Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3056
  Reference Plasmid   DSKIN0147-1_bin.9__k141_51874
  Reference Plasmid Size   8210
  Reference Plasmid GC Content   0.68
  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
M0070433 PGNAPDLM_00001 354 3 Skin 0.23 protein_coding synonymous_variant LOW 159C>G Ser53Ser
M0070434 PGNAPDLM_00001 930 3 Skin 0.23 protein_coding synonymous_variant LOW 735T>C Ala245Ala
M0070435 PGNAPDLM_00001 1260 3 Skin 0.23 protein_coding synonymous_variant LOW 1065C>T Cys355Cys
M0070436 PGNAPDLM_00001 1770 3 Skin 0.23 protein_coding missense_variant MODERATE 1575C>A Asp525Glu
M0070437 PGNAPDLM_00003 1879 3 Skin 0.23 protein_coding upstream_gene_variant MODIFIER -1654G>A None
M0070438 PGNAPDLM_00002 2337 3 Skin 0.23 protein_coding synonymous_variant LOW 1053C>G Ala351Ala
M0070439 PGNAPDLM_00002 2343 3 Skin 0.23 protein_coding synonymous_variant LOW 1047T>C Phe349Phe
M0070440 PGNAPDLM_00002 2357 3 Skin 0.23 protein_coding missense_variant MODERATE 1033G>A Ala345Thr
M0070441 PGNAPDLM_00002 2366 3 Skin 0.23 protein_coding missense_variant MODERATE 1024C>T Pro342Ser
M0070442 PGNAPDLM_00002 2388 3 Skin 0.23 protein_coding synonymous_variant LOW 1002T>A Ala334Ala
M0070443 PGNAPDLM_00002 2466 3 Skin 0.23 protein_coding synonymous_variant LOW 924C>G Ser308Ser
M0070444 PGNAPDLM_00002 2493 3 Skin 0.23 protein_coding synonymous_variant LOW 897C>T Ala299Ala
M0070445 PGNAPDLM_00002 2673 3 Skin 0.23 protein_coding synonymous_variant LOW 717G>A Ala239Ala
M0070446 PGNAPDLM_00002 2733 3 Skin 0.23 protein_coding synonymous_variant LOW 657T>C Phe219Phe
M0070447 PGNAPDLM_00001 450 3 Skin 0.23 protein_coding synonymous_variant LOW 255C>T Pro85Pro
M0070448 PGNAPDLM_00001 498 4 Skin 0.31 protein_coding synonymous_variant LOW 303G>C Val101Val
M0070449 PGNAPDLM_00001 528 4 Skin 0.31 protein_coding synonymous_variant LOW 333C>A Arg111Arg
M0070450 PGNAPDLM_00001 531 4 Skin 0.31 protein_coding synonymous_variant LOW 336G>A Glu112Glu
M0070451 PGNAPDLM_00001 738 3 Skin 0.23 protein_coding synonymous_variant LOW 543A>G Pro181Pro
M0070452 PGNAPDLM_00001 1304 3 Skin 0.23 protein_coding missense_variant MODERATE 1109C>T Ala370Val
M0070453 PGNAPDLM_00002 2787 5 Skin 0.38 protein_coding synonymous_variant LOW 603A>C Ala201Ala
M0070454 PGNAPDLM_00002 2963 8 Skin 0.62 protein_coding missense_variant MODERATE 427C>G Pro143Ala
M0070455 PGNAPDLM_00002 1969 3 Skin 0.23 protein_coding missense_variant MODERATE 1421T>C Val474Ala
M0070456 PGNAPDLM_00002 1992 3 Skin 0.23 protein_coding synonymous_variant LOW 1398A>G Ala466Ala
M0070457 PGNAPDLM_00002 2031 3 Skin 0.23 protein_coding synonymous_variant LOW 1359C>G Leu453Leu
M0070458 PGNAPDLM_00002 2034 3 Skin 0.23 protein_coding synonymous_variant LOW 1356A>G Glu452Glu
M0070459 PGNAPDLM_00002 2037 3 Skin 0.23 protein_coding synonymous_variant LOW 1353A>C Gly451Gly
M0070460 PGNAPDLM_00002 2040 3 Skin 0.23 protein_coding synonymous_variant LOW 1350G>A Glu450Glu
M0070461 PGNAPDLM_00002 2049 3 Skin 0.23 protein_coding synonymous_variant LOW 1341C>G Ala447Ala
M0070462 PGNAPDLM_00002 2052 3 Skin 0.23 protein_coding synonymous_variant LOW 1338T>C Asn446Asn
M0070463 PGNAPDLM_00002 2053 3 Skin 0.23 protein_coding missense_variant MODERATE 1337A>C Asn446Thr
M0070464 PGNAPDLM_00002 2082 3 Skin 0.23 protein_coding synonymous_variant LOW 1308C>G Val436Val
M0070465 PGNAPDLM_00002 2151 5 Skin 0.38 protein_coding synonymous_variant LOW 1239C>G Ser413Ser
M0070466 PGNAPDLM_00002 2211 5 Skin 0.38 protein_coding synonymous_variant LOW 1179C>T Gly393Gly
M0070467 PGNAPDLM_00002 2235 5 Skin 0.38 protein_coding synonymous_variant LOW 1155T>C Gly385Gly
M0070468 PGNAPDLM_00002 2244 5 Skin 0.38 protein_coding synonymous_variant LOW 1146C>G Ala382Ala
M0070469 PGNAPDLM_00002 2253 5 Skin 0.38 protein_coding synonymous_variant LOW 1137G>C Pro379Pro
M0070470 PGNAPDLM_00002 2265 5 Skin 0.38 protein_coding synonymous_variant LOW 1125G>T Ala375Ala
M0070471 PGNAPDLM_00002 2268 5 Skin 0.38 protein_coding synonymous_variant LOW 1122T>C Pro374Pro
M0070472 PGNAPDLM_00002 2277 5 Skin 0.38 protein_coding synonymous_variant LOW 1113G>A Glu371Glu
M0070473 PGNAPDLM_00002 2288 5 Skin 0.38 protein_coding missense_variant MODERATE 1102A>C Met368Leu
M0070474 PGNAPDLM_00002 2568 3 Skin 0.23 protein_coding synonymous_variant LOW 822C>G Leu274Leu
M0070475 PGNAPDLM_00002 3333 4 Skin 0.31 protein_coding synonymous_variant LOW 57T>C Val19Val
M0070476 PGNAPDLM_00003 3682 6 Skin 0.46 protein_coding synonymous_variant LOW 150G>C Arg50Arg
M0070477 PGNAPDLM_00003 3802 3 Skin 0.23 protein_coding synonymous_variant LOW 270C>T Asp90Asp
M0070478 PGNAPDLM_00002 4707 6 Skin 0.46 protein_coding upstream_gene_variant MODIFIER -1318T>C None
M0070479 PGNAPDLM_00002 4823 4 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -1434T>A None
M0070480 PGNAPDLM_00002 4828 4 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -1439G>A None
M0070481 PGNAPDLM_00005 4852 4 Skin 0.31 protein_coding missense_variant MODERATE 20T>C Ile7Thr
M0070482 PGNAPDLM_00005 5132 3 Skin 0.23 protein_coding synonymous_variant LOW 300G>T Gly100Gly
M0070483 PGNAPDLM_00005 5147 3 Skin 0.23 protein_coding synonymous_variant LOW 315A>G Ala105Ala
M0070484 PGNAPDLM_00005 5178 3 Skin 0.23 protein_coding synonymous_variant LOW 346T>C Leu116Leu
M0070485 PGNAPDLM_00005 5403 8 Skin 0.62 protein_coding missense_variant MODERATE 571T>A Cys191Ser
M0070486 PGNAPDLM_00005 5558 3 Skin 0.23 protein_coding missense_variant MODERATE 726G>T Lys242Asn
M0070487 PGNAPDLM_00005 5579 3 Skin 0.23 protein_coding synonymous_variant LOW 747T>C Asp249Asp
M0070488 PGNAPDLM_00005 5585 3 Skin 0.23 protein_coding synonymous_variant LOW 753C>A Ala251Ala
M0070489 PGNAPDLM_00006 6159 4 Skin 0.31 protein_coding synonymous_variant LOW 420C>T Arg140Arg
M0070490 PGNAPDLM_00006 6389 8 Skin 0.62 protein_coding missense_variant MODERATE 650G>T Gly217Val
M0070491 PGNAPDLM_00006 6489 5 Skin 0.38 protein_coding synonymous_variant LOW 750C>G Gly250Gly
M0070492 PGNAPDLM_00006 6628 5 Skin 0.38 protein_coding missense_variant MODERATE 889A>C Lys297Gln
M0070493 PGNAPDLM_00007 7211 7 Skin 0.54 protein_coding synonymous_variant LOW 75G>A Glu25Glu
M0070494 PGNAPDLM_00007 7604 6 Skin 0.46 protein_coding synonymous_variant LOW 468C>T Gly156Gly
M0070495 PGNAPDLM_00002 7675 5 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -4286T>C None
M0070496 PGNAPDLM_00002 7702 5 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -4313C>T None
M0070497 PGNAPDLM_00002 7741 4 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -4352A>G None
M0070498 PGNAPDLM_00002 7765 3 Skin 0.23 protein_coding upstream_gene_variant MODIFIER -4376A>G None
M0070499 PGNAPDLM_00002 7770 3 Skin 0.23 protein_coding upstream_gene_variant MODIFIER -4381G>A None
M0070500 PGNAPDLM_00002 7796 3 Skin 0.23 protein_coding upstream_gene_variant MODIFIER -4407C>T None
M0070501 PGNAPDLM_00002 7955 4 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -4566G>C None
M0070502 PGNAPDLM_00002 7959 4 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -4570G>T None
M0070503 PGNAPDLM_00002 8068 3 Skin 0.23 protein_coding upstream_gene_variant MODIFIER -4679A>G None
M0070504 PGNAPDLM_00002 8085 3 Skin 0.23 protein_coding upstream_gene_variant MODIFIER -4696C>T None
M0070505 PGNAPDLM_00002 8110 3 Skin 0.23 protein_coding upstream_gene_variant MODIFIER -4721G>A None
M0070506 PGNAPDLM_00002 3250 4 Skin 0.31 protein_coding missense_variant MODERATE 140A>G Lys47Arg
M0070507 PGNAPDLM_00002 3252 4 Skin 0.31 protein_coding synonymous_variant LOW 138C>G Ala46Ala
M0070508 PGNAPDLM_00002 4700 4 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -1311C>T None
M0070509 PGNAPDLM_00005 4919 6 Skin 0.46 protein_coding synonymous_variant LOW 87C>T Gly29Gly
M0070510 PGNAPDLM_00006 5756 4 Skin 0.31 protein_coding missense_variant MODERATE 17A>T Asp6Val
M0070511 PGNAPDLM_00002 3021 3 Skin 0.23 protein_coding synonymous_variant LOW 369C>T Gly123Gly
M0070512 PGNAPDLM_00005 4973 5 Skin 0.38 protein_coding synonymous_variant LOW 141C>G Ala47Ala
M0070513 PGNAPDLM_00005 4991 5 Skin 0.38 protein_coding synonymous_variant LOW 159C>T Cys53Cys
M0070514 PGNAPDLM_00002 4830 3 Skin 0.23 protein_coding upstream_gene_variant MODIFIER -1441G>A None
M0070515 PGNAPDLM_00005 5567 3 Skin 0.23 protein_coding synonymous_variant LOW 735G>A Gln245Gln
M0070516 PGNAPDLM_00002 3458 3 Skin 0.23 protein_coding upstream_gene_variant MODIFIER -69T>C None
M0070517 PGNAPDLM_00002 3484 3 Skin 0.23 protein_coding upstream_gene_variant MODIFIER -95A>C None
M0070518 PGNAPDLM_00005 5468 3 Skin 0.23 protein_coding synonymous_variant LOW 636G>A Gly212Gly






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