Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3093
  Reference Plasmid   MET0114_bin.4__k81_3932
  Reference Plasmid Size   87420
  Reference Plasmid GC Content   0.33
  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
M0074469 KFKDIIAG_00041 53911 5 Skin 0.29 protein_coding missense_variant MODERATE 928G>C Glu310Gln
M0074470 KFKDIIAG_00037 48087 3 Skin 0.18 protein_coding synonymous_variant LOW 306T>C Val102Val
M0074471 KFKDIIAG_00018 20337 3 Skin 0.18 protein_coding missense_variant MODERATE 1525G>A Val509Ile
M0074472 KFKDIIAG_00018 20350 3 Skin 0.18 protein_coding synonymous_variant LOW 1512C>T Val504Val
M0074473 KFKDIIAG_00018 20353 3 Skin 0.18 protein_coding synonymous_variant LOW 1509A>G Gln503Gln
M0074474 KFKDIIAG_00018 20356 3 Skin 0.18 protein_coding synonymous_variant LOW 1506G>A Thr502Thr
M0074475 KFKDIIAG_00018 20374 3 Skin 0.18 protein_coding synonymous_variant LOW 1488A>T Thr496Thr
M0074476 KFKDIIAG_00018 20377 3 Skin 0.18 protein_coding missense_variant MODERATE 1485A>T Lys495Asn
M0074477 KFKDIIAG_00018 20386 3 Skin 0.18 protein_coding synonymous_variant LOW 1476T>C His492His
M0074478 KFKDIIAG_00018 20395 3 Skin 0.18 protein_coding synonymous_variant LOW 1467C>G Val489Val
M0074479 KFKDIIAG_00018 20401 3 Skin 0.18 protein_coding synonymous_variant LOW 1461T>A Val487Val
M0074480 KFKDIIAG_00018 20404 3 Skin 0.18 protein_coding synonymous_variant LOW 1458C>T Val486Val
M0074481 KFKDIIAG_00018 20417 3 Skin 0.18 protein_coding missense_variant MODERATE 1445A>C Asn482Thr
M0074482 KFKDIIAG_00018 20419 3 Skin 0.18 protein_coding synonymous_variant LOW 1443A>T Ile481Ile
M0074483 KFKDIIAG_00018 20425 3 Skin 0.18 protein_coding synonymous_variant LOW 1437T>C Gly479Gly
M0074484 KFKDIIAG_00018 20481 3 Skin 0.18 protein_coding missense_variant MODERATE 1381C>G Gln461Glu
M0074485 KFKDIIAG_00018 20484 3 Skin 0.18 protein_coding missense_variant MODERATE 1378G>A Asp460Asn
M0074486 KFKDIIAG_00018 20485 3 Skin 0.18 protein_coding synonymous_variant LOW 1377T>G Thr459Thr
M0074487 KFKDIIAG_00018 20500 3 Skin 0.18 protein_coding synonymous_variant LOW 1362T>C Asn454Asn
M0074488 KFKDIIAG_00018 20518 3 Skin 0.18 protein_coding synonymous_variant LOW 1344A>G Ala448Ala
M0074489 KFKDIIAG_00018 20683 3 Skin 0.18 protein_coding synonymous_variant LOW 1179G>A Thr393Thr
M0074490 KFKDIIAG_00018 20698 3 Skin 0.18 protein_coding synonymous_variant LOW 1164T>C Asn388Asn
M0074491 KFKDIIAG_00018 20758 3 Skin 0.18 protein_coding synonymous_variant LOW 1104G>A Lys368Lys
M0074492 KFKDIIAG_00018 20767 3 Skin 0.18 protein_coding synonymous_variant LOW 1095A>T Gly365Gly
M0074493 KFKDIIAG_00018 20779 3 Skin 0.18 protein_coding synonymous_variant LOW 1083G>A Ser361Ser
M0074494 KFKDIIAG_00018 20802 3 Skin 0.18 protein_coding missense_variant MODERATE 1060A>C Lys354Gln
M0074495 KFKDIIAG_00018 20806 3 Skin 0.18 protein_coding synonymous_variant LOW 1056T>C Asn352Asn
M0074496 KFKDIIAG_00018 20871 3 Skin 0.18 protein_coding synonymous_variant LOW 991A>C Arg331Arg
M0074497 KFKDIIAG_00018 20883 3 Skin 0.18 protein_coding synonymous_variant LOW 979C>T Leu327Leu
M0074498 KFKDIIAG_00018 20884 3 Skin 0.18 protein_coding synonymous_variant LOW 978A>T Pro326Pro
M0074499 KFKDIIAG_00018 20932 3 Skin 0.18 protein_coding synonymous_variant LOW 930A>G Thr310Thr
M0074500 KFKDIIAG_00018 21010 3 Skin 0.18 protein_coding synonymous_variant LOW 852T>C Asp284Asp
M0074501 KFKDIIAG_00018 21034 3 Skin 0.18 protein_coding synonymous_variant LOW 828G>A Ser276Ser
M0074502 KFKDIIAG_00018 21043 3 Skin 0.18 protein_coding synonymous_variant LOW 819C>T Tyr273Tyr
M0074503 KFKDIIAG_00018 21069 3 Skin 0.18 protein_coding missense_variant MODERATE 793G>T Val265Leu
M0074504 KFKDIIAG_00018 21253 3 Skin 0.18 protein_coding synonymous_variant LOW 609T>G Pro203Pro
M0074505 KFKDIIAG_00018 21265 3 Skin 0.18 protein_coding synonymous_variant LOW 597A>T Ala199Ala
M0074506 KFKDIIAG_00018 21268 3 Skin 0.18 protein_coding synonymous_variant LOW 594T>A Leu198Leu
M0074507 KFKDIIAG_00018 21270 3 Skin 0.18 protein_coding missense_variant MODERATE 592C>T Leu198Phe
M0074508 KFKDIIAG_00018 21328 3 Skin 0.18 protein_coding synonymous_variant LOW 534A>G Thr178Thr
M0074509 KFKDIIAG_00018 21366 3 Skin 0.18 protein_coding missense_variant MODERATE 496C>T Pro166Ser
M0074510 KFKDIIAG_00018 21388 3 Skin 0.18 protein_coding synonymous_variant LOW 474G>A Ala158Ala
M0074511 KFKDIIAG_00018 21486 3 Skin 0.18 protein_coding missense_variant MODERATE 376G>A Asp126Asn
M0074512 KFKDIIAG_00018 21500 3 Skin 0.18 protein_coding missense_variant MODERATE 362T>C Leu121Pro
M0074513 KFKDIIAG_00018 21542 3 Skin 0.18 protein_coding missense_variant MODERATE 320C>A Thr107Asn
M0074514 KFKDIIAG_00018 21573 3 Skin 0.18 protein_coding missense_variant MODERATE 289G>A Ala97Thr
M0074515 KFKDIIAG_00018 21631 3 Skin 0.18 protein_coding synonymous_variant LOW 231G>T Thr77Thr
M0074516 KFKDIIAG_00015 22015 3 Skin 0.18 protein_coding upstream_gene_variant MODIFIER -4483G>A None
M0074517 KFKDIIAG_00015 22030 3 Skin 0.18 protein_coding upstream_gene_variant MODIFIER -4498C>T None
M0074518 KFKDIIAG_00015 22036 3 Skin 0.18 protein_coding upstream_gene_variant MODIFIER -4504C>A None
M0074519 KFKDIIAG_00015 22089 3 Skin 0.18 protein_coding upstream_gene_variant MODIFIER -4557G>T None
M0074520 KFKDIIAG_00019 22397 3 Skin 0.18 protein_coding synonymous_variant LOW 519G>A Gly173Gly
M0074521 KFKDIIAG_00019 22414 3 Skin 0.18 protein_coding missense_variant MODERATE 502A>C Ile168Leu
M0074522 KFKDIIAG_00019 22418 3 Skin 0.18 protein_coding synonymous_variant LOW 498T>C Cys166Cys
M0074523 KFKDIIAG_00019 22423 3 Skin 0.18 protein_coding missense_variant MODERATE 493T>A Leu165Ile
M0074524 KFKDIIAG_00019 22430 3 Skin 0.18 protein_coding synonymous_variant LOW 486T>C Ile162Ile
M0074525 KFKDIIAG_00019 22613 3 Skin 0.18 protein_coding synonymous_variant LOW 303T>C Asn101Asn
M0074526 KFKDIIAG_00020 23153 3 Skin 0.18 protein_coding missense_variant MODERATE 803C>T Ala268Val
M0074527 KFKDIIAG_00020 23575 3 Skin 0.18 protein_coding synonymous_variant LOW 381C>T Thr127Thr
M0074528 KFKDIIAG_00020 23582 3 Skin 0.18 protein_coding missense_variant MODERATE 374C>A Thr125Asn
M0074529 KFKDIIAG_00020 23586 3 Skin 0.18 protein_coding missense_variant MODERATE 370A>G Asn124Asp
M0074530 KFKDIIAG_00020 23587 3 Skin 0.18 protein_coding synonymous_variant LOW 369C>T Phe123Phe
M0074531 KFKDIIAG_00020 23800 3 Skin 0.18 protein_coding synonymous_variant LOW 156C>T Gly52Gly
M0074532 KFKDIIAG_00020 23868 3 Skin 0.18 protein_coding missense_variant MODERATE 88C>T Arg30Cys
M0074533 KFKDIIAG_00020 23906 3 Skin 0.18 protein_coding missense_variant MODERATE 50A>C Lys17Thr
M0074534 KFKDIIAG_00021 24097 3 Skin 0.18 protein_coding missense_variant MODERATE 1306T>A Ser436Thr
M0074535 KFKDIIAG_00021 24197 3 Skin 0.18 protein_coding synonymous_variant LOW 1206C>T Gly402Gly
M0074536 KFKDIIAG_00021 24481 3 Skin 0.18 protein_coding synonymous_variant LOW 922T>C Leu308Leu
M0074537 KFKDIIAG_00021 24744 3 Skin 0.18 protein_coding missense_variant MODERATE 659T>G Ile220Ser
M0074538 KFKDIIAG_00022 25762 3 Skin 0.18 protein_coding missense_variant MODERATE 742A>G Lys248Glu
M0074539 KFKDIIAG_00022 25855 3 Skin 0.18 protein_coding missense_variant MODERATE 649G>A Val217Ile
M0074540 KFKDIIAG_00022 26071 3 Skin 0.18 protein_coding synonymous_variant LOW 433C>T Leu145Leu
M0074541 KFKDIIAG_00022 26252 3 Skin 0.18 protein_coding synonymous_variant LOW 252A>G Gly84Gly
M0074542 KFKDIIAG_00022 26303 3 Skin 0.18 protein_coding synonymous_variant LOW 201T>A Ala67Ala
M0074543 KFKDIIAG_00018 26518 3 Skin 0.18 protein_coding upstream_gene_variant MODIFIER -4657A>G None
M0074544 KFKDIIAG_00023 26556 3 Skin 0.18 protein_coding synonymous_variant LOW 1216T>C Leu406Leu
M0074545 KFKDIIAG_00023 26598 3 Skin 0.18 protein_coding synonymous_variant LOW 1174T>C Leu392Leu
M0074546 KFKDIIAG_00023 26626 3 Skin 0.18 protein_coding synonymous_variant LOW 1146T>A Ile382Ile
M0074547 KFKDIIAG_00023 27160 3 Skin 0.18 protein_coding synonymous_variant LOW 612C>T Ile204Ile
M0074548 KFKDIIAG_00023 27450 3 Skin 0.18 protein_coding missense_variant MODERATE 322G>A Ala108Thr
M0074549 KFKDIIAG_00020 27941 3 Skin 0.18 protein_coding upstream_gene_variant MODIFIER -3986C>T None
M0074550 KFKDIIAG_00024 27959 3 Skin 0.18 protein_coding missense_variant MODERATE 157A>C Ile53Leu
M0074551 KFKDIIAG_00024 27965 3 Skin 0.18 protein_coding missense_variant MODERATE 151A>G Met51Val
M0074552 KFKDIIAG_00024 27973 3 Skin 0.18 protein_coding missense_variant MODERATE 143A>G His48Arg
M0074553 KFKDIIAG_00024 28001 3 Skin 0.18 protein_coding missense_variant MODERATE 115A>T Ile39Phe
M0074554 KFKDIIAG_00024 28071 3 Skin 0.18 protein_coding synonymous_variant LOW 45T>A Thr15Thr
M0074555 KFKDIIAG_00024 28090 3 Skin 0.18 protein_coding stop_gained HIGH 26T>A Leu9*
M0074556 KFKDIIAG_00025 28274 3 Skin 0.18 protein_coding synonymous_variant LOW 294C>T Val98Val
M0074557 KFKDIIAG_00025 28391 3 Skin 0.18 protein_coding synonymous_variant LOW 177G>A Glu59Glu
M0074558 KFKDIIAG_00025 28421 3 Skin 0.18 protein_coding synonymous_variant LOW 147A>T Leu49Leu
M0074559 KFKDIIAG_00025 28427 3 Skin 0.18 protein_coding synonymous_variant LOW 141G>A Lys47Lys






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
KFKDIIAG_00018 VFG001290 Clumping factor 96.6 0 1 877 1.0 0.9669 Adherence Clumping factor B, adhesin experiment
KFKDIIAG_00026 VFG001314 Aureolysin 99.8 1.3e-291 1 509 1.0 1 Exoenzyme zinc metalloproteinase aureolysin experiment
KFKDIIAG_00054 VFG001284 Intercellular adhesion proteins 100 2.4e-102 1 186 1.0 1 Biofilm ica operon transcriptional regulator IcaR experiment
KFKDIIAG_00055 VFG001285 Intercellular adhesion proteins 99.8 7.2e-237 1 412 1.0 1 Biofilm N-acetylglucosaminyltransferase, involved in polysaccharide intercellular adhesin(PIA) synthesis experiment
KFKDIIAG_00056 VFG001286 Intercellular adhesion proteins 100 1.9e-50 1 101 1.0 1 Biofilm intercellular adhesion protein D, involved in polysaccharide intercellular adhesin(PIA) synthesis experiment
KFKDIIAG_00059 VFG001288 Intercellular adhesion proteins 100 1.9e-190 1 350 1.0 1 Biofilm intercellular adhesion protein C, involved in polysaccharide intercellular adhesin(PIA) synthesis experiment
KFKDIIAG_00060 VFG004773 Lipase 99.4 0 2 681 0.9985 1 Exoenzyme triacylglycerol lipase precursor experiment
KFKDIIAG_00018 VFG001290 Clumping factor 96.6 0 1 877 1.0 0.9669 Adherence Clumping factor B, adhesin prediction
KFKDIIAG_00026 VFG001314 Aureolysin 99.8 9.5e-291 1 509 1.0 1 Exoenzyme zinc metalloproteinase aureolysin prediction
KFKDIIAG_00043 VFG043589 SraP 91.5 0 1 1639 0.9808 0.7249 Adherence serine-rich repeat glycoprotein adhesin SasA prediction
KFKDIIAG_00054 VFG001284 Intercellular adhesion proteins 100 1.8e-101 1 186 1.0 1 Biofilm ica operon transcriptional regulator IcaR prediction
KFKDIIAG_00055 VFG004543 Intercellular adhesion proteins 100 2.4e-236 1 412 1.0 1 Biofilm N-acetylglucosaminyltransferase, involved in polysaccharide intercellular adhesin(PIA) synthesis prediction
KFKDIIAG_00056 VFG001286 Intercellular adhesion proteins 100 1.4e-49 1 101 1.0 1 Biofilm intercellular adhesion protein D, involved in polysaccharide intercellular adhesin(PIA) synthesis prediction
KFKDIIAG_00059 VFG001288 Intercellular adhesion proteins 100 1.4e-189 1 350 1.0 1 Biofilm intercellular adhesion protein C, involved in polysaccharide intercellular adhesin(PIA) synthesis prediction
KFKDIIAG_00060 VFG004773 Lipase 99.4 0 2 681 0.9985 1 Exoenzyme triacylglycerol lipase precursor prediction







        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
KFKDIIAG_00018 PHI:4571 clfB 88 0 2 877 0.9989 0.9925 rodents community-acquired infection; nosocomial infection fibrinogen-binding protein reduced virulence
KFKDIIAG_00023 PHI:10470 arcA 100 4.4e-241 1 411 1.0000 1.0000 rodents skin infection arginine deiminase unaffected pathogenicity
KFKDIIAG_00026 PHI:11228 aur 93.5 2.3e-276 1 509 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease zinc metalloproteinase aureolysin increased virulence (hypervirulence)
KFKDIIAG_00027 PHI:6865 IsaB 99.4 1.2e-94 1 175 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease immunodominant surface antigen reduced virulence
KFKDIIAG_00052 PHI:7004 CapB2 99.1 2e-126 1 230 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease tyrosine kinase reduced virulence
KFKDIIAG_00054 PHI:12234 icaR 100 6.2e-102 1 186 1.0000 1.0000 moths endocarditis; osteomyelitis; pneumonia; septic shock biofilm operon icaADBC HTH-type negative transcriptional regulator reduced virulence
KFKDIIAG_00055 PHI:9883 icaA 100 8.6e-237 1 412 1.0000 1.0000 rodents abscess; sepsis poly-beta-1,6-N-acetyl-D-glucosamine synthase unaffected pathogenicity
KFKDIIAG_00056 PHI:9886 icaD 100 5.1e-50 1 101 1.0000 1.0000 rodents abscess; sepsis poly-beta-1,6-N-acetyl-D-glucosamine synthesis protein unaffected pathogenicity
KFKDIIAG_00057 PHI:9884 icaB 88.5 1.9e-73 8 163 0.9341 0.9862 rodents abscess; sepsis poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase unaffected pathogenicity
KFKDIIAG_00058 PHI:9884 icaB 99.2 1.8e-71 1 130 1.0000 0.9862 rodents abscess; sepsis poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase unaffected pathogenicity
KFKDIIAG_00059 PHI:9885 icaC 100 5.1e-190 1 350 1.0000 1.0000 rodents abscess; sepsis probable poly-beta-1,6-N-acetyl-D-glucosamine export protein 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
KFKDIIAG_00033 QEP01088.1|GH73 100 0 1 619 1 1
KFKDIIAG_00036 QHG58119.1|GT8 100 0 1 452 1 1
KFKDIIAG_00037 AKK59756.1|GT4 100 0 1 502 1 1
KFKDIIAG_00055 QCJ19683.1|GT2 100 2.23e-278 1 412 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
KFKDIIAG_00055 4.D.1.1.2 79.1 3.2e-191 1 412 1.0000 1.0000 4 Group Translocators 4.D Polysaccharide Synthase/Exporters 4.D.1 The Putative Vectorial Glycosyl Polymerization (VGP) Family
KFKDIIAG_00059 9.B.97.1.7 100 1.1e-189 1 350 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.97 The Acyltransferase-3/Putative Acetyl-CoA Transporter (ATAT) Family