Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C654
  Reference Plasmid   NZ_CP042181.1
  Reference Plasmid Size   116559
  Reference Plasmid GC Content   0.59
  Reference Plasmid Mobility Type   conjugative





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
M0096475 PAKKDGCM_00077 55530 22 Skin 0.67 protein_coding missense_variant MODERATE 2449A>C Thr817Pro
M0096476 PAKKDGCM_00077 55531 21 Skin 0.64 protein_coding synonymous_variant LOW 2448G>A Leu816Leu
M0096477 PAKKDGCM_00077 55546 21 Skin 0.64 protein_coding synonymous_variant LOW 2433G>A Ala811Ala
M0096478 PAKKDGCM_00077 55699 25 Skin 0.76 protein_coding synonymous_variant LOW 2280A>G Glu760Glu
M0096479 PAKKDGCM_00077 55705 25 Skin 0.76 protein_coding synonymous_variant LOW 2274C>T Thr758Thr
M0096480 PAKKDGCM_00077 55738 25 Skin 0.76 protein_coding synonymous_variant LOW 2241T>C Asn747Asn
M0096481 PAKKDGCM_00077 55777 24 Skin 0.73 protein_coding synonymous_variant LOW 2202T>C Asn734Asn
M0096482 PAKKDGCM_00077 55789 24 Skin 0.73 protein_coding synonymous_variant LOW 2190G>C Ala730Ala
M0096483 PAKKDGCM_00077 55918 22 Skin 0.67 protein_coding synonymous_variant LOW 2061C>T Ile687Ile
M0096484 PAKKDGCM_00077 55922 22 Skin 0.67 protein_coding missense_variant MODERATE 2057G>A Arg686Lys
M0096485 PAKKDGCM_00077 55924 21 Skin 0.64 protein_coding synonymous_variant LOW 2055C>A Ala685Ala
M0096486 PAKKDGCM_00077 55926 22 Skin 0.67 protein_coding missense_variant MODERATE 2053G>A Ala685Thr
M0096487 PAKKDGCM_00077 55928 22 Skin 0.67 protein_coding missense_variant MODERATE 2051T>G Val684Gly
M0096488 PAKKDGCM_00077 55930 22 Skin 0.67 protein_coding synonymous_variant LOW 2049A>G Ala683Ala
M0096489 PAKKDGCM_00077 55931 21 Skin 0.64 protein_coding missense_variant MODERATE 2048C>T Ala683Val
M0096490 PAKKDGCM_00077 55937 22 Skin 0.67 protein_coding missense_variant MODERATE 2042T>C Val681Ala
M0096491 PAKKDGCM_00077 55942 22 Skin 0.67 protein_coding synonymous_variant LOW 2037G>C Pro679Pro
M0096492 PAKKDGCM_00077 55959 21 Skin 0.64 protein_coding missense_variant MODERATE 2020A>G Ile674Val
M0096493 PAKKDGCM_00077 56001 22 Skin 0.67 protein_coding missense_variant MODERATE 1978G>A Gly660Ser
M0096494 PAKKDGCM_00077 56055 22 Skin 0.67 protein_coding synonymous_variant LOW 1924T>C Leu642Leu
M0096495 PAKKDGCM_00077 56071 20 Skin 0.61 protein_coding synonymous_variant LOW 1908G>A Ala636Ala
M0096496 PAKKDGCM_00077 56125 19 Skin 0.58 protein_coding synonymous_variant LOW 1854C>T Asp618Asp
M0096497 PAKKDGCM_00077 56271 21 Skin 0.64 protein_coding missense_variant MODERATE 1708G>A Val570Ile
M0096498 PAKKDGCM_00077 56278 20 Skin 0.61 protein_coding synonymous_variant LOW 1701G>A Gln567Gln
M0096499 PAKKDGCM_00077 56402 20 Skin 0.61 protein_coding missense_variant MODERATE 1577G>A Arg526Lys
M0096500 PAKKDGCM_00077 56410 20 Skin 0.61 protein_coding synonymous_variant LOW 1569T>C Tyr523Tyr
M0096501 PAKKDGCM_00077 56467 19 Skin 0.58 protein_coding synonymous_variant LOW 1512G>A Leu504Leu
M0096502 PAKKDGCM_00077 56509 20 Skin 0.61 protein_coding synonymous_variant LOW 1470C>G Ala490Ala
M0096503 PAKKDGCM_00077 56512 20 Skin 0.61 protein_coding synonymous_variant LOW 1467T>C Ile489Ile
M0096504 PAKKDGCM_00077 56542 19 Skin 0.58 protein_coding synonymous_variant LOW 1437C>A Arg479Arg
M0096505 PAKKDGCM_00077 56548 19 Skin 0.58 protein_coding synonymous_variant LOW 1431G>C Ala477Ala
M0096506 PAKKDGCM_00077 56623 18 Skin 0.55 protein_coding synonymous_variant LOW 1356C>G Val452Val
M0096507 PAKKDGCM_00077 56626 17 Skin 0.52 protein_coding synonymous_variant LOW 1353C>T Ala451Ala
M0096508 PAKKDGCM_00077 56632 17 Skin 0.52 protein_coding synonymous_variant LOW 1347C>T Tyr449Tyr
M0096509 PAKKDGCM_00077 56650 19 Skin 0.58 protein_coding synonymous_variant LOW 1329C>G Pro443Pro
M0096510 PAKKDGCM_00077 56699 19 Skin 0.58 protein_coding missense_variant MODERATE 1280G>A Arg427Lys
M0096511 PAKKDGCM_00077 56722 19 Skin 0.58 protein_coding synonymous_variant LOW 1257C>G Leu419Leu
M0096512 PAKKDGCM_00077 56724 19 Skin 0.58 protein_coding missense_variant MODERATE 1255C>T Leu419Phe
M0096513 PAKKDGCM_00077 56731 19 Skin 0.58 protein_coding synonymous_variant LOW 1248C>G Ala416Ala
M0096514 PAKKDGCM_00077 56762 19 Skin 0.58 protein_coding missense_variant MODERATE 1217C>T Ala406Val
M0096515 PAKKDGCM_00077 56848 19 Skin 0.58 protein_coding synonymous_variant LOW 1131G>C Leu377Leu
M0096516 PAKKDGCM_00077 56887 18 Skin 0.55 protein_coding synonymous_variant LOW 1092C>G Thr364Thr
M0096517 PAKKDGCM_00077 56893 18 Skin 0.55 protein_coding synonymous_variant LOW 1086C>T Asp362Asp
M0096518 PAKKDGCM_00077 56903 18 Skin 0.55 protein_coding missense_variant MODERATE 1076A>C Asn359Thr
M0096519 PAKKDGCM_00077 56904 18 Skin 0.55 protein_coding missense_variant MODERATE 1075A>G Asn359Asp
M0096520 PAKKDGCM_00077 56908 18 Skin 0.55 protein_coding synonymous_variant LOW 1071G>A Glu357Glu
M0096521 PAKKDGCM_00077 56940 18 Skin 0.55 protein_coding missense_variant MODERATE 1039C>G Leu347Val
M0096522 PAKKDGCM_00077 56941 18 Skin 0.55 protein_coding synonymous_variant LOW 1038G>C Pro346Pro
M0096523 PAKKDGCM_00077 56967 18 Skin 0.55 protein_coding missense_variant MODERATE 1012C>T Leu338Phe
M0096524 PAKKDGCM_00077 56989 18 Skin 0.55 protein_coding synonymous_variant LOW 990A>C Arg330Arg
M0096525 PAKKDGCM_00077 57052 18 Skin 0.55 protein_coding synonymous_variant LOW 927C>G Arg309Arg
M0096526 PAKKDGCM_00077 57076 18 Skin 0.55 protein_coding synonymous_variant LOW 903T>C Tyr301Tyr
M0096527 PAKKDGCM_00077 57124 16 Skin 0.48 protein_coding synonymous_variant LOW 855G>A Arg285Arg
M0096528 PAKKDGCM_00077 57145 18 Skin 0.55 protein_coding synonymous_variant LOW 834T>G Arg278Arg
M0096529 PAKKDGCM_00077 57175 18 Skin 0.55 protein_coding synonymous_variant LOW 804C>A Pro268Pro
M0096530 PAKKDGCM_00077 57262 16 Skin 0.48 protein_coding missense_variant MODERATE 717T>G Ile239Met
M0096531 PAKKDGCM_00077 57271 16 Skin 0.48 protein_coding synonymous_variant LOW 708C>T Phe236Phe
M0096532 PAKKDGCM_00077 57275 17 Skin 0.52 protein_coding missense_variant MODERATE 704G>C Ser235Thr
M0096533 PAKKDGCM_00077 57349 16 Skin 0.48 protein_coding synonymous_variant LOW 630T>C Ile210Ile
M0096534 PAKKDGCM_00077 57363 16 Skin 0.48 protein_coding missense_variant MODERATE 616A>T Thr206Ser
M0096535 PAKKDGCM_00077 57367 16 Skin 0.48 protein_coding synonymous_variant LOW 612T>C Val204Val
M0096536 PAKKDGCM_00077 57374 16 Skin 0.48 protein_coding missense_variant MODERATE 605T>C Val202Ala
M0096537 PAKKDGCM_00077 57424 16 Skin 0.48 protein_coding synonymous_variant LOW 555G>A Gln185Gln
M0096538 PAKKDGCM_00077 57433 16 Skin 0.48 protein_coding synonymous_variant LOW 546A>G Gln182Gln
M0096539 PAKKDGCM_00077 57452 16 Skin 0.48 protein_coding missense_variant MODERATE 527A>G His176Arg
M0096540 PAKKDGCM_00077 57472 16 Skin 0.48 protein_coding synonymous_variant LOW 507T>C Gly169Gly
M0096541 PAKKDGCM_00076 54557 21 Skin 0.64 protein_coding synonymous_variant LOW 723T>G Ala241Ala
M0096542 PAKKDGCM_00076 54583 22 Skin 0.67 protein_coding synonymous_variant LOW 697C>T Leu233Leu
M0096543 PAKKDGCM_00076 54656 22 Skin 0.67 protein_coding synonymous_variant LOW 624A>G Val208Val
M0096544 PAKKDGCM_00076 54707 22 Skin 0.67 protein_coding synonymous_variant LOW 573G>A Glu191Glu
M0096545 PAKKDGCM_00076 54758 22 Skin 0.67 protein_coding synonymous_variant LOW 522C>G Leu174Leu
M0096546 PAKKDGCM_00076 54761 22 Skin 0.67 protein_coding synonymous_variant LOW 519C>G Gly173Gly
M0096547 PAKKDGCM_00076 54881 22 Skin 0.67 protein_coding synonymous_variant LOW 399A>G Leu133Leu
M0096548 PAKKDGCM_00076 54896 22 Skin 0.67 protein_coding synonymous_variant LOW 384C>T Arg128Arg
M0096549 PAKKDGCM_00076 54902 22 Skin 0.67 protein_coding synonymous_variant LOW 378T>C Asp126Asp
M0096550 PAKKDGCM_00076 54905 22 Skin 0.67 protein_coding synonymous_variant LOW 375G>A Lys125Lys
M0096551 PAKKDGCM_00076 54917 22 Skin 0.67 protein_coding synonymous_variant LOW 363C>T His121His
M0096552 PAKKDGCM_00076 54941 22 Skin 0.67 protein_coding synonymous_variant LOW 339C>G Ser113Ser
M0096553 PAKKDGCM_00076 54944 22 Skin 0.67 protein_coding synonymous_variant LOW 336C>G Ala112Ala
M0096554 PAKKDGCM_00076 54947 22 Skin 0.67 protein_coding synonymous_variant LOW 333C>T Asp111Asp
M0096555 PAKKDGCM_00076 54968 23 Skin 0.70 protein_coding synonymous_variant LOW 312C>T Gly104Gly
M0096556 PAKKDGCM_00076 55001 23 Skin 0.70 protein_coding synonymous_variant LOW 279A>G Glu93Glu
M0096557 PAKKDGCM_00076 55015 23 Skin 0.70 protein_coding missense_variant MODERATE 265T>C Tyr89His
M0096558 PAKKDGCM_00076 55076 23 Skin 0.70 protein_coding synonymous_variant LOW 204C>G Leu68Leu
M0096559 PAKKDGCM_00076 55085 22 Skin 0.67 protein_coding synonymous_variant LOW 195C>T His65His
M0096560 PAKKDGCM_00076 55097 22 Skin 0.67 protein_coding missense_variant MODERATE 183C>G His61Gln
M0096561 PAKKDGCM_00076 55218 23 Skin 0.70 protein_coding missense_variant MODERATE 62G>C Gly21Ala
M0096562 PAKKDGCM_00076 55256 24 Skin 0.73 protein_coding synonymous_variant LOW 24A>C Ala8Ala
M0096563 PAKKDGCM_00077 55301 24 Skin 0.73 protein_coding missense_variant MODERATE 2678T>C Val893Ala
M0096564 PAKKDGCM_00077 55310 24 Skin 0.73 protein_coding missense_variant MODERATE 2669G>A Arg890Lys
M0096565 PAKKDGCM_00077 55344 24 Skin 0.73 protein_coding missense_variant MODERATE 2635G>A Glu879Lys
M0096566 PAKKDGCM_00077 55366 24 Skin 0.73 protein_coding synonymous_variant LOW 2613G>A Gln871Gln
M0096567 PAKKDGCM_00077 55384 24 Skin 0.73 protein_coding synonymous_variant LOW 2595C>A Gly865Gly






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
PAKKDGCM_00100 Nickel (Ni), Zinc (Zn) 100 2.4e-50 1 95 1.0000 1.0000 experiment
PAKKDGCM_00101 Nickel (Ni), Cadmium (Cd), Zinc (Zn), Cobalt (Co) 100 4.1e-218 1 377 1.0000 1.0000 experiment
PAKKDGCM_00113 Mercury (Hg) 100 8.9e-102 1 180 0.9945 0.8219 experiment
PAKKDGCM_00114 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 3.8e-79 1 144 1.0000 1.0000 experiment
AAJGMLHF_00100 Nickel (Ni), Zinc (Zn) 100 2.4e-50 1 95 1.0000 1.0000 experiment
AAJGMLHF_00101 Nickel (Ni), Cadmium (Cd), Zinc (Zn), Cobalt (Co) 100 4.1e-218 1 377 1.0000 1.0000 experiment
AAJGMLHF_00113 Mercury (Hg) 100 8.9e-102 1 180 0.9945 0.8219 experiment
AAJGMLHF_00114 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 3.8e-79 1 144 1.0000 1.0000 experiment
PAKKDGCM_00100 Nickel (Ni), Zinc (Zn) 100 5.6e-48 1 95 1.0000 1.0000 prediction
PAKKDGCM_00101 Nickel (Ni), Cadmium (Cd), Zinc (Zn), Cobalt (Co) 100 9.4e-216 1 377 1.0000 0.8788 prediction
PAKKDGCM_00113 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury], Methylmercury Acetate [class: Organo-mercury] 100 5.3e-100 1 181 1.0000 1.0000 prediction
PAKKDGCM_00114 Mercury (Hg) 100 8.6e-77 1 144 1.0000 1.0000 prediction
AAJGMLHF_00100 Nickel (Ni), Zinc (Zn) 100 5.6e-48 1 95 1.0000 1.0000 prediction
AAJGMLHF_00101 Nickel (Ni), Cadmium (Cd), Zinc (Zn), Cobalt (Co) 100 9.4e-216 1 377 1.0000 0.8788 prediction
AAJGMLHF_00113 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury], Methylmercury Acetate [class: Organo-mercury] 100 5.3e-100 1 181 1.0000 1.0000 prediction
AAJGMLHF_00114 Mercury (Hg) 100 8.6e-77 1 144 1.0000 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
PAKKDGCM_00014 PHI:10215 pumA 72.9 2e-38 1 96 0.9600 0.9697 nematodes nosocomial infection putative addiction module killer protein increased virulence (hypervirulence)
PAKKDGCM_00060 PHI:3165 hopA1 85.7 1.6e-149 1 293 1.0000 1.0000 eudicots leaf spot (celery); leaf spot (eggplant); leaf spot (sweet pepper); wilt rot (muskmelon); stem rot (muskmelon); stem rot (chrysanthemum); leaf spot (soybean) effector (plant avirulence determinant) effector (plant avirulence determinant)
AAJGMLHF_00014 PHI:10215 pumA 72.9 2e-38 1 96 0.9600 0.9697 nematodes nosocomial infection putative addiction module killer protein increased virulence (hypervirulence)
AAJGMLHF_00060 PHI:3165 hopA1 85.7 1.6e-149 1 293 1.0000 1.0000 eudicots leaf spot (celery); leaf spot (eggplant); leaf spot (sweet pepper); wilt rot (muskmelon); stem rot (muskmelon); stem rot (chrysanthemum); leaf spot (soybean) effector (plant avirulence determinant) effector (plant avirulence determinant)






        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
PAKKDGCM_00078 CAC86814.1|GH23 100 0 1 482 1 1
PAKKDGCM_00128 QDW60992.1|GH23 100 8.77e-206 1 305 1 1
AAJGMLHF_00078 CAC86814.1|GH23 100 0 1 482 1 1
AAJGMLHF_00128 QDW60992.1|GH23 100 8.77e-206 1 305 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
PAKKDGCM_00087 1.B.9.2.1 99.3 1.3e-237 1 411 1.0000 0.8839 1 Channels/Pores 1.B β-Barrel Porins 1.B.9 The FadL Outer Membrane Protein (FadL) Family
AAJGMLHF_00087 1.B.9.2.1 99.3 1.3e-237 1 411 1.0000 0.8839 1 Channels/Pores 1.B β-Barrel Porins 1.B.9 The FadL Outer Membrane Protein (FadL) Family