Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C492
  Reference Plasmid   NZ_CP023732.1
  Reference Plasmid Size   93276
  Reference Plasmid GC Content   0.48
  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
M0167339 LPPIKEPL_00071 54410 3 Gut 0.75 protein_coding synonymous_variant LOW 699C>A Arg233Arg
M0167340 LPPIKEPL_00077 56589 3 Gut 0.75 protein_coding synonymous_variant LOW 186G>A Thr62Thr
M0167341 LPPIKEPL_00077 56721 3 Gut 0.75 protein_coding synonymous_variant LOW 318T>C Thr106Thr
M0167342 LPPIKEPL_00077 56724 3 Gut 0.75 protein_coding synonymous_variant LOW 321C>A Gly107Gly
M0167343 LPPIKEPL_00077 56750 3 Gut 0.75 protein_coding missense_variant MODERATE 347C>A Ala116Asp
M0167344 LPPIKEPL_00077 56775 3 Gut 0.75 protein_coding synonymous_variant LOW 372T>C Ser124Ser
M0167345 LPPIKEPL_00078 56797 3 Gut 0.75 protein_coding synonymous_variant LOW 9C>T Arg3Arg
M0167346 LPPIKEPL_00078 56858 3 Gut 0.75 protein_coding missense_variant MODERATE 70A>G Lys24Glu
M0167347 LPPIKEPL_00079 57025 3 Gut 0.75 protein_coding synonymous_variant LOW 30G>A Gln10Gln
M0167348 LPPIKEPL_00079 57472 3 Gut 0.75 protein_coding synonymous_variant LOW 477T>C Gly159Gly
M0167349 LPPIKEPL_00079 57893 3 Gut 0.75 protein_coding synonymous_variant LOW 898T>C Leu300Leu
M0167350 LPPIKEPL_00080 58211 3 Gut 0.75 protein_coding synonymous_variant LOW 84T>C Ile28Ile
M0167351 LPPIKEPL_00080 58412 3 Gut 0.75 protein_coding synonymous_variant LOW 285T>C Arg95Arg
M0167352 LPPIKEPL_00081 58686 3 Gut 0.75 protein_coding synonymous_variant LOW 21A>G Lys7Lys
M0167353 LPPIKEPL_00081 58809 3 Gut 0.75 protein_coding synonymous_variant LOW 144T>A Thr48Thr
M0167354 LPPIKEPL_00081 58873 3 Gut 0.75 protein_coding missense_variant MODERATE 208T>G Ser70Ala
M0167355 LPPIKEPL_00081 58886 3 Gut 0.75 protein_coding missense_variant MODERATE 221A>G His74Arg
M0167356 LPPIKEPL_00081 58899 3 Gut 0.75 protein_coding synonymous_variant LOW 234T>C His78His
M0167357 LPPIKEPL_00081 58904 3 Gut 0.75 protein_coding missense_variant MODERATE 239C>T Ala80Val
M0167358 LPPIKEPL_00081 58917 3 Gut 0.75 protein_coding synonymous_variant LOW 252G>T Ala84Ala
M0167359 LPPIKEPL_00081 58926 3 Gut 0.75 protein_coding synonymous_variant LOW 261G>A Gln87Gln
M0167360 LPPIKEPL_00081 58938 3 Gut 0.75 protein_coding synonymous_variant LOW 273C>T Ala91Ala
M0167361 LPPIKEPL_00081 58962 3 Gut 0.75 protein_coding synonymous_variant LOW 297T>C Asn99Asn
M0167362 LPPIKEPL_00081 58965 3 Gut 0.75 protein_coding synonymous_variant LOW 300G>T Ala100Ala
M0167363 LPPIKEPL_00081 58998 3 Gut 0.75 protein_coding synonymous_variant LOW 333A>T Ser111Ser
M0167364 LPPIKEPL_00081 59031 3 Gut 0.75 protein_coding synonymous_variant LOW 366G>T Arg122Arg
M0167365 LPPIKEPL_00081 59034 3 Gut 0.75 protein_coding synonymous_variant LOW 369T>C Thr123Thr
M0167366 LPPIKEPL_00081 59097 3 Gut 0.75 protein_coding synonymous_variant LOW 432G>T Ala144Ala
M0167367 LPPIKEPL_00081 59157 3 Gut 0.75 protein_coding synonymous_variant LOW 492T>G Arg164Arg
M0167368 LPPIKEPL_00081 59163 3 Gut 0.75 protein_coding synonymous_variant LOW 498A>G Gly166Gly
M0167369 LPPIKEPL_00081 59166 3 Gut 0.75 protein_coding synonymous_variant LOW 501T>C Ala167Ala
M0167370 LPPIKEPL_00081 59247 3 Gut 0.75 protein_coding synonymous_variant LOW 582C>T Arg194Arg
M0167371 LPPIKEPL_00081 59499 3 Gut 0.75 protein_coding synonymous_variant LOW 834G>A Ala278Ala
M0167372 LPPIKEPL_00081 59523 3 Gut 0.75 protein_coding synonymous_variant LOW 858A>C Gly286Gly
M0167373 LPPIKEPL_00081 59526 3 Gut 0.75 protein_coding synonymous_variant LOW 861A>G Gly287Gly
M0167374 LPPIKEPL_00081 59727 3 Gut 0.75 protein_coding synonymous_variant LOW 1062T>C Ile354Ile
M0167375 LPPIKEPL_00082 60386 3 Gut 0.75 protein_coding synonymous_variant LOW 528T>C Thr176Thr
M0167376 LPPIKEPL_00082 60422 3 Gut 0.75 protein_coding synonymous_variant LOW 564A>G Leu188Leu
M0167377 LPPIKEPL_00082 60464 3 Gut 0.75 protein_coding synonymous_variant LOW 606T>A Thr202Thr
M0167378 LPPIKEPL_00082 60626 3 Gut 0.75 protein_coding synonymous_variant LOW 768A>C Gly256Gly
M0167379 LPPIKEPL_00082 60683 3 Gut 0.75 protein_coding synonymous_variant LOW 825G>A Ala275Ala
M0167380 LPPIKEPL_00082 60798 3 Gut 0.75 protein_coding synonymous_variant LOW 940A>C Arg314Arg
M0167381 LPPIKEPL_00082 61049 3 Gut 0.75 protein_coding synonymous_variant LOW 1191G>A Lys397Lys
M0167382 LPPIKEPL_00082 61091 3 Gut 0.75 protein_coding synonymous_variant LOW 1233A>T Ser411Ser
M0167383 LPPIKEPL_00083 62914 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -695T>C None
M0167384 LPPIKEPL_00083 62952 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -733T>A None
M0167385 LPPIKEPL_00083 62954 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -735T>A None
M0167386 LPPIKEPL_00085 63232 3 Gut 0.75 protein_coding synonymous_variant LOW 97T>C Leu33Leu
M0167387 LPPIKEPL_00085 63272 3 Gut 0.75 protein_coding missense_variant MODERATE 137A>G His46Arg
M0167388 LPPIKEPL_00086 63694 3 Gut 0.75 protein_coding synonymous_variant LOW 330T>C Ser110Ser
M0167389 LPPIKEPL_00086 63877 3 Gut 0.75 protein_coding synonymous_variant LOW 513A>G Leu171Leu
M0167390 LPPIKEPL_00086 63985 3 Gut 0.75 protein_coding synonymous_variant LOW 621A>T Ala207Ala
M0167391 LPPIKEPL_00083 64874 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -2655A>T None
M0167392 LPPIKEPL_00083 64915 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -2696T>A None
M0167393 LPPIKEPL_00088 65212 3 Gut 0.75 protein_coding synonymous_variant LOW 207G>A Lys69Lys
M0167394 LPPIKEPL_00088 65243 3 Gut 0.75 protein_coding missense_variant MODERATE 238T>C Ser80Pro
M0167395 LPPIKEPL_00088 65248 3 Gut 0.75 protein_coding synonymous_variant LOW 243A>G Thr81Thr
M0167396 LPPIKEPL_00088 65332 3 Gut 0.75 protein_coding synonymous_variant LOW 327A>G Val109Val
M0167397 LPPIKEPL_00089 65815 3 Gut 0.75 protein_coding synonymous_variant LOW 60T>G Ala20Ala
M0167398 LPPIKEPL_00089 65836 3 Gut 0.75 protein_coding synonymous_variant LOW 81A>G Leu27Leu
M0167399 LPPIKEPL_00092 68429 3 Gut 0.75 protein_coding synonymous_variant LOW 57C>G Leu19Leu
M0167400 LPPIKEPL_00093 68855 3 Gut 0.75 protein_coding synonymous_variant LOW 6432G>A Glu2144Glu
M0167401 LPPIKEPL_00093 69083 3 Gut 0.75 protein_coding synonymous_variant LOW 6204T>C Gly2068Gly
M0167402 LPPIKEPL_00093 69232 3 Gut 0.75 protein_coding missense_variant MODERATE 6055T>G Ser2019Ala
M0167403 LPPIKEPL_00093 69233 3 Gut 0.75 protein_coding synonymous_variant LOW 6054T>C Val2018Val
M0167404 LPPIKEPL_00093 69257 3 Gut 0.75 protein_coding synonymous_variant LOW 6030C>G Arg2010Arg
M0167405 LPPIKEPL_00093 69284 3 Gut 0.75 protein_coding synonymous_variant LOW 6003T>A Ala2001Ala
M0167406 LPPIKEPL_00093 69295 3 Gut 0.75 protein_coding missense_variant MODERATE 5992T>G Ser1998Ala
M0167407 LPPIKEPL_00093 69299 3 Gut 0.75 protein_coding synonymous_variant LOW 5988A>G Lys1996Lys
M0167408 LPPIKEPL_00093 69395 3 Gut 0.75 protein_coding synonymous_variant LOW 5892T>C Ala1964Ala
M0167409 LPPIKEPL_00093 69436 3 Gut 0.75 protein_coding missense_variant MODERATE 5851G>T Ala1951Ser
M0167410 LPPIKEPL_00093 69713 3 Gut 0.75 protein_coding synonymous_variant LOW 5574C>T Ile1858Ile
M0167411 LPPIKEPL_00093 70095 3 Gut 0.75 protein_coding missense_variant MODERATE 5192C>A Ala1731Asp
M0167412 LPPIKEPL_00093 70266 3 Gut 0.75 protein_coding missense_variant MODERATE 5021T>C Met1674Thr
M0167413 LPPIKEPL_00093 70358 3 Gut 0.75 protein_coding missense_variant MODERATE 4929C>G Asp1643Glu
M0167414 LPPIKEPL_00093 70397 3 Gut 0.75 protein_coding synonymous_variant LOW 4890G>A Leu1630Leu
M0167415 LPPIKEPL_00093 70498 3 Gut 0.75 protein_coding missense_variant MODERATE 4789A>C Lys1597Gln
M0167416 LPPIKEPL_00093 70502 3 Gut 0.75 protein_coding synonymous_variant LOW 4785T>C Ala1595Ala
M0167417 LPPIKEPL_00093 70586 3 Gut 0.75 protein_coding synonymous_variant LOW 4701C>T Asp1567Asp
M0167418 LPPIKEPL_00093 70691 3 Gut 0.75 protein_coding synonymous_variant LOW 4596G>T Gly1532Gly
M0167419 LPPIKEPL_00093 70736 3 Gut 0.75 protein_coding synonymous_variant LOW 4551T>C Gly1517Gly
M0167420 LPPIKEPL_00093 70787 3 Gut 0.75 protein_coding synonymous_variant LOW 4500G>A Pro1500Pro
M0167421 LPPIKEPL_00093 70799 3 Gut 0.75 protein_coding synonymous_variant LOW 4488C>T His1496His
M0167422 LPPIKEPL_00093 70802 3 Gut 0.75 protein_coding synonymous_variant LOW 4485C>T His1495His
M0167423 LPPIKEPL_00093 70808 3 Gut 0.75 protein_coding synonymous_variant LOW 4479T>C Asp1493Asp
M0167424 LPPIKEPL_00093 70811 3 Gut 0.75 protein_coding synonymous_variant LOW 4476G>T Thr1492Thr
M0167425 LPPIKEPL_00093 71065 3 Gut 0.75 protein_coding missense_variant MODERATE 4222A>G Thr1408Ala
M0167426 LPPIKEPL_00093 71318 3 Gut 0.75 protein_coding synonymous_variant LOW 3969A>G Leu1323Leu
M0167427 LPPIKEPL_00093 71546 3 Gut 0.75 protein_coding synonymous_variant LOW 3741G>A Lys1247Lys
M0167428 LPPIKEPL_00093 71606 3 Gut 0.75 protein_coding synonymous_variant LOW 3681A>C Ala1227Ala
M0167429 LPPIKEPL_00093 71609 3 Gut 0.75 protein_coding synonymous_variant LOW 3678A>G Ala1226Ala
M0167430 LPPIKEPL_00093 72053 3 Gut 0.75 protein_coding synonymous_variant LOW 3234A>G Val1078Val
M0167431 LPPIKEPL_00093 72245 3 Gut 0.75 protein_coding synonymous_variant LOW 3042T>C His1014His
M0167432 LPPIKEPL_00093 72251 3 Gut 0.75 protein_coding synonymous_variant LOW 3036T>C Asp1012Asp
M0167433 LPPIKEPL_00093 72257 3 Gut 0.75 protein_coding synonymous_variant LOW 3030T>C Asp1010Asp
M0167434 LPPIKEPL_00093 72599 3 Gut 0.75 protein_coding synonymous_variant LOW 2688T>A Ala896Ala
M0167435 LPPIKEPL_00093 72835 3 Gut 0.75 protein_coding missense_variant MODERATE 2452C>T Pro818Ser
M0167436 LPPIKEPL_00093 72887 3 Gut 0.75 protein_coding synonymous_variant LOW 2400A>G Glu800Glu
M0167437 LPPIKEPL_00093 73202 3 Gut 0.75 protein_coding synonymous_variant LOW 2085T>G Leu695Leu
M0167438 LPPIKEPL_00093 73355 3 Gut 0.75 protein_coding synonymous_variant LOW 1932C>T Gly644Gly
M0167439 LPPIKEPL_00093 73373 3 Gut 0.75 protein_coding synonymous_variant LOW 1914T>C Leu638Leu
M0167440 LPPIKEPL_00093 73391 3 Gut 0.75 protein_coding synonymous_variant LOW 1896A>T Ala632Ala
M0167441 LPPIKEPL_00093 73466 3 Gut 0.75 protein_coding synonymous_variant LOW 1821C>T Gly607Gly
M0167442 LPPIKEPL_00093 73499 3 Gut 0.75 protein_coding missense_variant MODERATE 1788C>A Asp596Glu
M0167443 LPPIKEPL_00093 73565 3 Gut 0.75 protein_coding synonymous_variant LOW 1722T>C Thr574Thr
M0167444 LPPIKEPL_00093 73574 3 Gut 0.75 protein_coding synonymous_variant LOW 1713T>C Ser571Ser
M0167445 LPPIKEPL_00093 73577 3 Gut 0.75 protein_coding synonymous_variant LOW 1710C>T Tyr570Tyr
M0167446 LPPIKEPL_00093 73622 3 Gut 0.75 protein_coding synonymous_variant LOW 1665C>A Ala555Ala
M0167447 LPPIKEPL_00093 73646 3 Gut 0.75 protein_coding synonymous_variant LOW 1641A>G Lys547Lys
M0167448 LPPIKEPL_00093 74150 3 Gut 0.75 protein_coding synonymous_variant LOW 1137T>C Gly379Gly
M0167449 LPPIKEPL_00093 74357 3 Gut 0.75 protein_coding synonymous_variant LOW 930T>C Asp310Asp
M0167450 LPPIKEPL_00093 74422 3 Gut 0.75 protein_coding missense_variant MODERATE 865G>A Gly289Ser
M0167451 LPPIKEPL_00093 74519 3 Gut 0.75 protein_coding synonymous_variant LOW 768C>T Gly256Gly
M0167452 LPPIKEPL_00093 74537 3 Gut 0.75 protein_coding synonymous_variant LOW 750T>C Ala250Ala
M0167453 LPPIKEPL_00093 74540 3 Gut 0.75 protein_coding synonymous_variant LOW 747C>T Gly249Gly
M0167454 LPPIKEPL_00093 74558 3 Gut 0.75 protein_coding synonymous_variant LOW 729T>G Arg243Arg
M0167455 LPPIKEPL_00093 74561 3 Gut 0.75 protein_coding synonymous_variant LOW 726C>A Ser242Ser
M0167456 LPPIKEPL_00094 76963 3 Gut 0.75 protein_coding synonymous_variant LOW 1602T>G Ala534Ala
M0167457 LPPIKEPL_00095 77348 3 Gut 0.75 protein_coding synonymous_variant LOW 285T>C Ser95Ser
M0167458 LPPIKEPL_00095 77933 3 Gut 0.75 protein_coding synonymous_variant LOW 870A>T Val290Val
M0167459 LPPIKEPL_00095 77939 3 Gut 0.75 protein_coding synonymous_variant LOW 876G>A Thr292Thr
M0167460 LPPIKEPL_00095 78003 3 Gut 0.75 protein_coding missense_variant MODERATE 940A>G Ile314Val
M0167461 LPPIKEPL_00095 78032 3 Gut 0.75 protein_coding synonymous_variant LOW 969A>G Pro323Pro
M0167462 LPPIKEPL_00093 78104 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -2818T>C None
M0167463 LPPIKEPL_00093 78317 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -3031T>C None
M0167464 LPPIKEPL_00096 78612 3 Gut 0.75 protein_coding synonymous_variant LOW 321T>C Ser107Ser
M0167465 LPPIKEPL_00096 78714 3 Gut 0.75 protein_coding synonymous_variant LOW 219A>C Thr73Thr
M0167466 LPPIKEPL_00096 78774 3 Gut 0.75 protein_coding synonymous_variant LOW 159A>G Ala53Ala
M0167467 LPPIKEPL_00093 79071 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -3785T>G 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







        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
LPPIKEPL_00006 AXI37841.1|GH23 100 0 1 1140 1 1
LPPIKEPL_00093 AYL89119.1|GH24 96.2 0 1753 2255 0.2231 0.9031
LPPIKEPL_00096 QHN01840.1|GH24 100 2.31e-139 1 185 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
LPPIKEPL_00108 1.E.4.1.1 100 1.3e-54 1 109 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.4 The LydA Holin (LydA Holin) Family