Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2553
  Reference Plasmid   1111525849852394_bin.3__k141_245397
  Reference Plasmid Size   9776
  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
M0046981 LCNLFEPP_00002 1651 13 Skin 0.14 protein_coding synonymous_variant LOW 462T>G Arg154Arg
M0046982 LCNLFEPP_00002 1654 13 Skin 0.14 protein_coding synonymous_variant LOW 465C>T Gly155Gly
M0046983 LCNLFEPP_00002 1720 14 Skin 0.16 protein_coding synonymous_variant LOW 531G>C Thr177Thr
M0046984 LCNLFEPP_00002 1729 14 Skin 0.16 protein_coding synonymous_variant LOW 540T>G Gly180Gly
M0046985 LCNLFEPP_00002 1753 14 Skin 0.16 protein_coding synonymous_variant LOW 564T>C His188His
M0046986 LCNLFEPP_00002 1771 15 Skin 0.17 protein_coding synonymous_variant LOW 582T>C Gly194Gly
M0046987 LCNLFEPP_00002 1777 15 Skin 0.17 protein_coding synonymous_variant LOW 588A>G Glu196Glu
M0046988 LCNLFEPP_00002 1778 15 Skin 0.17 protein_coding missense_variant MODERATE 589A>G Ile197Val
M0046989 LCNLFEPP_00002 1780 15 Skin 0.17 protein_coding missense_variant MODERATE 591C>G Ile197Met
M0046990 LCNLFEPP_00002 1783 15 Skin 0.17 protein_coding synonymous_variant LOW 594T>G Gly198Gly
M0046991 LCNLFEPP_00002 1795 15 Skin 0.17 protein_coding synonymous_variant LOW 606A>G Leu202Leu
M0046992 LCNLFEPP_00002 1800 15 Skin 0.17 protein_coding missense_variant MODERATE 611G>A Ser204Asn
M0046993 LCNLFEPP_00002 1828 15 Skin 0.17 protein_coding synonymous_variant LOW 639C>G Val213Val
M0046994 LCNLFEPP_00002 1834 15 Skin 0.17 protein_coding synonymous_variant LOW 645A>G Ala215Ala
M0046995 LCNLFEPP_00002 1841 15 Skin 0.17 protein_coding missense_variant MODERATE 652A>G Thr218Ala
M0046996 LCNLFEPP_00002 1844 14 Skin 0.16 protein_coding missense_variant MODERATE 655G>C Glu219Gln
M0046997 LCNLFEPP_00001 1918 10 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -846A>C None
M0046998 LCNLFEPP_00001 1930 11 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -858T>C None
M0046999 LCNLFEPP_00001 1952 16 Skin 0.18 protein_coding upstream_gene_variant MODIFIER -880A>G None
M0047000 LCNLFEPP_00001 1984 11 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -912T>G None
M0047001 LCNLFEPP_00001 1996 11 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -924G>A None
M0047002 LCNLFEPP_00001 2068 16 Skin 0.18 protein_coding upstream_gene_variant MODIFIER -996A>G None
M0047003 LCNLFEPP_00003 2541 60 Skin 0.67 protein_coding synonymous_variant LOW 471G>A Leu157Leu
M0047004 LCNLFEPP_00004 3403 52 Skin 0.58 protein_coding synonymous_variant LOW 132C>T His44His
M0047005 LCNLFEPP_00004 3412 52 Skin 0.58 protein_coding synonymous_variant LOW 123C>A Gly41Gly
M0047006 LCNLFEPP_00005 3839 30 Skin 0.33 protein_coding synonymous_variant LOW 2070T>C Gly690Gly
M0047007 LCNLFEPP_00005 3857 30 Skin 0.33 protein_coding synonymous_variant LOW 2052T>C Arg684Arg
M0047008 LCNLFEPP_00005 3884 27 Skin 0.30 protein_coding synonymous_variant LOW 2025T>C Thr675Thr
M0047009 LCNLFEPP_00005 3908 24 Skin 0.27 protein_coding synonymous_variant LOW 2001T>C Arg667Arg
M0047010 LCNLFEPP_00005 4016 31 Skin 0.34 protein_coding synonymous_variant LOW 1893T>C Gly631Gly
M0047011 LCNLFEPP_00005 4052 26 Skin 0.29 protein_coding synonymous_variant LOW 1857C>G Val619Val
M0047012 LCNLFEPP_00005 4070 26 Skin 0.29 protein_coding synonymous_variant LOW 1839G>T Pro613Pro
M0047013 LCNLFEPP_00005 4523 36 Skin 0.40 protein_coding synonymous_variant LOW 1386G>C Ser462Ser
M0047014 LCNLFEPP_00005 4526 36 Skin 0.40 protein_coding synonymous_variant LOW 1383A>G Val461Val
M0047015 LCNLFEPP_00005 4565 40 Skin 0.44 protein_coding synonymous_variant LOW 1344A>G Ala448Ala
M0047016 LCNLFEPP_00005 4568 40 Skin 0.44 protein_coding synonymous_variant LOW 1341T>C Ile447Ile
M0047017 LCNLFEPP_00005 4772 23 Skin 0.26 protein_coding synonymous_variant LOW 1137C>T Asp379Asp
M0047018 LCNLFEPP_00005 4805 21 Skin 0.23 protein_coding synonymous_variant LOW 1104A>G Thr368Thr
M0047019 LCNLFEPP_00005 5051 14 Skin 0.16 protein_coding synonymous_variant LOW 858C>T Ile286Ile
M0047020 LCNLFEPP_00005 5066 14 Skin 0.16 protein_coding synonymous_variant LOW 843A>G Pro281Pro
M0047021 LCNLFEPP_00005 5084 14 Skin 0.16 protein_coding synonymous_variant LOW 825G>A Ser275Ser
M0047022 LCNLFEPP_00005 5093 14 Skin 0.16 protein_coding synonymous_variant LOW 816T>C Gly272Gly
M0047023 LCNLFEPP_00005 5096 13 Skin 0.14 protein_coding synonymous_variant LOW 813G>C Ala271Ala
M0047024 LCNLFEPP_00005 5099 13 Skin 0.14 protein_coding synonymous_variant LOW 810T>C Gly270Gly
M0047025 LCNLFEPP_00005 5108 13 Skin 0.14 protein_coding synonymous_variant LOW 801G>A Lys267Lys
M0047026 LCNLFEPP_00005 5138 15 Skin 0.17 protein_coding synonymous_variant LOW 771G>A Ala257Ala
M0047027 LCNLFEPP_00005 5228 36 Skin 0.40 protein_coding synonymous_variant LOW 681T>C Gly227Gly
M0047028 LCNLFEPP_00005 5231 36 Skin 0.40 protein_coding synonymous_variant LOW 678A>G Glu226Glu
M0047029 LCNLFEPP_00005 5237 36 Skin 0.40 protein_coding synonymous_variant LOW 672C>T Asn224Asn
M0047030 LCNLFEPP_00005 5243 36 Skin 0.40 protein_coding synonymous_variant LOW 666T>C Tyr222Tyr
M0047031 LCNLFEPP_00005 5378 15 Skin 0.17 protein_coding synonymous_variant LOW 531T>C Gly177Gly
M0047032 LCNLFEPP_00005 5399 13 Skin 0.14 protein_coding synonymous_variant LOW 510T>C Gly170Gly
M0047033 LCNLFEPP_00004 6201 11 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -2667C>T None
M0047034 LCNLFEPP_00004 6213 11 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -2679A>C None
M0047035 LCNLFEPP_00008 7709 8 Skin 0.09 protein_coding synonymous_variant LOW 48G>C Leu16Leu
M0047036 LCNLFEPP_00008 7745 8 Skin 0.09 protein_coding synonymous_variant LOW 84C>A Pro28Pro
M0047037 LCNLFEPP_00008 7754 8 Skin 0.09 protein_coding synonymous_variant LOW 93T>C Ser31Ser
M0047038 LCNLFEPP_00009 8915 6 Skin 0.07 protein_coding missense_variant MODERATE 199G>A Asp67Asn
M0047039 LCNLFEPP_00009 8925 6 Skin 0.07 protein_coding synonymous_variant LOW 189T>C Asp63Asp
M0047040 LCNLFEPP_00009 8937 6 Skin 0.07 protein_coding missense_variant MODERATE 177C>G Asp59Glu
M0047041 LCNLFEPP_00005 9435 4 Skin 0.04 protein_coding upstream_gene_variant MODIFIER -3527T>A None
M0047042 LCNLFEPP_00005 9440 5 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -3532G>A None
M0047043 LCNLFEPP_00005 9448 5 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -3540G>C None
M0047044 LCNLFEPP_00005 9476 16 Skin 0.18 protein_coding upstream_gene_variant MODIFIER -3568A>G None
M0047045 LCNLFEPP_00005 9480 5 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -3572T>A None
M0047046 LCNLFEPP_00005 9520 5 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -3612T>C None
M0047047 LCNLFEPP_00005 9574 4 Skin 0.04 protein_coding upstream_gene_variant MODIFIER -3666G>A None
M0047048 LCNLFEPP_00005 9576 4 Skin 0.04 protein_coding upstream_gene_variant MODIFIER -3668T>A None
M0047049 LCNLFEPP_00003 2244 23 Skin 0.26 protein_coding synonymous_variant LOW 174C>T Asp58Asp
M0047050 LCNLFEPP_00003 2340 30 Skin 0.33 protein_coding synonymous_variant LOW 270G>C Pro90Pro
M0047051 LCNLFEPP_00003 2358 30 Skin 0.33 protein_coding synonymous_variant LOW 288G>A Glu96Glu
M0047052 LCNLFEPP_00003 2387 31 Skin 0.34 protein_coding missense_variant MODERATE 317C>G Thr106Ser
M0047053 LCNLFEPP_00003 2417 32 Skin 0.36 protein_coding missense_variant MODERATE 347T>G Leu116Arg
M0047054 LCNLFEPP_00003 2425 32 Skin 0.36 protein_coding missense_variant MODERATE 355C>G Leu119Val
M0047055 LCNLFEPP_00003 2432 32 Skin 0.36 protein_coding missense_variant MODERATE 362G>A Arg121Gln
M0047056 LCNLFEPP_00003 2487 22 Skin 0.24 protein_coding synonymous_variant LOW 417A>G Gly139Gly
M0047057 LCNLFEPP_00003 2758 24 Skin 0.27 protein_coding synonymous_variant LOW 688T>C Leu230Leu
M0047058 LCNLFEPP_00001 698 4 Skin 0.04 protein_coding synonymous_variant LOW 375C>T Asp125Asp
M0047059 LCNLFEPP_00001 713 4 Skin 0.04 protein_coding synonymous_variant LOW 360G>C Ser120Ser
M0047060 LCNLFEPP_00001 719 4 Skin 0.04 protein_coding synonymous_variant LOW 354C>T Arg118Arg
M0047061 LCNLFEPP_00001 722 4 Skin 0.04 protein_coding synonymous_variant LOW 351G>A Leu117Leu
M0047062 LCNLFEPP_00001 724 4 Skin 0.04 protein_coding synonymous_variant LOW 349T>C Leu117Leu
M0047063 LCNLFEPP_00004 3076 23 Skin 0.26 protein_coding synonymous_variant LOW 459A>G Val153Val
M0047064 LCNLFEPP_00004 3127 25 Skin 0.28 protein_coding synonymous_variant LOW 408G>C Leu136Leu
M0047065 LCNLFEPP_00004 3134 26 Skin 0.29 protein_coding missense_variant MODERATE 401T>A Leu134Gln
M0047066 LCNLFEPP_00004 3151 25 Skin 0.28 protein_coding synonymous_variant LOW 384C>T His128His
M0047067 LCNLFEPP_00005 5683 16 Skin 0.18 protein_coding missense_variant MODERATE 226C>G Leu76Val
M0047068 LCNLFEPP_00005 5753 15 Skin 0.17 protein_coding synonymous_variant LOW 156T>G Gly52Gly
M0047069 LCNLFEPP_00005 5765 15 Skin 0.17 protein_coding synonymous_variant LOW 144T>C Ser48Ser
M0047070 LCNLFEPP_00001 6030 12 Skin 0.13 protein_coding upstream_gene_variant MODIFIER -4958A>G None
M0047071 LCNLFEPP_00001 6035 12 Skin 0.13 protein_coding upstream_gene_variant MODIFIER -4963C>T None
M0047072 LCNLFEPP_00001 6037 12 Skin 0.13 protein_coding upstream_gene_variant MODIFIER -4965A>C None
M0047073 LCNLFEPP_00001 6039 12 Skin 0.13 protein_coding upstream_gene_variant MODIFIER -4967C>G None
M0047074 LCNLFEPP_00002 1675 12 Skin 0.13 protein_coding synonymous_variant LOW 486T>A Gly162Gly
M0047075 LCNLFEPP_00004 2882 22 Skin 0.24 protein_coding missense_variant MODERATE 653C>T Ser218Phe
M0047076 LCNLFEPP_00004 2891 20 Skin 0.22 protein_coding missense_variant MODERATE 644A>C Glu215Ala
M0047077 LCNLFEPP_00004 2977 16 Skin 0.18 protein_coding synonymous_variant LOW 558A>G Glu186Glu
M0047078 LCNLFEPP_00004 3289 17 Skin 0.19 protein_coding synonymous_variant LOW 246C>T Cys82Cys
M0047079 LCNLFEPP_00004 3295 21 Skin 0.23 protein_coding synonymous_variant LOW 240A>G Leu80Leu
M0047080 LCNLFEPP_00004 3299 17 Skin 0.19 protein_coding missense_variant MODERATE 236C>T Thr79Met
M0047081 LCNLFEPP_00004 3333 18 Skin 0.20 protein_coding synonymous_variant LOW 202C>T Leu68Leu
M0047082 LCNLFEPP_00001 3659 25 Skin 0.28 protein_coding upstream_gene_variant MODIFIER -2587G>C None
M0047083 LCNLFEPP_00005 3704 23 Skin 0.26 protein_coding synonymous_variant LOW 2205T>C Asp735Asp
M0047084 LCNLFEPP_00005 3734 24 Skin 0.27 protein_coding synonymous_variant LOW 2175A>C Ala725Ala
M0047085 LCNLFEPP_00005 3743 24 Skin 0.27 protein_coding synonymous_variant LOW 2166G>A Val722Val
M0047086 LCNLFEPP_00005 4130 26 Skin 0.29 protein_coding synonymous_variant LOW 1779C>T His593His
M0047087 LCNLFEPP_00004 6704 14 Skin 0.16 protein_coding upstream_gene_variant MODIFIER -3170A>T None
M0047088 LCNLFEPP_00004 6725 14 Skin 0.16 protein_coding upstream_gene_variant MODIFIER -3191C>T None
M0047089 LCNLFEPP_00004 6751 13 Skin 0.14 protein_coding upstream_gene_variant MODIFIER -3217G>T None
M0047090 LCNLFEPP_00004 6752 13 Skin 0.14 protein_coding upstream_gene_variant MODIFIER -3218G>A None
M0047091 LCNLFEPP_00009 8853 6 Skin 0.07 protein_coding missense_variant MODERATE 261T>A Asn87Lys
M0047092 LCNLFEPP_00005 9322 16 Skin 0.18 protein_coding upstream_gene_variant MODIFIER -3414G>A None
M0047093 LCNLFEPP_00002 1468 7 Skin 0.08 protein_coding synonymous_variant LOW 279C>G Ala93Ala
M0047094 LCNLFEPP_00002 1501 7 Skin 0.08 protein_coding synonymous_variant LOW 312C>T Tyr104Tyr
M0047095 LCNLFEPP_00002 1531 8 Skin 0.09 protein_coding synonymous_variant LOW 342C>G Ala114Ala
M0047096 LCNLFEPP_00002 1570 9 Skin 0.10 protein_coding synonymous_variant LOW 381C>G Gly127Gly
M0047097 LCNLFEPP_00002 1571 9 Skin 0.10 protein_coding missense_variant MODERATE 382A>C Met128Leu
M0047098 LCNLFEPP_00002 1591 9 Skin 0.10 protein_coding synonymous_variant LOW 402C>T Leu134Leu
M0047099 LCNLFEPP_00002 1610 9 Skin 0.10 protein_coding synonymous_variant LOW 421C>T Leu141Leu
M0047100 LCNLFEPP_00002 1614 9 Skin 0.10 protein_coding missense_variant MODERATE 425G>C Gly142Ala
M0047101 LCNLFEPP_00004 3022 27 Skin 0.30 protein_coding synonymous_variant LOW 513T>C Tyr171Tyr
M0047102 LCNLFEPP_00004 6976 10 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -3442C>T None
M0047103 LCNLFEPP_00004 7013 9 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -3479A>G None
M0047104 LCNLFEPP_00007 7467 8 Skin 0.09 protein_coding synonymous_variant LOW 423T>C Arg141Arg
M0047105 LCNLFEPP_00009 8643 9 Skin 0.10 protein_coding synonymous_variant LOW 471C>A Ala157Ala
M0047106 LCNLFEPP_00009 8652 9 Skin 0.10 protein_coding synonymous_variant LOW 462T>C Gly154Gly
M0047107 LCNLFEPP_00009 8661 9 Skin 0.10 protein_coding synonymous_variant LOW 453T>C Val151Val
M0047108 LCNLFEPP_00009 8700 8 Skin 0.09 protein_coding synonymous_variant LOW 414C>A Gly138Gly
M0047109 LCNLFEPP_00009 9025 8 Skin 0.09 protein_coding missense_variant MODERATE 89T>C Val30Ala
M0047110 LCNLFEPP_00005 5588 14 Skin 0.16 protein_coding synonymous_variant LOW 321C>T Arg107Arg
M0047111 LCNLFEPP_00005 5624 15 Skin 0.17 protein_coding synonymous_variant LOW 285T>C Phe95Phe
M0047112 LCNLFEPP_00004 6137 11 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -2603C>A None
M0047113 LCNLFEPP_00004 6143 11 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -2609A>G None
M0047114 LCNLFEPP_00008 7913 6 Skin 0.07 protein_coding synonymous_variant LOW 252A>T Arg84Arg
M0047115 LCNLFEPP_00001 1958 3 Skin 0.03 protein_coding upstream_gene_variant MODIFIER -886G>A None
M0047116 LCNLFEPP_00001 1965 3 Skin 0.03 protein_coding upstream_gene_variant MODIFIER -893A>G None
M0047117 LCNLFEPP_00001 1974 3 Skin 0.03 protein_coding upstream_gene_variant MODIFIER -902G>C None
M0047118 LCNLFEPP_00003 2655 25 Skin 0.28 protein_coding synonymous_variant LOW 585T>C Gly195Gly
M0047119 LCNLFEPP_00003 2684 23 Skin 0.26 protein_coding missense_variant MODERATE 614G>A Arg205Gln
M0047120 LCNLFEPP_00001 2767 3 Skin 0.03 protein_coding upstream_gene_variant MODIFIER -1695C>A None
M0047121 LCNLFEPP_00005 4385 3 Skin 0.03 protein_coding synonymous_variant LOW 1524G>A Val508Val
M0047122 LCNLFEPP_00006 6333 9 Skin 0.10 protein_coding missense_variant MODERATE 72C>G His24Gln
M0047123 LCNLFEPP_00009 8607 8 Skin 0.09 protein_coding missense_variant MODERATE 507T>G Ile169Met
M0047124 LCNLFEPP_00005 4580 5 Skin 0.06 protein_coding synonymous_variant LOW 1329C>T Asp443Asp
M0047125 LCNLFEPP_00007 7610 8 Skin 0.09 protein_coding missense_variant MODERATE 566A>G Gln189Arg
M0047126 LCNLFEPP_00008 8022 3 Skin 0.03 protein_coding missense_variant MODERATE 361A>G Ile121Val
M0047127 LCNLFEPP_00001 644 3 Skin 0.03 protein_coding synonymous_variant LOW 429T>C Asp143Asp






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