Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2088
  Reference Plasmid   1111525849740170_bin.34__k141_115987
  Reference Plasmid Size   48903
  Reference Plasmid GC Content   0.39
  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
M0024369 LNICLLLP_00014 12994 3 Skin 0.33 protein_coding synonymous_variant LOW 747T>A Gly249Gly
M0024370 LNICLLLP_00014 13705 4 Skin 0.44 protein_coding synonymous_variant LOW 36T>C Ser12Ser
M0024371 LNICLLLP_00011 13787 4 Skin 0.44 protein_coding upstream_gene_variant MODIFIER -4193A>G None
M0024372 LNICLLLP_00015 13904 3 Skin 0.33 protein_coding synonymous_variant LOW 1254T>A Pro418Pro
M0024373 LNICLLLP_00027 26325 4 Skin 0.44 protein_coding synonymous_variant LOW 30A>C Val10Val
M0024374 LNICLLLP_00029 27685 4 Skin 0.44 protein_coding synonymous_variant LOW 90A>G Lys30Lys
M0024375 LNICLLLP_00030 28350 3 Skin 0.33 protein_coding synonymous_variant LOW 468C>A Leu156Leu
M0024376 LNICLLLP_00030 28482 3 Skin 0.33 protein_coding synonymous_variant LOW 600C>T His200His
M0024377 LNICLLLP_00030 28485 3 Skin 0.33 protein_coding synonymous_variant LOW 603T>G Ala201Ala
M0024378 LNICLLLP_00030 28594 4 Skin 0.44 protein_coding missense_variant MODERATE 712G>C Ala238Pro
M0024379 LNICLLLP_00030 28662 3 Skin 0.33 protein_coding synonymous_variant LOW 780G>A Lys260Lys
M0024380 LNICLLLP_00024 28677 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -4888T>C None
M0024381 LNICLLLP_00024 28683 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -4894A>G None
M0024382 LNICLLLP_00024 28688 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -4899T>C None
M0024383 LNICLLLP_00012 10288 3 Skin 0.33 protein_coding synonymous_variant LOW 555T>C His185His
M0024384 LNICLLLP_00010 11093 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -3267T>C None
M0024385 LNICLLLP_00014 18725 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -4985A>T None
M0024386 LNICLLLP_00022 21199 3 Skin 0.33 protein_coding missense_variant MODERATE 632A>G Lys211Arg
M0024387 LNICLLLP_00022 21208 3 Skin 0.33 protein_coding missense_variant MODERATE 623C>A Pro208His
M0024388 LNICLLLP_00022 21609 3 Skin 0.33 protein_coding synonymous_variant LOW 222A>G Glu74Glu
M0024389 LNICLLLP_00022 21615 3 Skin 0.33 protein_coding synonymous_variant LOW 216T>A Pro72Pro
M0024390 LNICLLLP_00024 22485 3 Skin 0.33 protein_coding synonymous_variant LOW 1305G>A Gln435Gln
M0024391 LNICLLLP_00024 22788 3 Skin 0.33 protein_coding synonymous_variant LOW 1002C>T Ser334Ser
M0024392 LNICLLLP_00024 22863 3 Skin 0.33 protein_coding synonymous_variant LOW 927A>C Arg309Arg
M0024393 LNICLLLP_00024 23163 3 Skin 0.33 protein_coding synonymous_variant LOW 627G>A Glu209Glu
M0024394 LNICLLLP_00024 23214 3 Skin 0.33 protein_coding synonymous_variant LOW 576A>G Gln192Gln
M0024395 LNICLLLP_00024 23241 3 Skin 0.33 protein_coding synonymous_variant LOW 549T>C Thr183Thr
M0024396 LNICLLLP_00024 23264 3 Skin 0.33 protein_coding missense_variant MODERATE 526A>G Lys176Glu
M0024397 LNICLLLP_00024 23271 3 Skin 0.33 protein_coding synonymous_variant LOW 519C>A Pro173Pro
M0024398 LNICLLLP_00024 23391 3 Skin 0.33 protein_coding synonymous_variant LOW 399C>T Asp133Asp
M0024399 LNICLLLP_00024 23415 3 Skin 0.33 protein_coding synonymous_variant LOW 375A>C Ser125Ser
M0024400 LNICLLLP_00024 23610 3 Skin 0.33 protein_coding synonymous_variant LOW 180T>C Ser60Ser
M0024401 LNICLLLP_00025 24063 3 Skin 0.33 protein_coding synonymous_variant LOW 730T>C Leu244Leu
M0024402 LNICLLLP_00025 24067 3 Skin 0.33 protein_coding synonymous_variant LOW 726G>A Lys242Lys
M0024403 LNICLLLP_00025 24106 3 Skin 0.33 protein_coding synonymous_variant LOW 687T>C Phe229Phe
M0024404 LNICLLLP_00025 24462 4 Skin 0.44 protein_coding missense_variant MODERATE 331A>C Thr111Pro
M0024405 LNICLLLP_00020 24923 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -4952T>C None
M0024406 LNICLLLP_00026 25127 3 Skin 0.33 protein_coding synonymous_variant LOW 100T>C Leu34Leu
M0024407 LNICLLLP_00027 25382 4 Skin 0.44 protein_coding synonymous_variant LOW 973C>T Leu325Leu
M0024408 LNICLLLP_00027 25565 3 Skin 0.33 protein_coding missense_variant MODERATE 790T>G Ser264Ala
M0024409 LNICLLLP_00027 25731 3 Skin 0.33 protein_coding synonymous_variant LOW 624T>C Gly208Gly
M0024410 LNICLLLP_00027 25794 3 Skin 0.33 protein_coding synonymous_variant LOW 561G>A Gly187Gly
M0024411 LNICLLLP_00027 26031 3 Skin 0.33 protein_coding synonymous_variant LOW 324A>G Ala108Ala
M0024412 LNICLLLP_00027 26079 3 Skin 0.33 protein_coding synonymous_variant LOW 276C>T Arg92Arg
M0024413 LNICLLLP_00027 26202 3 Skin 0.33 protein_coding synonymous_variant LOW 153C>T Gly51Gly
M0024414 LNICLLLP_00027 26234 3 Skin 0.33 protein_coding missense_variant MODERATE 121T>C Phe41Leu
M0024415 LNICLLLP_00028 26696 4 Skin 0.44 protein_coding synonymous_variant LOW 231A>G Glu77Glu
M0024416 LNICLLLP_00028 26855 3 Skin 0.33 protein_coding synonymous_variant LOW 390G>A Glu130Glu
M0024417 LNICLLLP_00028 27287 3 Skin 0.33 protein_coding synonymous_variant LOW 822T>C Ala274Ala
M0024418 LNICLLLP_00028 27385 3 Skin 0.33 protein_coding missense_variant MODERATE 920C>G Ala307Gly
M0024419 LNICLLLP_00024 27543 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -3754T>C None
M0024420 LNICLLLP_00030 28021 3 Skin 0.33 protein_coding missense_variant MODERATE 139T>C Tyr47His
M0024421 LNICLLLP_00031 29215 3 Skin 0.33 protein_coding synonymous_variant LOW 285C>T Ala95Ala
M0024422 LNICLLLP_00031 29590 3 Skin 0.33 protein_coding synonymous_variant LOW 660T>C Gly220Gly
M0024423 LNICLLLP_00031 29602 3 Skin 0.33 protein_coding synonymous_variant LOW 672A>G Glu224Glu
M0024424 LNICLLLP_00031 29659 3 Skin 0.33 protein_coding synonymous_variant LOW 729T>C Asn243Asn
M0024425 LNICLLLP_00031 29677 3 Skin 0.33 protein_coding synonymous_variant LOW 747T>C Tyr249Tyr
M0024426 LNICLLLP_00031 29734 3 Skin 0.33 protein_coding synonymous_variant LOW 804G>A Leu268Leu
M0024427 LNICLLLP_00031 29834 3 Skin 0.33 protein_coding synonymous_variant LOW 904T>C Leu302Leu
M0024428 LNICLLLP_00031 30013 4 Skin 0.44 protein_coding synonymous_variant LOW 1083G>A Ala361Ala
M0024429 LNICLLLP_00031 30592 3 Skin 0.33 protein_coding synonymous_variant LOW 1662T>C Thr554Thr
M0024430 LNICLLLP_00031 30694 3 Skin 0.33 protein_coding synonymous_variant LOW 1764C>T Asp588Asp
M0024431 LNICLLLP_00031 30769 3 Skin 0.33 protein_coding synonymous_variant LOW 1839T>G Leu613Leu
M0024432 LNICLLLP_00021 20314 3 Skin 0.33 protein_coding synonymous_variant LOW 483C>T Gly161Gly
M0024433 LNICLLLP_00024 23109 3 Skin 0.33 protein_coding synonymous_variant LOW 681C>T Ala227Ala






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






        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
LNICLLLP_00014 1.B.25.1.38 78.5 1.2e-196 1 417 1.0000 0.9928 1 Channels/Pores 1.B β-Barrel Porins 1.B.25 The Outer Membrane Porin (Opr) Family
LNICLLLP_00020 2.A.46.1.1 80.9 2.6e-177 1 392 0.9679 0.9975 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.46 The Benzoate:H+ Symporter (BenE) Family