Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2525
  Reference Plasmid   1111525849772552_bin.4__k141_66191
  Reference Plasmid Size   21285
  Reference Plasmid GC Content   0.54
  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
M0045626 PGKONOMK_00007 237 3 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -4288G>A None
M0045627 PGKONOMK_00001 396 3 Skin 0.50 protein_coding synonymous_variant LOW 906A>C Gly302Gly
M0045628 PGKONOMK_00001 414 3 Skin 0.50 protein_coding synonymous_variant LOW 888A>C Ala296Ala
M0045629 PGKONOMK_00001 429 3 Skin 0.50 protein_coding synonymous_variant LOW 873A>G Leu291Leu
M0045630 PGKONOMK_00001 465 3 Skin 0.50 protein_coding synonymous_variant LOW 837C>A Gly279Gly
M0045631 PGKONOMK_00001 483 3 Skin 0.50 protein_coding synonymous_variant LOW 819G>A Glu273Glu
M0045632 PGKONOMK_00001 564 3 Skin 0.50 protein_coding synonymous_variant LOW 738T>C Tyr246Tyr
M0045633 PGKONOMK_00001 645 3 Skin 0.50 protein_coding synonymous_variant LOW 657T>C Ala219Ala
M0045634 PGKONOMK_00001 707 3 Skin 0.50 protein_coding synonymous_variant LOW 595T>C Leu199Leu
M0045635 PGKONOMK_00001 774 3 Skin 0.50 protein_coding synonymous_variant LOW 528A>G Ala176Ala
M0045636 PGKONOMK_00001 884 4 Skin 0.67 protein_coding synonymous_variant LOW 418A>C Arg140Arg
M0045637 PGKONOMK_00001 912 4 Skin 0.67 protein_coding synonymous_variant LOW 390A>C Arg130Arg
M0045638 PGKONOMK_00001 939 4 Skin 0.67 protein_coding synonymous_variant LOW 363T>C Thr121Thr
M0045639 PGKONOMK_00001 944 4 Skin 0.67 protein_coding missense_variant MODERATE 358A>G Thr120Ala
M0045640 PGKONOMK_00001 987 3 Skin 0.50 protein_coding synonymous_variant LOW 315C>T Cys105Cys
M0045641 PGKONOMK_00001 998 4 Skin 0.67 protein_coding missense_variant MODERATE 304T>C Phe102Leu
M0045642 PGKONOMK_00001 1110 4 Skin 0.67 protein_coding synonymous_variant LOW 192T>C Arg64Arg
M0045643 PGKONOMK_00002 1457 3 Skin 0.50 protein_coding synonymous_variant LOW 1239A>G Pro413Pro
M0045644 PGKONOMK_00002 1541 3 Skin 0.50 protein_coding synonymous_variant LOW 1155A>C Gly385Gly
M0045645 PGKONOMK_00002 1562 3 Skin 0.50 protein_coding synonymous_variant LOW 1134A>G Ala378Ala
M0045646 PGKONOMK_00002 1847 3 Skin 0.50 protein_coding synonymous_variant LOW 849C>T Ile283Ile
M0045647 PGKONOMK_00002 1868 3 Skin 0.50 protein_coding synonymous_variant LOW 828T>C Phe276Phe
M0045648 PGKONOMK_00002 1919 3 Skin 0.50 protein_coding synonymous_variant LOW 777C>T Arg259Arg
M0045649 PGKONOMK_00002 1952 3 Skin 0.50 protein_coding synonymous_variant LOW 744C>T Asp248Asp
M0045650 PGKONOMK_00002 2021 4 Skin 0.67 protein_coding synonymous_variant LOW 675T>G Ala225Ala
M0045651 PGKONOMK_00002 2024 4 Skin 0.67 protein_coding synonymous_variant LOW 672G>C Gly224Gly
M0045652 PGKONOMK_00002 2036 4 Skin 0.67 protein_coding synonymous_variant LOW 660T>C Gly220Gly
M0045653 PGKONOMK_00002 2051 3 Skin 0.50 protein_coding synonymous_variant LOW 645T>G Arg215Arg
M0045654 PGKONOMK_00002 2057 4 Skin 0.67 protein_coding synonymous_variant LOW 639A>G Pro213Pro
M0045655 PGKONOMK_00002 2075 4 Skin 0.67 protein_coding synonymous_variant LOW 621A>G Gly207Gly
M0045656 PGKONOMK_00002 2204 4 Skin 0.67 protein_coding synonymous_variant LOW 492T>C Arg164Arg
M0045657 PGKONOMK_00002 2207 4 Skin 0.67 protein_coding synonymous_variant LOW 489A>G Pro163Pro
M0045658 PGKONOMK_00002 2208 4 Skin 0.67 protein_coding missense_variant MODERATE 488C>A Pro163Gln
M0045659 PGKONOMK_00002 2237 4 Skin 0.67 protein_coding synonymous_variant LOW 459A>G Ser153Ser
M0045660 PGKONOMK_00002 2495 3 Skin 0.50 protein_coding synonymous_variant LOW 201G>A Lys67Lys
M0045661 PGKONOMK_00002 2501 4 Skin 0.67 protein_coding synonymous_variant LOW 195T>C Gly65Gly
M0045662 PGKONOMK_00002 2542 3 Skin 0.50 protein_coding synonymous_variant LOW 154C>T Leu52Leu
M0045663 PGKONOMK_00002 2543 3 Skin 0.50 protein_coding synonymous_variant LOW 153A>G Arg51Arg
M0045664 PGKONOMK_00002 2549 4 Skin 0.67 protein_coding synonymous_variant LOW 147A>G Gly49Gly
M0045665 PGKONOMK_00002 2615 3 Skin 0.50 protein_coding synonymous_variant LOW 81C>A Leu27Leu
M0045666 PGKONOMK_00002 2618 3 Skin 0.50 protein_coding synonymous_variant LOW 78A>G Gly26Gly
M0045667 PGKONOMK_00002 2624 3 Skin 0.50 protein_coding synonymous_variant LOW 72A>G Val24Val
M0045668 PGKONOMK_00003 2810 4 Skin 0.67 protein_coding synonymous_variant LOW 210C>A Gly70Gly
M0045669 PGKONOMK_00005 3439 4 Skin 0.67 protein_coding synonymous_variant LOW 195C>T Asp65Asp
M0045670 PGKONOMK_00005 3466 3 Skin 0.50 protein_coding synonymous_variant LOW 168C>T Arg56Arg
M0045671 PGKONOMK_00001 3680 4 Skin 0.67 protein_coding upstream_gene_variant MODIFIER -2379A>G None
M0045672 PGKONOMK_00006 3760 4 Skin 0.67 protein_coding synonymous_variant LOW 598T>C Leu200Leu
M0045673 PGKONOMK_00006 4064 3 Skin 0.50 protein_coding synonymous_variant LOW 294T>C Thr98Thr
M0045674 PGKONOMK_00006 3932 3 Skin 0.50 protein_coding synonymous_variant LOW 426T>C Arg142Arg
M0045675 PGKONOMK_00007 4653 3 Skin 0.50 protein_coding missense_variant MODERATE 129T>G Asp43Glu
M0045676 PGKONOMK_00007 4710 3 Skin 0.50 protein_coding synonymous_variant LOW 186A>G Ser62Ser
M0045677 PGKONOMK_00008 5658 3 Skin 0.50 protein_coding synonymous_variant LOW 1221T>A Gly407Gly
M0045678 PGKONOMK_00008 5679 3 Skin 0.50 protein_coding synonymous_variant LOW 1200A>G Ala400Ala
M0045679 PGKONOMK_00008 5685 3 Skin 0.50 protein_coding synonymous_variant LOW 1194A>C Gly398Gly
M0045680 PGKONOMK_00008 5733 3 Skin 0.50 protein_coding synonymous_variant LOW 1146G>A Thr382Thr
M0045681 PGKONOMK_00008 5799 3 Skin 0.50 protein_coding synonymous_variant LOW 1080A>G Ser360Ser
M0045682 PGKONOMK_00008 5907 3 Skin 0.50 protein_coding synonymous_variant LOW 972T>C Val324Val
M0045683 PGKONOMK_00008 5940 3 Skin 0.50 protein_coding synonymous_variant LOW 939G>A Gly313Gly
M0045684 PGKONOMK_00008 6096 3 Skin 0.50 protein_coding synonymous_variant LOW 783A>G Leu261Leu
M0045685 PGKONOMK_00009 7006 3 Skin 0.50 protein_coding synonymous_variant LOW 1068T>C Ala356Ala
M0045686 PGKONOMK_00009 7303 3 Skin 0.50 protein_coding synonymous_variant LOW 771A>G Leu257Leu
M0045687 PGKONOMK_00009 7456 3 Skin 0.50 protein_coding synonymous_variant LOW 618G>C Val206Val
M0045688 PGKONOMK_00009 7525 3 Skin 0.50 protein_coding synonymous_variant LOW 549T>C Ala183Ala
M0045689 PGKONOMK_00009 7600 3 Skin 0.50 protein_coding synonymous_variant LOW 474C>T Asp158Asp
M0045690 PGKONOMK_00009 7623 3 Skin 0.50 protein_coding synonymous_variant LOW 451T>C Leu151Leu
M0045691 PGKONOMK_00010 8337 3 Skin 0.50 protein_coding synonymous_variant LOW 93A>G Leu31Leu
M0045692 PGKONOMK_00010 8925 3 Skin 0.50 protein_coding synonymous_variant LOW 681T>C Arg227Arg
M0045693 PGKONOMK_00010 9063 3 Skin 0.50 protein_coding missense_variant MODERATE 819A>C Lys273Asn
M0045694 PGKONOMK_00010 9196 3 Skin 0.50 protein_coding synonymous_variant LOW 952C>T Leu318Leu
M0045695 PGKONOMK_00010 9249 3 Skin 0.50 protein_coding synonymous_variant LOW 1005A>C Arg335Arg
M0045696 PGKONOMK_00010 9267 3 Skin 0.50 protein_coding synonymous_variant LOW 1023T>C Leu341Leu
M0045697 PGKONOMK_00010 9730 3 Skin 0.50 protein_coding missense_variant MODERATE 1486A>G Lys496Glu
M0045698 PGKONOMK_00010 10239 3 Skin 0.50 protein_coding synonymous_variant LOW 1995A>G Leu665Leu
M0045699 PGKONOMK_00010 10421 3 Skin 0.50 protein_coding missense_variant MODERATE 2177G>A Arg726Gln
M0045700 PGKONOMK_00010 10479 3 Skin 0.50 protein_coding synonymous_variant LOW 2235G>T Leu745Leu
M0045701 PGKONOMK_00010 10533 3 Skin 0.50 protein_coding synonymous_variant LOW 2289A>G Leu763Leu
M0045702 PGKONOMK_00010 10534 3 Skin 0.50 protein_coding missense_variant MODERATE 2290C>A Gln764Lys
M0045703 PGKONOMK_00010 10536 3 Skin 0.50 protein_coding missense_variant MODERATE 2292G>T Gln764His
M0045704 PGKONOMK_00010 10541 3 Skin 0.50 protein_coding splice_region_variant&stop_retained_variant LOW 2297A>G Ter766Ter
M0045705 PGKONOMK_00008 10544 3 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -3666T>C None
M0045706 PGKONOMK_00008 10559 3 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -3681G>A None
M0045707 PGKONOMK_00008 10564 3 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -3686T>A None
M0045708 PGKONOMK_00008 10569 3 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -3691G>A None
M0045709 PGKONOMK_00008 10570 3 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -3692T>C None
M0045710 PGKONOMK_00008 11156 3 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -4278A>C None
M0045711 PGKONOMK_00012 11569 3 Skin 0.50 protein_coding synonymous_variant LOW 381C>T Phe127Phe
M0045712 PGKONOMK_00012 11590 3 Skin 0.50 protein_coding synonymous_variant LOW 402T>C Asn134Asn
M0045713 PGKONOMK_00012 11614 3 Skin 0.50 protein_coding synonymous_variant LOW 426C>T Val142Val
M0045714 PGKONOMK_00012 12106 3 Skin 0.50 protein_coding synonymous_variant LOW 918T>C Thr306Thr
M0045715 PGKONOMK_00012 12439 3 Skin 0.50 protein_coding synonymous_variant LOW 1251G>T Pro417Pro
M0045716 PGKONOMK_00012 12466 3 Skin 0.50 protein_coding synonymous_variant LOW 1278T>A Arg426Arg
M0045717 PGKONOMK_00012 12469 3 Skin 0.50 protein_coding synonymous_variant LOW 1281A>G Leu427Leu
M0045718 PGKONOMK_00012 12475 3 Skin 0.50 protein_coding synonymous_variant LOW 1287T>C Asp429Asp
M0045719 PGKONOMK_00012 12614 3 Skin 0.50 protein_coding missense_variant MODERATE 1426A>G Ile476Val
M0045720 PGKONOMK_00013 12862 3 Skin 0.50 protein_coding synonymous_variant LOW 31T>C Leu11Leu
M0045721 PGKONOMK_00013 12951 3 Skin 0.50 protein_coding synonymous_variant LOW 120A>G Leu40Leu






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
PGKONOMK_00015 Arsenic (As) 91.4 6.6e-126 1 232 1.0000 1.0000 experiment
PGKONOMK_00016 Arsenic (As) 88.8 2.9e-44 1 89 0.8396 0.7607 experiment
PGKONOMK_00017 Arsenic (As) 90.9 4.8e-215 1 429 1.0000 1.0000 experiment
PGKONOMK_00018 Arsenic (As), Antimony (Sb) 83.7 4.1e-70 1 141 1.0000 1.0000 experiment
PGKONOMK_00015 Arsenic (As) 99.1 9.5e-134 1 232 1.0000 1.0000 prediction
PGKONOMK_00016 Arsenic (As) 91.5 4.1e-52 1 106 1.0000 1.0000 prediction
PGKONOMK_00017 Arsenic (As), Antimony (Sb) 98.6 2.6e-230 1 429 1.0000 1.0000 prediction
PGKONOMK_00018 Arsenic (As) 86.5 1.1e-68 1 141 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
PGKONOMK_00003 PHI:7660 pspD 79.2 1.6e-26 1 72 1.0000 1.0000 rodents salmonellosis phage-shock protein reduced virulence
PGKONOMK_00005 PHI:7658 pspB 81.1 2.8e-29 1 74 1.0000 1.0000 rodents salmonellosis phage-shock protein reduced virulence
PGKONOMK_00006 PHI:7657 pspA 91.9 6.3e-101 1 222 1.0000 1.0000 rodents salmonellosis phage-shock protein reduced virulence






        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
PGKONOMK_00010 QTK90621.1|GH0 99.5 0 1 765 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
PGKONOMK_00006 9.B.100.1.1 91.9 1.4e-100 1 222 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.100 The Phage Shock Protein (Psp) Family
PGKONOMK_00012 3.A.1.5.5 85.4 3e-277 1 548 1.0000 2.0485 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
PGKONOMK_00013 3.A.1.5.5 90.3 4.9e-163 1 321 1.0000 1.1978 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
PGKONOMK_00017 3.A.4.1.1 88.3 1.7e-211 1 429 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family