Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2447
  Reference Plasmid   1111525849768046_bin.37__k141_41301
  Reference Plasmid Size   5202
  Reference Plasmid GC Content   0.38
  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
M0126547 PJDEFLKM_00001 4757 6 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -3529G>T None
M0126548 PJDEFLKM_00001 4779 5 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -3551T>C None
M0126549 PJDEFLKM_00001 5003 6 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -3775A>G None
M0126550 PJDEFLKM_00001 5111 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -3883G>A None
M0126551 PJDEFLKM_00001 5114 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -3886T>C None
M0126552 PJDEFLKM_00001 725 4 Oral 0.40 protein_coding synonymous_variant LOW 504G>A Leu168Leu
M0126553 PJDEFLKM_00002 1829 7 Oral 0.70 protein_coding synonymous_variant LOW 1221T>A Ile407Ile
M0126554 PJDEFLKM_00002 1940 5 Oral 0.50 protein_coding synonymous_variant LOW 1110T>C Asp370Asp
M0126555 PJDEFLKM_00002 2003 8 Oral 0.80 protein_coding synonymous_variant LOW 1047T>A Ala349Ala
M0126556 PJDEFLKM_00002 2090 4 Oral 0.40 protein_coding synonymous_variant LOW 960A>G Leu320Leu
M0126557 PJDEFLKM_00002 2264 4 Oral 0.40 protein_coding synonymous_variant LOW 786T>A Ala262Ala
M0126558 PJDEFLKM_00002 2569 7 Oral 0.70 protein_coding missense_variant MODERATE 481A>C Asn161His
M0126559 PJDEFLKM_00002 2591 4 Oral 0.40 protein_coding synonymous_variant LOW 459C>T Asn153Asn
M0126560 PJDEFLKM_00002 2765 6 Oral 0.60 protein_coding synonymous_variant LOW 285A>T Pro95Pro
M0126561 PJDEFLKM_00003 3095 6 Oral 0.60 protein_coding splice_region_variant&stop_retained_variant LOW 996G>A Ter332Ter
M0126562 PJDEFLKM_00003 3122 5 Oral 0.50 protein_coding synonymous_variant LOW 969A>T Thr323Thr
M0126563 PJDEFLKM_00003 3194 4 Oral 0.40 protein_coding synonymous_variant LOW 897T>C Leu299Leu
M0126564 PJDEFLKM_00001 338 6 Oral 0.60 protein_coding synonymous_variant LOW 891C>T Ile297Ile
M0126565 PJDEFLKM_00001 368 3 Oral 0.30 protein_coding synonymous_variant LOW 861G>A Ala287Ala
M0126566 PJDEFLKM_00001 389 3 Oral 0.30 protein_coding synonymous_variant LOW 840C>T Ser280Ser
M0126567 PJDEFLKM_00001 395 3 Oral 0.30 protein_coding synonymous_variant LOW 834A>G Glu278Glu
M0126568 PJDEFLKM_00001 653 3 Oral 0.30 protein_coding synonymous_variant LOW 576G>A Leu192Leu
M0126569 PJDEFLKM_00001 665 4 Oral 0.40 protein_coding synonymous_variant LOW 564T>C Asn188Asn
M0126570 PJDEFLKM_00001 692 4 Oral 0.40 protein_coding synonymous_variant LOW 537C>T Thr179Thr
M0126571 PJDEFLKM_00001 917 4 Oral 0.40 protein_coding synonymous_variant LOW 312C>T Phe104Phe
M0126572 PJDEFLKM_00002 2390 3 Oral 0.30 protein_coding synonymous_variant LOW 660C>A Ile220Ile
M0126573 PJDEFLKM_00002 2465 4 Oral 0.40 protein_coding synonymous_variant LOW 585A>T Val195Val
M0126574 PJDEFLKM_00002 2906 3 Oral 0.30 protein_coding synonymous_variant LOW 144T>C Phe48Phe
M0126575 PJDEFLKM_00003 3227 3 Oral 0.30 protein_coding synonymous_variant LOW 864C>T Gly288Gly
M0126576 PJDEFLKM_00003 3239 3 Oral 0.30 protein_coding synonymous_variant LOW 852G>A Leu284Leu
M0126577 PJDEFLKM_00003 3564 3 Oral 0.30 protein_coding missense_variant MODERATE 527T>C Val176Ala
M0126578 PJDEFLKM_00003 3674 3 Oral 0.30 protein_coding synonymous_variant LOW 417C>T Cys139Cys
M0126579 PJDEFLKM_00003 3677 4 Oral 0.40 protein_coding synonymous_variant LOW 414T>C Gly138Gly
M0126580 PJDEFLKM_00003 3752 3 Oral 0.30 protein_coding synonymous_variant LOW 339T>A Val113Val
M0126581 PJDEFLKM_00003 3929 4 Oral 0.40 protein_coding synonymous_variant LOW 162A>G Gly54Gly
M0126582 PJDEFLKM_00003 3962 4 Oral 0.40 protein_coding synonymous_variant LOW 129C>T Asn43Asn
M0126583 PJDEFLKM_00003 4004 5 Oral 0.50 protein_coding synonymous_variant LOW 87T>C Phe29Phe
M0126584 PJDEFLKM_00001 4094 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -2866T>C None
M0126585 PJDEFLKM_00001 4097 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -2869T>C None
M0126586 PJDEFLKM_00001 4140 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -2912T>C None
M0126587 PJDEFLKM_00001 458 4 Oral 0.40 protein_coding synonymous_variant LOW 771C>T Ile257Ile
M0126588 PJDEFLKM_00001 677 3 Oral 0.30 protein_coding synonymous_variant LOW 552A>G Ser184Ser
M0126589 PJDEFLKM_00001 749 4 Oral 0.40 protein_coding synonymous_variant LOW 480T>C Asp160Asp
M0126590 PJDEFLKM_00001 755 3 Oral 0.30 protein_coding synonymous_variant LOW 474C>T Asn158Asn
M0126591 PJDEFLKM_00002 2174 5 Oral 0.50 protein_coding synonymous_variant LOW 876A>G Lys292Lys
M0126592 PJDEFLKM_00002 2837 4 Oral 0.40 protein_coding synonymous_variant LOW 213T>C Ile71Ile
M0126593 PJDEFLKM_00001 3087 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -1859T>G None
M0126594 PJDEFLKM_00003 3332 3 Oral 0.30 protein_coding synonymous_variant LOW 759C>T Cys253Cys
M0126595 PJDEFLKM_00003 3446 4 Oral 0.40 protein_coding synonymous_variant LOW 645T>C Val215Val
M0126596 PJDEFLKM_00003 3479 5 Oral 0.50 protein_coding synonymous_variant LOW 612C>T Asn204Asn
M0126597 PJDEFLKM_00003 3488 5 Oral 0.50 protein_coding synonymous_variant LOW 603A>T Thr201Thr
M0126598 PJDEFLKM_00003 3497 3 Oral 0.30 protein_coding synonymous_variant LOW 594A>G Val198Val
M0126599 PJDEFLKM_00003 3716 3 Oral 0.30 protein_coding synonymous_variant LOW 375G>A Glu125Glu
M0126600 PJDEFLKM_00003 3830 4 Oral 0.40 protein_coding synonymous_variant LOW 261T>G Val87Val
M0126601 PJDEFLKM_00001 5102 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -3874C>T None
M0126602 PJDEFLKM_00004 40 5 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -4416A>T None
M0126603 PJDEFLKM_00004 56 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -4400T>A None
M0126604 PJDEFLKM_00001 4424 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -3196C>T None
M0126605 PJDEFLKM_00002 2436 3 Oral 0.30 protein_coding missense_variant MODERATE 614A>G Lys205Arg






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