Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C375
  Reference Plasmid   NZ_AP023419.1
  Reference Plasmid Size   4032
  Reference Plasmid GC Content   0.58
  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
M0163462 LLKHPLFM_00004 125 3 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -2973G>A None
M0163463 LLKHPLFM_00001 411 4 Gut 0.13 protein_coding missense_variant MODERATE 985C>A Leu329Met
M0163464 LLKHPLFM_00001 541 6 Gut 0.19 protein_coding synonymous_variant LOW 855G>A Glu285Glu
M0163465 LLKHPLFM_00001 547 8 Gut 0.25 protein_coding synonymous_variant LOW 849G>A Thr283Thr
M0163466 LLKHPLFM_00001 556 14 Gut 0.44 protein_coding synonymous_variant LOW 840T>C Ser280Ser
M0163467 LLKHPLFM_00001 571 11 Gut 0.34 protein_coding synonymous_variant LOW 825C>T Tyr275Tyr
M0163468 LLKHPLFM_00001 630 9 Gut 0.28 protein_coding missense_variant MODERATE 766A>C Ile256Leu
M0163469 LLKHPLFM_00001 1440 6 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -45A>G None
M0163470 LLKHPLFM_00001 1482 9 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -87C>T None
M0163471 LLKHPLFM_00001 1545 9 Gut 0.28 protein_coding upstream_gene_variant MODIFIER -150C>T None
M0163472 LLKHPLFM_00001 1584 4 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -189T>G None
M0163473 LLKHPLFM_00001 1585 3 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -190T>A None
M0163474 LLKHPLFM_00002 1733 10 Gut 0.31 protein_coding synonymous_variant LOW 1050G>T Thr350Thr
M0163475 LLKHPLFM_00002 1763 11 Gut 0.34 protein_coding synonymous_variant LOW 1020T>G Leu340Leu
M0163476 LLKHPLFM_00002 1826 17 Gut 0.53 protein_coding synonymous_variant LOW 957C>T Tyr319Tyr
M0163477 LLKHPLFM_00002 1841 12 Gut 0.38 protein_coding synonymous_variant LOW 942C>T Asn314Asn
M0163478 LLKHPLFM_00002 1874 9 Gut 0.28 protein_coding synonymous_variant LOW 909T>C Ala303Ala
M0163479 LLKHPLFM_00002 1919 17 Gut 0.53 protein_coding synonymous_variant LOW 864T>C Tyr288Tyr
M0163480 LLKHPLFM_00002 1920 17 Gut 0.53 protein_coding missense_variant MODERATE 863A>T Tyr288Phe
M0163481 LLKHPLFM_00002 1928 17 Gut 0.53 protein_coding synonymous_variant LOW 855T>C Pro285Pro
M0163482 LLKHPLFM_00002 1934 17 Gut 0.53 protein_coding synonymous_variant LOW 849C>T Asp283Asp
M0163483 LLKHPLFM_00002 1961 15 Gut 0.47 protein_coding synonymous_variant LOW 822C>T Ile274Ile
M0163484 LLKHPLFM_00002 2084 3 Gut 0.09 protein_coding synonymous_variant LOW 699C>T Val233Val
M0163485 LLKHPLFM_00002 2192 7 Gut 0.22 protein_coding synonymous_variant LOW 591T>C Asp197Asp
M0163486 LLKHPLFM_00002 2204 10 Gut 0.31 protein_coding synonymous_variant LOW 579G>A Val193Val
M0163487 LLKHPLFM_00002 2240 7 Gut 0.22 protein_coding synonymous_variant LOW 543C>T Gly181Gly
M0163488 LLKHPLFM_00002 2291 4 Gut 0.13 protein_coding synonymous_variant LOW 492C>T Gly164Gly
M0163489 LLKHPLFM_00002 2354 12 Gut 0.38 protein_coding synonymous_variant LOW 429A>G Ala143Ala
M0163490 LLKHPLFM_00002 2384 13 Gut 0.41 protein_coding synonymous_variant LOW 399C>T Ser133Ser
M0163491 LLKHPLFM_00002 2504 17 Gut 0.53 protein_coding synonymous_variant LOW 279T>C Tyr93Tyr
M0163492 LLKHPLFM_00002 2720 3 Gut 0.09 protein_coding synonymous_variant LOW 63C>T Ala21Ala
M0163493 LLKHPLFM_00002 2723 4 Gut 0.13 protein_coding synonymous_variant LOW 60C>T Pro20Pro
M0163494 LLKHPLFM_00002 2726 4 Gut 0.13 protein_coding synonymous_variant LOW 57A>G Val19Val
M0163495 LLKHPLFM_00002 2729 4 Gut 0.13 protein_coding synonymous_variant LOW 54C>A Ala18Ala
M0163496 LLKHPLFM_00002 2735 3 Gut 0.09 protein_coding synonymous_variant LOW 48G>A Val16Val
M0163497 LLKHPLFM_00002 1967 6 Gut 0.19 protein_coding synonymous_variant LOW 816C>T Gly272Gly
M0163498 LLKHPLFM_00002 2045 12 Gut 0.38 protein_coding synonymous_variant LOW 738C>T Asp246Asp
M0163499 LLKHPLFM_00002 2118 10 Gut 0.31 protein_coding missense_variant MODERATE 665G>C Ser222Thr
M0163500 LLKHPLFM_00002 2119 10 Gut 0.31 protein_coding missense_variant MODERATE 664A>T Ser222Cys
M0163501 LLKHPLFM_00002 2168 7 Gut 0.22 protein_coding synonymous_variant LOW 615C>T Ala205Ala
M0163502 LLKHPLFM_00002 2486 3 Gut 0.09 protein_coding synonymous_variant LOW 297C>T His99His
M0163503 LLKHPLFM_00002 2614 15 Gut 0.47 protein_coding missense_variant MODERATE 169G>A Val57Ile
M0163504 LLKHPLFM_00002 2651 6 Gut 0.19 protein_coding synonymous_variant LOW 132T>C Gly44Gly
M0163505 LLKHPLFM_00002 2675 4 Gut 0.13 protein_coding synonymous_variant LOW 108A>G Glu36Glu
M0163506 LLKHPLFM_00004 192 11 Gut 0.34 protein_coding upstream_gene_variant MODIFIER -2906G>T None
M0163507 LLKHPLFM_00004 194 11 Gut 0.34 protein_coding upstream_gene_variant MODIFIER -2904A>G None
M0163508 LLKHPLFM_00001 284 6 Gut 0.19 protein_coding missense_variant MODERATE 1112G>T Gly371Val
M0163509 LLKHPLFM_00001 352 6 Gut 0.19 protein_coding synonymous_variant LOW 1044C>T Ser348Ser
M0163510 LLKHPLFM_00001 365 7 Gut 0.22 protein_coding missense_variant MODERATE 1031G>A Ser344Asn
M0163511 LLKHPLFM_00001 384 4 Gut 0.13 protein_coding missense_variant MODERATE 1012A>C Lys338Gln
M0163512 LLKHPLFM_00001 424 10 Gut 0.31 protein_coding missense_variant MODERATE 972G>C Met324Ile
M0163513 LLKHPLFM_00001 427 10 Gut 0.31 protein_coding synonymous_variant LOW 969T>C Ala323Ala
M0163514 LLKHPLFM_00001 662 11 Gut 0.34 protein_coding missense_variant MODERATE 734A>C Asn245Thr
M0163515 LLKHPLFM_00001 915 12 Gut 0.38 protein_coding missense_variant MODERATE 481T>G Ser161Ala
M0163516 LLKHPLFM_00001 925 6 Gut 0.19 protein_coding synonymous_variant LOW 471C>T Leu157Leu
M0163517 LLKHPLFM_00001 1240 5 Gut 0.16 protein_coding synonymous_variant LOW 156T>C Ile52Ile
M0163518 LLKHPLFM_00001 1300 13 Gut 0.41 protein_coding synonymous_variant LOW 96C>T Gly32Gly
M0163519 LLKHPLFM_00001 1421 4 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -26C>T None
M0163520 LLKHPLFM_00001 1592 4 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -197T>C None
M0163521 LLKHPLFM_00002 2087 7 Gut 0.22 protein_coding synonymous_variant LOW 696C>T Asp232Asp
M0163522 LLKHPLFM_00002 2159 3 Gut 0.09 protein_coding synonymous_variant LOW 624G>A Lys208Lys
M0163523 LLKHPLFM_00002 2411 9 Gut 0.28 protein_coding synonymous_variant LOW 372C>T Gly124Gly
M0163524 LLKHPLFM_00002 2558 5 Gut 0.16 protein_coding synonymous_variant LOW 225G>A Glu75Glu
M0163525 LLKHPLFM_00004 107 8 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -2991A>G None
M0163526 LLKHPLFM_00001 811 6 Gut 0.19 protein_coding synonymous_variant LOW 585C>T Tyr195Tyr
M0163527 LLKHPLFM_00001 967 5 Gut 0.16 protein_coding synonymous_variant LOW 429C>T Ala143Ala
M0163528 LLKHPLFM_00002 2222 5 Gut 0.16 protein_coding synonymous_variant LOW 561C>T Ala187Ala
M0163529 LLKHPLFM_00002 2234 10 Gut 0.31 protein_coding synonymous_variant LOW 549T>C Ala183Ala
M0163530 LLKHPLFM_00002 2460 10 Gut 0.31 protein_coding missense_variant MODERATE 323G>A Gly108Asp
M0163531 LLKHPLFM_00002 2461 8 Gut 0.25 protein_coding missense_variant MODERATE 322G>A Gly108Ser
M0163532 LLKHPLFM_00004 224 5 Gut 0.16 protein_coding upstream_gene_variant MODIFIER -2874A>C None
M0163533 LLKHPLFM_00001 291 8 Gut 0.25 protein_coding missense_variant MODERATE 1105T>C Phe369Leu
M0163534 LLKHPLFM_00001 300 8 Gut 0.25 protein_coding missense_variant MODERATE 1096C>T Arg366Cys
M0163535 LLKHPLFM_00001 308 13 Gut 0.41 protein_coding missense_variant MODERATE 1088G>A Gly363Asp
M0163536 LLKHPLFM_00001 466 3 Gut 0.09 protein_coding synonymous_variant LOW 930C>T Ile310Ile
M0163537 LLKHPLFM_00001 481 5 Gut 0.16 protein_coding synonymous_variant LOW 915C>T Asn305Asn
M0163538 LLKHPLFM_00001 483 5 Gut 0.16 protein_coding missense_variant MODERATE 913A>G Asn305Asp
M0163539 LLKHPLFM_00001 521 10 Gut 0.31 protein_coding missense_variant MODERATE 875T>C Val292Ala
M0163540 LLKHPLFM_00001 522 9 Gut 0.28 protein_coding missense_variant MODERATE 874G>A Val292Ile
M0163541 LLKHPLFM_00001 523 9 Gut 0.28 protein_coding synonymous_variant LOW 873C>T Val291Val
M0163542 LLKHPLFM_00001 538 11 Gut 0.34 protein_coding synonymous_variant LOW 858T>C Ala286Ala
M0163543 LLKHPLFM_00001 692 10 Gut 0.31 protein_coding missense_variant MODERATE 704C>A Ser235Tyr
M0163544 LLKHPLFM_00001 693 10 Gut 0.31 protein_coding missense_variant MODERATE 703T>G Ser235Ala
M0163545 LLKHPLFM_00001 694 10 Gut 0.31 protein_coding synonymous_variant LOW 702A>C Gly234Gly
M0163546 LLKHPLFM_00001 784 10 Gut 0.31 protein_coding missense_variant MODERATE 612C>G Phe204Leu
M0163547 LLKHPLFM_00001 786 10 Gut 0.31 protein_coding missense_variant MODERATE 610T>C Phe204Leu
M0163548 LLKHPLFM_00001 845 8 Gut 0.25 protein_coding missense_variant MODERATE 551A>C Asp184Ala
M0163549 LLKHPLFM_00001 856 7 Gut 0.22 protein_coding missense_variant MODERATE 540G>C Glu180Asp
M0163550 LLKHPLFM_00001 880 3 Gut 0.09 protein_coding synonymous_variant LOW 516C>T Gly172Gly
M0163551 LLKHPLFM_00001 1006 4 Gut 0.13 protein_coding synonymous_variant LOW 390C>T Pro130Pro
M0163552 LLKHPLFM_00001 1065 8 Gut 0.25 protein_coding missense_variant MODERATE 331G>A Val111Ile
M0163553 LLKHPLFM_00001 1210 8 Gut 0.25 protein_coding synonymous_variant LOW 186C>T Ile62Ile
M0163554 LLKHPLFM_00001 1213 8 Gut 0.25 protein_coding synonymous_variant LOW 183C>T Phe61Phe
M0163555 LLKHPLFM_00001 1214 8 Gut 0.25 protein_coding missense_variant MODERATE 182T>A Phe61Tyr
M0163556 LLKHPLFM_00001 1216 8 Gut 0.25 protein_coding synonymous_variant LOW 180T>C Asp60Asp
M0163557 LLKHPLFM_00001 1219 8 Gut 0.25 protein_coding synonymous_variant LOW 177C>T Ala59Ala
M0163558 LLKHPLFM_00001 1225 8 Gut 0.25 protein_coding synonymous_variant LOW 171C>T Gly57Gly
M0163559 LLKHPLFM_00001 1344 12 Gut 0.38 protein_coding synonymous_variant LOW 52C>T Leu18Leu
M0163560 LLKHPLFM_00001 1356 3 Gut 0.09 protein_coding missense_variant MODERATE 40A>G Ile14Val
M0163561 LLKHPLFM_00001 1234 7 Gut 0.22 protein_coding synonymous_variant LOW 162T>C Ser54Ser
M0163562 LLKHPLFM_00001 1243 7 Gut 0.22 protein_coding missense_variant MODERATE 153C>G Ile51Met
M0163563 LLKHPLFM_00001 1245 7 Gut 0.22 protein_coding missense_variant MODERATE 151A>C Ile51Leu
M0163564 LLKHPLFM_00001 1246 7 Gut 0.22 protein_coding synonymous_variant LOW 150C>T Gly50Gly
M0163565 LLKHPLFM_00001 1252 5 Gut 0.16 protein_coding synonymous_variant LOW 144C>T Phe48Phe
M0163566 LLKHPLFM_00001 1267 3 Gut 0.09 protein_coding synonymous_variant LOW 129C>T Asp43Asp
M0163567 LLKHPLFM_00004 55 3 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -3043A>T None
M0163568 LLKHPLFM_00001 874 3 Gut 0.09 protein_coding synonymous_variant LOW 522C>T Gly174Gly
M0163569 LLKHPLFM_00001 1032 3 Gut 0.09 protein_coding synonymous_variant LOW 364C>T Leu122Leu
M0163570 LLKHPLFM_00001 1126 3 Gut 0.09 protein_coding synonymous_variant LOW 270G>A Lys90Lys
M0163571 LLKHPLFM_00002 1688 3 Gut 0.09 protein_coding synonymous_variant LOW 1095C>T Ala365Ala
M0163572 LLKHPLFM_00001 294 6 Gut 0.19 protein_coding missense_variant MODERATE 1102C>T Arg368Cys
M0163573 LLKHPLFM_00001 997 4 Gut 0.13 protein_coding synonymous_variant LOW 399T>C Asp133Asp
M0163574 LLKHPLFM_00001 1048 3 Gut 0.09 protein_coding synonymous_variant LOW 348C>T Ser116Ser
M0163575 LLKHPLFM_00001 1222 3 Gut 0.09 protein_coding synonymous_variant LOW 174T>C Asn58Asn
M0163576 LLKHPLFM_00001 241 4 Gut 0.13 protein_coding stop_lost&splice_region_variant HIGH 1155A>G Ter385Trpext*?
M0163577 LLKHPLFM_00001 412 5 Gut 0.16 protein_coding synonymous_variant LOW 984T>C Ser328Ser
M0163578 LLKHPLFM_00001 282 5 Gut 0.16 protein_coding missense_variant MODERATE 1114C>T Leu372Phe
M0163579 LLKHPLFM_00001 539 4 Gut 0.13 protein_coding missense_variant MODERATE 857C>G Ala286Gly
M0163580 LLKHPLFM_00001 558 4 Gut 0.13 protein_coding missense_variant MODERATE 838T>A Ser280Thr
M0163581 LLKHPLFM_00001 584 4 Gut 0.13 protein_coding missense_variant MODERATE 812C>A Thr271Asn
M0163582 LLKHPLFM_00001 586 4 Gut 0.13 protein_coding synonymous_variant LOW 810G>A Val270Val
M0163583 LLKHPLFM_00001 588 6 Gut 0.19 protein_coding missense_variant MODERATE 808G>A Val270Met
M0163584 LLKHPLFM_00001 590 4 Gut 0.13 protein_coding missense_variant MODERATE 806C>T Ala269Val
M0163585 LLKHPLFM_00001 594 4 Gut 0.13 protein_coding missense_variant MODERATE 802A>G Ile268Val
M0163586 LLKHPLFM_00001 603 4 Gut 0.13 protein_coding missense_variant MODERATE 793C>G Leu265Val
M0163587 LLKHPLFM_00001 610 4 Gut 0.13 protein_coding synonymous_variant LOW 786C>T Ile262Ile
M0163588 LLKHPLFM_00001 674 4 Gut 0.13 protein_coding missense_variant MODERATE 722G>A Arg241His
M0163589 LLKHPLFM_00001 675 4 Gut 0.13 protein_coding missense_variant MODERATE 721C>A Arg241Ser
M0163590 LLKHPLFM_00001 730 4 Gut 0.13 protein_coding synonymous_variant LOW 666G>A Glu222Glu
M0163591 LLKHPLFM_00002 1856 4 Gut 0.13 protein_coding synonymous_variant LOW 927C>T Ser309Ser
M0163592 LLKHPLFM_00002 1889 3 Gut 0.09 protein_coding synonymous_variant LOW 894C>T Asp298Asp
M0163593 LLKHPLFM_00002 2039 5 Gut 0.16 protein_coding synonymous_variant LOW 744T>C Ile248Ile
M0163594 LLKHPLFM_00002 2429 5 Gut 0.16 protein_coding synonymous_variant LOW 354T>C Asp118Asp
M0163595 LLKHPLFM_00001 636 3 Gut 0.09 protein_coding missense_variant MODERATE 760T>G Ser254Ala
M0163596 LLKHPLFM_00001 373 4 Gut 0.13 protein_coding synonymous_variant LOW 1023T>C Gly341Gly
M0163597 LLKHPLFM_00001 463 5 Gut 0.16 protein_coding synonymous_variant LOW 933G>A Gln311Gln
M0163598 LLKHPLFM_00001 468 4 Gut 0.13 protein_coding missense_variant MODERATE 928A>G Ile310Val
M0163599 LLKHPLFM_00001 1086 4 Gut 0.13 protein_coding missense_variant MODERATE 310A>G Ile104Val






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