Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1539
  Reference Plasmid   1111525849479042_bin.21__k141_789772
  Reference Plasmid Size   3588
  Reference Plasmid GC Content   0.31
  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
M0006308 LEEGCGPK_00002 1666 7 Skin 0.47 protein_coding synonymous_variant LOW 594G>A Ser198Ser
M0006309 LEEGCGPK_00002 1852 6 Skin 0.40 protein_coding synonymous_variant LOW 408A>G Lys136Lys
M0006310 LEEGCGPK_00003 2341 3 Skin 0.20 protein_coding missense_variant MODERATE 221G>T Trp74Leu
M0006311 LEEGCGPK_00004 2842 5 Skin 0.33 protein_coding missense_variant MODERATE 733C>A Leu245Ile
M0006312 LEEGCGPK_00004 2864 9 Skin 0.60 protein_coding synonymous_variant LOW 711G>T Ser237Ser
M0006313 LEEGCGPK_00004 2923 10 Skin 0.67 protein_coding missense_variant MODERATE 652C>T Pro218Ser
M0006314 LEEGCGPK_00004 2954 10 Skin 0.67 protein_coding synonymous_variant LOW 621C>T Gly207Gly
M0006315 LEEGCGPK_00004 3248 10 Skin 0.67 protein_coding synonymous_variant LOW 327T>C Ile109Ile
M0006316 LEEGCGPK_00001 126 8 Skin 0.53 protein_coding downstream_gene_variant MODIFIER *210C>A None
M0006317 LEEGCGPK_00001 137 8 Skin 0.53 protein_coding downstream_gene_variant MODIFIER *199C>T None
M0006318 LEEGCGPK_00001 144 8 Skin 0.53 protein_coding downstream_gene_variant MODIFIER *192G>C None
M0006319 LEEGCGPK_00001 147 8 Skin 0.53 protein_coding downstream_gene_variant MODIFIER *189A>T None
M0006320 LEEGCGPK_00001 148 8 Skin 0.53 protein_coding downstream_gene_variant MODIFIER *188T>A None
M0006321 LEEGCGPK_00001 150 3 Skin 0.20 protein_coding downstream_gene_variant MODIFIER *186C>T None
M0006322 LEEGCGPK_00001 170 3 Skin 0.20 protein_coding downstream_gene_variant MODIFIER *166G>A None
M0006323 LEEGCGPK_00001 277 4 Skin 0.27 protein_coding downstream_gene_variant MODIFIER *59T>A None
M0006324 LEEGCGPK_00001 432 3 Skin 0.20 protein_coding synonymous_variant LOW 972C>A Val324Val
M0006325 LEEGCGPK_00001 441 3 Skin 0.20 protein_coding synonymous_variant LOW 963T>C Cys321Cys
M0006326 LEEGCGPK_00001 485 3 Skin 0.20 protein_coding missense_variant MODERATE 919A>C Ile307Leu
M0006327 LEEGCGPK_00001 496 3 Skin 0.20 protein_coding missense_variant MODERATE 908A>T Glu303Val
M0006328 LEEGCGPK_00001 622 3 Skin 0.20 protein_coding missense_variant MODERATE 782G>T Gly261Val
M0006329 LEEGCGPK_00001 681 3 Skin 0.20 protein_coding synonymous_variant LOW 723C>T Val241Val
M0006330 LEEGCGPK_00001 697 3 Skin 0.20 protein_coding missense_variant MODERATE 707G>A Ser236Asn
M0006331 LEEGCGPK_00001 702 3 Skin 0.20 protein_coding synonymous_variant LOW 702C>T Ser234Ser
M0006332 LEEGCGPK_00001 948 11 Skin 0.73 protein_coding synonymous_variant LOW 456A>G Leu152Leu
M0006333 LEEGCGPK_00001 973 4 Skin 0.27 protein_coding missense_variant MODERATE 431G>A Arg144Lys
M0006334 LEEGCGPK_00002 1516 4 Skin 0.27 protein_coding synonymous_variant LOW 744G>T Gly248Gly
M0006335 LEEGCGPK_00002 1522 4 Skin 0.27 protein_coding synonymous_variant LOW 738A>G Gln246Gln
M0006336 LEEGCGPK_00002 1558 3 Skin 0.20 protein_coding synonymous_variant LOW 702C>T Asp234Asp
M0006337 LEEGCGPK_00002 1592 4 Skin 0.27 protein_coding missense_variant MODERATE 668G>A Arg223His
M0006338 LEEGCGPK_00002 1604 3 Skin 0.20 protein_coding missense_variant MODERATE 656C>A Pro219Gln
M0006339 LEEGCGPK_00002 1612 4 Skin 0.27 protein_coding synonymous_variant LOW 648A>G Lys216Lys
M0006340 LEEGCGPK_00002 1614 4 Skin 0.27 protein_coding missense_variant MODERATE 646A>G Lys216Glu
M0006341 LEEGCGPK_00002 1659 4 Skin 0.27 protein_coding missense_variant MODERATE 601T>A Ser201Thr
M0006342 LEEGCGPK_00002 1759 5 Skin 0.33 protein_coding synonymous_variant LOW 501T>C Asp167Asp
M0006343 LEEGCGPK_00002 1812 4 Skin 0.27 protein_coding missense_variant MODERATE 448A>G Ile150Val
M0006344 LEEGCGPK_00002 1987 5 Skin 0.33 protein_coding synonymous_variant LOW 273C>T His91His
M0006345 LEEGCGPK_00003 2502 4 Skin 0.27 protein_coding synonymous_variant LOW 60G>A Arg20Arg
M0006346 LEEGCGPK_00003 2514 5 Skin 0.33 protein_coding synonymous_variant LOW 48A>G Leu16Leu
M0006347 LEEGCGPK_00004 2605 4 Skin 0.27 protein_coding missense_variant MODERATE 970G>A Ala324Thr
M0006348 LEEGCGPK_00004 2909 7 Skin 0.47 protein_coding synonymous_variant LOW 666T>C Thr222Thr
M0006349 LEEGCGPK_00004 3007 4 Skin 0.27 protein_coding missense_variant MODERATE 568G>A Val190Met
M0006350 LEEGCGPK_00004 3017 4 Skin 0.27 protein_coding synonymous_variant LOW 558C>T Cys186Cys
M0006351 LEEGCGPK_00004 3052 4 Skin 0.27 protein_coding missense_variant MODERATE 523G>C Asp175His
M0006352 LEEGCGPK_00004 3279 4 Skin 0.27 protein_coding missense_variant MODERATE 296G>T Gly99Val
M0006353 LEEGCGPK_00004 3368 7 Skin 0.47 protein_coding synonymous_variant LOW 207T>C Cys69Cys
M0006354 LEEGCGPK_00004 3422 4 Skin 0.27 protein_coding synonymous_variant LOW 153A>G Lys51Lys
M0006355 LEEGCGPK_00001 1127 3 Skin 0.20 protein_coding synonymous_variant LOW 277T>C Leu93Leu
M0006356 LEEGCGPK_00001 1128 3 Skin 0.20 protein_coding synonymous_variant LOW 276C>T Gly92Gly
M0006357 LEEGCGPK_00001 1350 5 Skin 0.33 protein_coding synonymous_variant LOW 54A>C Ile18Ile
M0006358 LEEGCGPK_00001 1214 7 Skin 0.47 protein_coding synonymous_variant LOW 190C>T Leu64Leu
M0006359 LEEGCGPK_00004 3080 3 Skin 0.20 protein_coding synonymous_variant LOW 495T>C Ile165Ile
M0006360 LEEGCGPK_00004 3182 4 Skin 0.27 protein_coding synonymous_variant LOW 393T>A Leu131Leu
M0006361 LEEGCGPK_00004 3476 4 Skin 0.27 protein_coding missense_variant MODERATE 99C>A Asp33Glu
M0006362 LEEGCGPK_00004 3008 3 Skin 0.20 protein_coding synonymous_variant LOW 567A>G Leu189Leu
M0006363 LEEGCGPK_00004 3020 3 Skin 0.20 protein_coding synonymous_variant LOW 555A>T Leu185Leu
M0006364 LEEGCGPK_00004 3023 3 Skin 0.20 protein_coding synonymous_variant LOW 552T>A Ala184Ala
M0006365 LEEGCGPK_00004 3026 3 Skin 0.20 protein_coding synonymous_variant LOW 549T>C Arg183Arg
M0006366 LEEGCGPK_00001 236 4 Skin 0.27 protein_coding downstream_gene_variant MODIFIER *100C>T None






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
LEEGCGPK_00001 VFG001288 Intercellular adhesion proteins 74.9 1.3e-146 1 350 0.9859 1 Biofilm intercellular adhesion protein C, involved in polysaccharide intercellular adhesin(PIA) synthesis experiment
LEEGCGPK_00004 VFG001285 Intercellular adhesion proteins 82.8 5.5e-169 6 349 0.9857 0.835 Biofilm N-acetylglucosaminyltransferase, involved in polysaccharide intercellular adhesin(PIA) synthesis experiment
LEEGCGPK_00001 VFG004513 Intercellular adhesion proteins 100 4.1e-192 1 355 1.0 1 Biofilm intercellular adhesion protein C, involved in polysaccharide intercellular adhesin(PIA) synthesis prediction
LEEGCGPK_00002 VFG004523 Intercellular adhesion proteins 100 8.3e-167 1 289 1.0 1 Biofilm N-deacetylase, involved in polysaccharide intercellular adhesin(PIA) synthesis prediction
LEEGCGPK_00003 VFG004533 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
LEEGCGPK_00004 VFG004542 Intercellular adhesion proteins 100 1.3e-198 6 349 0.9857 0.835 Biofilm N-acetylglucosaminyltransferase, involved in polysaccharide intercellular adhesin(PIA) synthesis 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
LEEGCGPK_00001 PHI:9885 icaC 74.9 3.5e-146 1 350 0.9859 1.0000 rodents abscess; sepsis probable poly-beta-1,6-N-acetyl-D-glucosamine export protein unaffected pathogenicity
LEEGCGPK_00004 PHI:9883 icaA 82.8 1.4e-168 6 349 0.9857 0.8350 rodents abscess; sepsis poly-beta-1,6-N-acetyl-D-glucosamine synthase 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
LEEGCGPK_00002 QRJ31245.1|CE4 100 1.6e-209 1 289 1 1
LEEGCGPK_00004 AVG08313.1|GT2 100 1.24e-247 6 349 0.9857 0.835





        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
LEEGCGPK_00001 9.B.97.1.7 74.9 7.9e-146 1 350 0.9859 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.97 The Acyltransferase-3/Putative Acetyl-CoA Transporter (ATAT) Family
LEEGCGPK_00004 4.D.1.1.2 100 1e-198 6 349 0.9857 0.8350 4 Group Translocators 4.D Polysaccharide Synthase/Exporters 4.D.1 The Putative Vectorial Glycosyl Polymerization (VGP) Family