein_coding synonymous_variant LOW 2004G>A Pro668Pro
M0023718 IFJFGEKM_00010 11529 4 Skin 0.04 protein_coding missense_variant MODERATE 2151G>T Lys717Asn
M0023719 IFJFGEKM_00010 11544 4 Skin 0.04 protein_coding synonymous_variant LOW 2166A>G Glu722Glu
M0023720 IFJFGEKM_00011 12560 3 Skin 0.03 protein_coding synonymous_variant LOW 814T>C Leu272Leu
M0023721 IFJFGEKM_00011 12584 3 Skin 0.03 protein_coding stop_gained HIGH 838C>T Gln280*
M0023722 IFJFGEKM_00013 14381 6 Skin 0.05 protein_coding synonymous_variant LOW 717G>A Ser239Ser
M0023723 IFJFGEKM_00013 14392 6 Skin 0.05 protein_coding missense_variant MODERATE 728A>G Asp243Gly
M0023724 IFJFGEKM_00013 14403 6 Skin 0.05 protein_coding missense_variant MODERATE 739G>A Ala247Thr
M0023725 IFJFGEKM_00013 14420 6 Skin 0.05 protein_coding synonymous_variant LOW 756G>A Gly252Gly
M0023726 IFJFGEKM_00013 14765 4 Skin 0.04 protein_coding synonymous_variant LOW 1101G>A Gln367Gln
M0023727 IFJFGEKM_00013 14771 4 Skin 0.04 protein_coding synonymous_variant LOW 1107A>G Arg369Arg
M0023728 IFJFGEKM_00015 16152 4 Skin 0.04 protein_coding synonymous_variant LOW 1200T>G Pro400Pro
M0023729 IFJFGEKM_00015 16158 4 Skin 0.04 protein_coding synonymous_variant LOW 1194T>C Ala398Ala
M0023730 IFJFGEKM_00015 16218 5 Skin 0.05 protein_coding synonymous_variant LOW 1134C>T Gly378Gly
M0023731 IFJFGEKM_00015 16251 4 Skin 0.04 protein_coding synonymous_variant LOW 1101G>A Leu367Leu
M0023732 IFJFGEKM_00015 16257 4 Skin 0.04 protein_coding synonymous_variant LOW 1095T>C Tyr365Tyr
M0023733 IFJFGEKM_00017 18343 3 Skin 0.03 protein_coding missense_variant MODERATE 190C>A His64Asn
M0023734 IFJFGEKM_00017 18388 4 Skin 0.04 protein_coding missense_variant MODERATE 235A>G Ser79Gly
M0023735 IFJFGEKM_00017 18405 4 Skin 0.04 protein_coding synonymous_variant LOW 252T>C Cys84Cys
M0023736 IFJFGEKM_00018 19068 4 Skin 0.04 protein_coding synonymous_variant LOW 318T>C Gly106Gly
M0023737 IFJFGEKM_00019 19697 4 Skin 0.04 protein_coding synonymous_variant LOW 504A>G Gly168Gly
M0023738 IFJFGEKM_00004 3507 3 Skin 0.03 protein_coding missense_variant MODERATE 669C>A Ser223Arg
M0023739 IFJFGEKM_00005 3922 3 Skin 0.03 protein_coding missense_variant MODERATE 62A>C Glu21Ala
M0023740 IFJFGEKM_00006 4311 9 Skin 0.08 protein_coding synonymous_variant LOW 285A>G Leu95Leu
M0023741 IFJFGEKM_00008 6028 4 Skin 0.04 protein_coding missense_variant MODERATE 812A>C Glu271Ala
M0023742 IFJFGEKM_00008 6029 4 Skin 0.04 protein_coding missense_variant MODERATE 813G>C Glu271Asp
M0023743 IFJFGEKM_00012 13663 7 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -202G>C None
M0023744 IFJFGEKM_00026 30095 5 Skin 0.05 protein_coding synonymous_variant LOW 525A>G Leu175Leu
M0023745 IFJFGEKM_00012 13309 4 Skin 0.04 protein_coding synonymous_variant LOW 153G>A Thr51Thr
M0023746 IFJFGEKM_00013 13757 3 Skin 0.03 protein_coding synonymous_variant LOW 93G>A Leu31Leu
M0023747 IFJFGEKM_00015 17314 3 Skin 0.03 protein_coding missense_variant MODERATE 38A>C Glu13Ala
M0023748 IFJFGEKM_00016 17773 3 Skin 0.03 protein_coding missense_variant MODERATE 250G>A Ala84Thr
M0023749 IFJFGEKM_00015 18626 3 Skin 0.03 protein_coding upstream_gene_variant MODIFIER -1275G>A None
M0023750 IFJFGEKM_00019 19786 3 Skin 0.03 protein_coding missense_variant MODERATE 415T>C Cys139Arg
M0023751 IFJFGEKM_00021 21933 3 Skin 0.03 protein_coding synonymous_variant LOW 921T>C Ala307Ala
M0023752 IFJFGEKM_00021 22339 3 Skin 0.03 protein_coding missense_variant MODERATE 515G>C Ser172Thr
M0023753 IFJFGEKM_00021 22397 3 Skin 0.03 protein_coding missense_variant MODERATE 457T>G Tyr153Asp
M0023754 IFJFGEKM_00022 23703 3 Skin 0.03 protein_coding synonymous_variant LOW 483G>A Glu161Glu
M0023755 IFJFGEKM_00024 25049 3 Skin 0.03 protein_coding synonymous_variant LOW 387C>T His129His
M0023756 IFJFGEKM_00024 25319 4 Skin 0.04 protein_coding synonymous_variant LOW 117A>G Glu39Glu
M0023757 IFJFGEKM_00025 25501 7 Skin 0.06 protein_coding stop_lost&splice_region_variant HIGH 3163T>C Ter1055Glnext*?
M0023758 IFJFGEKM_00025 26759 4 Skin 0.04 protein_coding synonymous_variant LOW 1905C>T Gly635Gly
M0023759 IFJFGEKM_00025 26966 4 Skin 0.04 protein_coding synonymous_variant LOW 1698C>T Gly566Gly
M0023760 IFJFGEKM_00025 27086 4 Skin 0.04 protein_coding synonymous_variant LOW 1578G>A Pro526Pro
M0023761 IFJFGEKM_00026 29572 3 Skin 0.03 protein_coding missense_variant MODERATE 1048G>A Glu350Lys
M0023762 IFJFGEKM_00026 29793 4 Skin 0.04 protein_coding missense_variant MODERATE 827G>A Gly276Asp
M0023763 IFJFGEKM_00009 6586 6 Skin 0.05 protein_coding synonymous_variant LOW 153C>T Arg51Arg
M0023764 IFJFGEKM_00009 6600 6 Skin 0.05 protein_coding missense_variant MODERATE 167T>C Val56Ala
M0023765 IFJFGEKM_00043 50535 5 Skin 0.05 protein_coding synonymous_variant LOW 678A>C Gly226Gly
M0023766 IFJFGEKM_00046 52721 5 Skin 0.05 protein_coding stop_lost&splice_region_variant HIGH 371A>C Ter124Serext*?
M0023767 IFJFGEKM_00009 8308 4 Skin 0.04 protein_coding synonymous_variant LOW 1875C>A Ala625Ala
M0023768 IFJFGEKM_00008 6254 5 Skin 0.05 protein_coding synonymous_variant LOW 1038A>C Ala346Ala
M0023769 IFJFGEKM_00009 6917 3 Skin 0.03 protein_coding missense_variant MODERATE 484A>T Ser162Cys
M0023770 IFJFGEKM_00009 7534 3 Skin 0.03 protein_coding synonymous_variant LOW 1101C>T Arg367Arg
M0023771 IFJFGEKM_00010 11271 8 Skin 0.07 protein_coding synonymous_variant LOW 1893T>C Ser631Ser
M0023772 IFJFGEKM_00023 24407 6 Skin 0.05 protein_coding synonymous_variant LOW 580C>T Leu194Leu
M0023773 IFJFGEKM_00003 144 3 Skin 0.03 protein_coding upstream_gene_variant MODIFIER -1160G>A None
M0023774 IFJFGEKM_00003 159 3 Skin 0.03 protein_coding upstream_gene_variant MODIFIER -1145T>C None
M0023775 IFJFGEKM_00014 15629 4 Skin 0.04 protein_coding synonymous_variant LOW 507A>G Ala169Ala
M0023776 IFJFGEKM_00009 7225 7 Skin 0.06 protein_coding synonymous_variant LOW 792G>A Glu264Glu
M0023777 IFJFGEKM_00009 7234 7 Skin 0.06 protein_coding synonymous_variant LOW 801A>G Pro267Pro
M0023778 IFJFGEKM_00009 7237 7 Skin 0.06 protein_coding synonymous_variant LOW 804A>G Gln268Gln
M0023779 IFJFGEKM_00009 7369 4 Skin 0.04 protein_coding synonymous_variant LOW 936C>G Ser312Ser
M0023780 IFJFGEKM_00020 20660 3 Skin 0.03 protein_coding missense_variant MODERATE 614T>C Val205Ala
M0023781 IFJFGEKM_00020 20674 3 Skin 0.03 protein_coding synonymous_variant LOW 600T>C Thr200Thr
M0023782 IFJFGEKM_00020 21165 3 Skin 0.03 protein_coding synonymous_variant LOW 109T>C Leu37Leu
M0023783 IFJFGEKM_00022 23727 3 Skin 0.03 protein_coding synonymous_variant LOW 459T>G Pro153Pro
M0023784 IFJFGEKM_00025 26282 3 Skin 0.03 protein_coding synonymous_variant LOW 2382A>G Thr794Thr
M0023785 IFJFGEKM_00025 26294 3 Skin 0.03 protein_coding synonymous_variant LOW 2370T>C Thr790Thr
M0023786 IFJFGEKM_00025 26306 3 Skin 0.03 protein_coding synonymous_variant LOW 2358T>A Thr786Thr
M0023787 IFJFGEKM_00025 28556 3 Skin 0.03 protein_coding synonymous_variant LOW 108C>T Asp36Asp
M0023788 IFJFGEKM_00001 383 5 Skin 0.05 protein_coding synonymous_variant LOW 558T>C Asn186Asn
M0023789 IFJFGEKM_00010 10822 3 Skin 0.03 protein_coding missense_variant MODERATE 1444G>A Ala482Thr
M0023790 IFJFGEKM_00009 7435 3 Skin 0.03 protein_coding missense_variant MODERATE 1002T>G Ile334Met






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
IFJFGEKM_00023 PHI:10580 PccS1_003516 76.2 3.7e-96 8 230 0.9654 0.8511 monocots soft rot transcriptional regulator, GntR family unaffected pathogenicity






        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
IFJFGEKM_00062 SMZ55713.1|GH13_5 96.2 0 1 496 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
IFJFGEKM_00042 2.A.1.14.33 76.7 5.4e-200 1 447 0.9889 0.9868 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)