Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1822
  Reference Plasmid   1111525849649836_bin.8__k141_395676
  Reference Plasmid Size   20738
  Reference Plasmid GC Content   0.62
  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
M0017932 EMLDNIJJ_00003 2525 17 Skin 0.17 protein_coding synonymous_variant LOW 12A>T Leu4Leu
M0017933 EMLDNIJJ_00016 11571 22 Skin 0.22 protein_coding synonymous_variant LOW 2193G>A Ala731Ala
M0017934 EMLDNIJJ_00016 11970 10 Skin 0.10 protein_coding synonymous_variant LOW 1794C>T Gly598Gly
M0017935 EMLDNIJJ_00016 12176 27 Skin 0.27 protein_coding missense_variant MODERATE 1588C>G Pro530Ala
M0017936 EMLDNIJJ_00016 12339 19 Skin 0.19 protein_coding synonymous_variant LOW 1425A>G Glu475Glu
M0017937 EMLDNIJJ_00016 12360 19 Skin 0.19 protein_coding synonymous_variant LOW 1404C>T Arg468Arg
M0017938 EMLDNIJJ_00016 12378 19 Skin 0.19 protein_coding synonymous_variant LOW 1386A>G Pro462Pro
M0017939 EMLDNIJJ_00016 12384 19 Skin 0.19 protein_coding synonymous_variant LOW 1380T>C Gly460Gly
M0017940 EMLDNIJJ_00016 12672 8 Skin 0.08 protein_coding synonymous_variant LOW 1092C>T Asp364Asp
M0017941 EMLDNIJJ_00016 13107 17 Skin 0.17 protein_coding synonymous_variant LOW 657C>T Cys219Cys
M0017942 EMLDNIJJ_00016 13476 7 Skin 0.07 protein_coding synonymous_variant LOW 288A>G Val96Val
M0017943 EMLDNIJJ_00016 13480 7 Skin 0.07 protein_coding missense_variant MODERATE 284T>C Val95Ala
M0017944 EMLDNIJJ_00016 13497 7 Skin 0.07 protein_coding synonymous_variant LOW 267G>A Val89Val
M0017945 EMLDNIJJ_00016 13512 7 Skin 0.07 protein_coding synonymous_variant LOW 252C>T Ile84Ile
M0017946 EMLDNIJJ_00016 13611 7 Skin 0.07 protein_coding synonymous_variant LOW 153C>T Arg51Arg
M0017947 EMLDNIJJ_00016 13677 19 Skin 0.19 protein_coding synonymous_variant LOW 87T>C Ser29Ser
M0017948 EMLDNIJJ_00017 13875 21 Skin 0.21 protein_coding synonymous_variant LOW 429C>T Gly143Gly
M0017949 EMLDNIJJ_00018 14531 7 Skin 0.07 protein_coding synonymous_variant LOW 2043C>T Gly681Gly
M0017950 EMLDNIJJ_00018 14591 9 Skin 0.09 protein_coding synonymous_variant LOW 1983G>C Val661Val
M0017951 EMLDNIJJ_00018 14609 9 Skin 0.09 protein_coding synonymous_variant LOW 1965C>G Arg655Arg
M0017952 EMLDNIJJ_00018 14717 5 Skin 0.05 protein_coding synonymous_variant LOW 1857A>G Gly619Gly
M0017953 EMLDNIJJ_00018 14722 5 Skin 0.05 protein_coding missense_variant MODERATE 1852C>G Gln618Glu
M0017954 EMLDNIJJ_00018 14933 15 Skin 0.15 protein_coding synonymous_variant LOW 1641T>C Tyr547Tyr
M0017955 EMLDNIJJ_00018 14945 15 Skin 0.15 protein_coding synonymous_variant LOW 1629C>T His543His
M0017956 EMLDNIJJ_00018 14953 15 Skin 0.15 protein_coding synonymous_variant LOW 1621C>T Leu541Leu
M0017957 EMLDNIJJ_00018 14969 15 Skin 0.15 protein_coding synonymous_variant LOW 1605C>T His535His
M0017958 EMLDNIJJ_00018 14979 22 Skin 0.22 protein_coding missense_variant MODERATE 1595T>G Ile532Ser
M0017959 EMLDNIJJ_00018 14999 15 Skin 0.15 protein_coding synonymous_variant LOW 1575G>A Glu525Glu
M0017960 EMLDNIJJ_00018 15182 6 Skin 0.06 protein_coding synonymous_variant LOW 1392C>T Gly464Gly
M0017961 EMLDNIJJ_00018 15968 4 Skin 0.04 protein_coding synonymous_variant LOW 606T>C Phe202Phe
M0017962 EMLDNIJJ_00018 16001 5 Skin 0.05 protein_coding synonymous_variant LOW 573C>T Asp191Asp
M0017963 EMLDNIJJ_00019 17038 11 Skin 0.11 protein_coding synonymous_variant LOW 234C>A Ala78Ala
M0017964 EMLDNIJJ_00016 11763 12 Skin 0.12 protein_coding synonymous_variant LOW 2001C>T Ala667Ala
M0017965 EMLDNIJJ_00016 11796 12 Skin 0.12 protein_coding synonymous_variant LOW 1968A>G Pro656Pro
M0017966 EMLDNIJJ_00016 13227 6 Skin 0.06 protein_coding synonymous_variant LOW 537G>C Leu179Leu
M0017967 EMLDNIJJ_00018 15436 6 Skin 0.06 protein_coding missense_variant MODERATE 1138A>G Asn380Asp
M0017968 EMLDNIJJ_00018 16379 17 Skin 0.17 protein_coding synonymous_variant LOW 195G>A Pro65Pro
M0017969 EMLDNIJJ_00020 17581 12 Skin 0.12 protein_coding missense_variant MODERATE 289A>G Ile97Val
M0017970 EMLDNIJJ_00020 17621 15 Skin 0.15 protein_coding missense_variant MODERATE 329C>T Pro110Leu
M0017971 EMLDNIJJ_00021 17683 17 Skin 0.17 protein_coding missense_variant MODERATE 977C>T Thr326Ile
M0017972 EMLDNIJJ_00021 17904 12 Skin 0.12 protein_coding synonymous_variant LOW 756A>G Arg252Arg
M0017973 EMLDNIJJ_00021 17915 12 Skin 0.12 protein_coding missense_variant MODERATE 745C>T Pro249Ser
M0017974 EMLDNIJJ_00021 17945 12 Skin 0.12 protein_coding missense_variant MODERATE 715A>C Asn239His
M0017975 EMLDNIJJ_00021 17967 12 Skin 0.12 protein_coding synonymous_variant LOW 693T>C Ile231Ile
M0017976 EMLDNIJJ_00021 18011 10 Skin 0.10 protein_coding missense_variant MODERATE 649G>T Ala217Ser
M0017977 EMLDNIJJ_00021 18033 10 Skin 0.10 protein_coding synonymous_variant LOW 627A>G Gln209Gln
M0017978 EMLDNIJJ_00021 18057 9 Skin 0.09 protein_coding synonymous_variant LOW 603T>C Gly201Gly
M0017979 EMLDNIJJ_00021 18060 9 Skin 0.09 protein_coding synonymous_variant LOW 600C>T Ile200Ile
M0017980 EMLDNIJJ_00015 11117 4 Skin 0.04 protein_coding synonymous_variant LOW 249G>A Ala83Ala
M0017981 EMLDNIJJ_00016 11697 9 Skin 0.09 protein_coding synonymous_variant LOW 2067T>C Asp689Asp
M0017982 EMLDNIJJ_00016 11718 8 Skin 0.08 protein_coding synonymous_variant LOW 2046C>T Ser682Ser
M0017983 EMLDNIJJ_00016 11730 8 Skin 0.08 protein_coding synonymous_variant LOW 2034C>T Asn678Asn
M0017984 EMLDNIJJ_00016 12173 8 Skin 0.08 protein_coding missense_variant MODERATE 1591G>C Asp531His
M0017985 EMLDNIJJ_00016 13368 16 Skin 0.16 protein_coding synonymous_variant LOW 396C>T Arg132Arg
M0017986 EMLDNIJJ_00016 13401 15 Skin 0.15 protein_coding synonymous_variant LOW 363A>G Arg121Arg
M0017987 EMLDNIJJ_00019 16978 3 Skin 0.03 protein_coding synonymous_variant LOW 174G>A Glu58Glu
M0017988 EMLDNIJJ_00021 17681 5 Skin 0.05 protein_coding missense_variant MODERATE 979A>G Thr327Ala
M0017989 EMLDNIJJ_00021 17700 5 Skin 0.05 protein_coding synonymous_variant LOW 960T>C Gly320Gly
M0017990 EMLDNIJJ_00021 17730 6 Skin 0.06 protein_coding synonymous_variant LOW 930G>A Glu310Glu
M0017991 EMLDNIJJ_00021 18230 5 Skin 0.05 protein_coding missense_variant MODERATE 430A>G Thr144Ala
M0017992 EMLDNIJJ_00021 18644 3 Skin 0.03 protein_coding missense_variant MODERATE 16G>A Ala6Thr
M0017993 EMLDNIJJ_00016 18705 4 Skin 0.04 protein_coding upstream_gene_variant MODIFIER -4942C>A None
M0017994 EMLDNIJJ_00016 18708 4 Skin 0.04 protein_coding upstream_gene_variant MODIFIER -4945A>C None
M0017995 EMLDNIJJ_00022 18808 3 Skin 0.03 protein_coding synonymous_variant LOW 78T>C Ile26Ile
M0017996 EMLDNIJJ_00023 19137 11 Skin 0.11 protein_coding splice_region_variant&stop_retained_variant LOW 530A>G Ter177Ter
M0017997 EMLDNIJJ_00023 19139 11 Skin 0.11 protein_coding synonymous_variant LOW 528C>G Arg176Arg
M0017998 EMLDNIJJ_00023 19442 5 Skin 0.05 protein_coding synonymous_variant LOW 225T>A Val75Val
M0017999 EMLDNIJJ_00023 19451 5 Skin 0.05 protein_coding synonymous_variant LOW 216C>A Ala72Ala
M0018000 EMLDNIJJ_00023 19658 5 Skin 0.05 protein_coding synonymous_variant LOW 9C>T Tyr3Tyr
M0018001 EMLDNIJJ_00018 19706 7 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -3133C>T None
M0018002 EMLDNIJJ_00018 19723 7 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -3150G>A None
M0018003 EMLDNIJJ_00018 20367 10 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -3794T>C None
M0018004 EMLDNIJJ_00018 20694 10 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4121G>A None
M0018005 EMLDNIJJ_00018 20707 10 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4134A>G None
M0018006 EMLDNIJJ_00016 11412 9 Skin 0.09 protein_coding synonymous_variant LOW 2352G>A Gln784Gln
M0018007 EMLDNIJJ_00015 11170 7 Skin 0.07 protein_coding missense_variant MODERATE 196G>A Ala66Thr
M0018008 EMLDNIJJ_00015 11177 7 Skin 0.07 protein_coding synonymous_variant LOW 189T>C Asp63Asp
M0018009 EMLDNIJJ_00015 11180 7 Skin 0.07 protein_coding synonymous_variant LOW 186C>T Asp62Asp
M0018010 EMLDNIJJ_00017 14079 7 Skin 0.07 protein_coding synonymous_variant LOW 225A>G Val75Val
M0018011 EMLDNIJJ_00019 16915 4 Skin 0.04 protein_coding synonymous_variant LOW 111C>T Asn37Asn
M0018012 EMLDNIJJ_00019 17113 5 Skin 0.05 protein_coding synonymous_variant LOW 309C>T Asp103Asp
M0018013 EMLDNIJJ_00021 17817 4 Skin 0.04 protein_coding synonymous_variant LOW 843A>G Gln281Gln
M0018014 EMLDNIJJ_00005 3177 13 Skin 0.13 protein_coding synonymous_variant LOW 147A>G Leu49Leu
M0018015 EMLDNIJJ_00006 3599 7 Skin 0.07 protein_coding synonymous_variant LOW 267G>A Glu89Glu
M0018016 EMLDNIJJ_00018 14603 3 Skin 0.03 protein_coding synonymous_variant LOW 1971C>T Arg657Arg
M0018017 EMLDNIJJ_00018 15317 3 Skin 0.03 protein_coding synonymous_variant LOW 1257T>C Ala419Ala
M0018018 EMLDNIJJ_00024 19860 7 Skin 0.07 protein_coding missense_variant MODERATE 29A>G Gln10Arg
M0018019 EMLDNIJJ_00024 20124 8 Skin 0.08 protein_coding missense_variant MODERATE 293T>C Val98Ala
M0018020 EMLDNIJJ_00024 20186 11 Skin 0.11 protein_coding missense_variant MODERATE 355A>G Thr119Ala
M0018021 EMLDNIJJ_00024 20218 10 Skin 0.10 protein_coding synonymous_variant LOW 387T>C Phe129Phe
M0018022 EMLDNIJJ_00018 20436 9 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -3863A>C None
M0018023 EMLDNIJJ_00018 20456 9 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -3883C>T None
M0018024 EMLDNIJJ_00018 20523 11 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -3950A>G None
M0018025 EMLDNIJJ_00018 20526 11 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -3953A>G None
M0018026 EMLDNIJJ_00018 20585 9 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -4012G>A None
M0018027 EMLDNIJJ_00018 20601 9 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -4028C>A None
M0018028 EMLDNIJJ_00018 20605 9 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -4032G>C None
M0018029 EMLDNIJJ_00018 20613 9 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -4040A>G None
M0018030 EMLDNIJJ_00018 20616 9 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -4043G>T None
M0018031 EMLDNIJJ_00007 4481 9 Skin 0.09 protein_coding synonymous_variant LOW 27T>C Gly9Gly
M0018032 EMLDNIJJ_00015 13796 5 Skin 0.05 protein_coding upstream_gene_variant MODIFIER -2431A>T None
M0018033 EMLDNIJJ_00018 15503 4 Skin 0.04 protein_coding synonymous_variant LOW 1071G>A Val357Val
M0018034 EMLDNIJJ_00022 19075 3 Skin 0.03 protein_coding synonymous_variant LOW 345C>G Gly115Gly
M0018035 EMLDNIJJ_00022 19076 3 Skin 0.03 protein_coding missense_variant MODERATE 346C>A Arg116Ser
M0018036 EMLDNIJJ_00023 19167 4 Skin 0.04 protein_coding missense_variant MODERATE 500A>C Asp167Ala
M0018037 EMLDNIJJ_00023 19169 4 Skin 0.04 protein_coding synonymous_variant LOW 498T>C Ala166Ala
M0018038 EMLDNIJJ_00023 19208 3 Skin 0.03 protein_coding synonymous_variant LOW 459C>T Thr153Thr
M0018039 EMLDNIJJ_00023 19217 3 Skin 0.03 protein_coding synonymous_variant LOW 450C>T Gly150Gly
M0018040 EMLDNIJJ_00015 10940 3 Skin 0.03 protein_coding synonymous_variant LOW 426G>A Pro142Pro
M0018041 EMLDNIJJ_00016 17220 5 Skin 0.05 protein_coding upstream_gene_variant MODIFIER -3457T>A None
M0018042 EMLDNIJJ_00023 19286 3 Skin 0.03 protein_coding synonymous_variant LOW 381C>G Gly127Gly
M0018043 EMLDNIJJ_00023 19289 3 Skin 0.03 protein_coding synonymous_variant LOW 378T>C Arg126Arg
M0018044 EMLDNIJJ_00023 19571 4 Skin 0.04 protein_coding synonymous_variant LOW 96G>A Glu32Glu
M0018045 EMLDNIJJ_00024 19924 5 Skin 0.05 protein_coding synonymous_variant LOW 93T>C Leu31Leu
M0018046 EMLDNIJJ_00024 19942 5 Skin 0.05 protein_coding synonymous_variant LOW 111A>G Ala37Ala
M0018047 EMLDNIJJ_00024 19948 5 Skin 0.05 protein_coding synonymous_variant LOW 117T>C Asp39Asp
M0018048 EMLDNIJJ_00023 19341 5 Skin 0.05 protein_coding missense_variant MODERATE 326A>C Asn109Thr






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
EMLDNIJJ_00005 Nickel (Ni), Zinc (Zn) 86.6 7e-45 1 97 1.0000 1.0211 experiment
EMLDNIJJ_00006 Nickel (Ni), Cadmium (Cd), Zinc (Zn), Cobalt (Co) 88.6 1.6e-193 1 373 1.0107 1.0000 experiment
EMLDNIJJ_00011 Chromium (Cr) 75.1 4.8e-197 19 452 0.9647 0.9541 experiment
EMLDNIJJ_00005 Nickel (Ni), Zinc (Zn) 100 2.7e-50 1 97 1.0000 1.0000 prediction
EMLDNIJJ_00006 Nickel (Ni), Cadmium (Cd), Zinc (Zn), Cobalt (Co) 89.1 1.4e-192 1 373 1.0107 1.0000 prediction
EMLDNIJJ_00011 Chromium (Cr) 99.8 3e-261 1 453 1.0000 1.0000 prediction
EMLDNIJJ_00012 Chromium (Cr), Methyl Viologen [class: Paraquat], Menadione [class: Naphthoquinone] 96.1 2.3e-167 9 314 0.9745 1.0000 prediction






        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
EMLDNIJJ_00011 2.A.51.1.4 74.8 1.5e-197 1 452 0.9978 0.9934 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.51 The Chromate Ion Transporter (CHR) Family