Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3351
  Reference Plasmid   MGYG000298844__MGYG000298844_14
  Reference Plasmid Size   14365
  Reference Plasmid GC Content   0.41
  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
M0136491 HALCJMND_00001 1016 3 Oral 0.30 protein_coding synonymous_variant LOW 450C>T Gly150Gly
M0136492 HALCJMND_00001 1100 3 Oral 0.30 protein_coding missense_variant MODERATE 534A>C Glu178Asp
M0136493 HALCJMND_00001 1139 4 Oral 0.40 protein_coding synonymous_variant LOW 573T>C Gly191Gly
M0136494 HALCJMND_00002 1287 4 Oral 0.40 protein_coding missense_variant MODERATE 10C>A Gln4Lys
M0136495 HALCJMND_00002 1427 4 Oral 0.40 protein_coding synonymous_variant LOW 150G>T Val50Val
M0136496 HALCJMND_00002 1448 4 Oral 0.40 protein_coding synonymous_variant LOW 171G>A Gly57Gly
M0136497 HALCJMND_00002 1469 3 Oral 0.30 protein_coding synonymous_variant LOW 192G>A Leu64Leu
M0136498 HALCJMND_00002 1522 4 Oral 0.40 protein_coding missense_variant MODERATE 245A>G Asn82Ser
M0136499 HALCJMND_00002 1526 3 Oral 0.30 protein_coding synonymous_variant LOW 249C>T Asp83Asp
M0136500 HALCJMND_00002 1565 4 Oral 0.40 protein_coding synonymous_variant LOW 288A>G Leu96Leu
M0136501 HALCJMND_00009 8304 3 Oral 0.30 protein_coding synonymous_variant LOW 42G>T Ala14Ala
M0136502 HALCJMND_00009 8346 3 Oral 0.30 protein_coding synonymous_variant LOW 84A>T Ala28Ala
M0136503 HALCJMND_00009 8403 4 Oral 0.40 protein_coding synonymous_variant LOW 141T>C Ala47Ala
M0136504 HALCJMND_00009 8944 4 Oral 0.40 protein_coding missense_variant MODERATE 682A>G Ile228Val
M0136505 HALCJMND_00009 9027 3 Oral 0.30 protein_coding synonymous_variant LOW 765G>A Val255Val
M0136506 HALCJMND_00009 9204 3 Oral 0.30 protein_coding synonymous_variant LOW 942T>C Gly314Gly
M0136507 HALCJMND_00009 9276 4 Oral 0.40 protein_coding synonymous_variant LOW 1014T>A Val338Val
M0136508 HALCJMND_00009 9315 3 Oral 0.30 protein_coding synonymous_variant LOW 1053C>T Ala351Ala
M0136509 HALCJMND_00009 9327 4 Oral 0.40 protein_coding synonymous_variant LOW 1065G>T Ser355Ser
M0136510 HALCJMND_00008 9555 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -1464A>G None
M0136511 HALCJMND_00008 9665 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -1574T>G None
M0136512 HALCJMND_00008 9683 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -1592C>T None
M0136513 HALCJMND_00010 9961 3 Oral 0.30 protein_coding synonymous_variant LOW 207C>T Thr69Thr
M0136514 HALCJMND_00003 2733 4 Oral 0.40 protein_coding synonymous_variant LOW 477C>T Asn159Asn
M0136515 HALCJMND_00003 2748 3 Oral 0.30 protein_coding synonymous_variant LOW 492T>C Cys164Cys
M0136516 HALCJMND_00004 2855 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -130T>A None
M0136517 HALCJMND_00004 2862 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -123T>C None
M0136518 HALCJMND_00004 2937 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -48T>G None
M0136519 HALCJMND_00004 3500 3 Oral 0.30 protein_coding synonymous_variant LOW 516C>T Tyr172Tyr
M0136520 HALCJMND_00004 3812 3 Oral 0.30 protein_coding synonymous_variant LOW 828A>T Thr276Thr
M0136521 HALCJMND_00005 4020 3 Oral 0.30 protein_coding missense_variant MODERATE 25C>T Leu9Phe
M0136522 HALCJMND_00005 4073 3 Oral 0.30 protein_coding synonymous_variant LOW 78A>G Val26Val
M0136523 HALCJMND_00005 4163 4 Oral 0.40 protein_coding synonymous_variant LOW 168G>A Arg56Arg
M0136524 HALCJMND_00005 4191 4 Oral 0.40 protein_coding missense_variant MODERATE 196G>A Val66Ile
M0136525 HALCJMND_00001 540 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -27A>G None
M0136526 HALCJMND_00001 564 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -3A>G None
M0136527 HALCJMND_00001 665 3 Oral 0.30 protein_coding synonymous_variant LOW 99T>C Pro33Pro
M0136528 HALCJMND_00002 1994 3 Oral 0.30 protein_coding synonymous_variant LOW 717T>G Thr239Thr
M0136529 HALCJMND_00002 2065 3 Oral 0.30 protein_coding missense_variant MODERATE 788G>A Arg263Lys
M0136530 HALCJMND_00002 2138 3 Oral 0.30 protein_coding synonymous_variant LOW 861T>C Ser287Ser
M0136531 HALCJMND_00002 2198 3 Oral 0.30 protein_coding synonymous_variant LOW 921T>A Gly307Gly
M0136532 HALCJMND_00003 2311 3 Oral 0.30 protein_coding missense_variant MODERATE 55C>G Pro19Ala
M0136533 HALCJMND_00003 2373 3 Oral 0.30 protein_coding synonymous_variant LOW 117A>G Glu39Glu
M0136534 HALCJMND_00003 2484 3 Oral 0.30 protein_coding synonymous_variant LOW 228G>T Arg76Arg
M0136535 HALCJMND_00003 2495 3 Oral 0.30 protein_coding missense_variant MODERATE 239A>C Asn80Thr
M0136536 HALCJMND_00003 2500 3 Oral 0.30 protein_coding synonymous_variant LOW 244C>T Leu82Leu
M0136537 HALCJMND_00003 2577 3 Oral 0.30 protein_coding synonymous_variant LOW 321A>T Ala107Ala
M0136538 HALCJMND_00003 2579 3 Oral 0.30 protein_coding missense_variant MODERATE 323A>T Lys108Met
M0136539 HALCJMND_00004 2967 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -18A>T None
M0136540 HALCJMND_00005 4520 3 Oral 0.30 protein_coding synonymous_variant LOW 525T>C Phe175Phe
M0136541 HALCJMND_00006 5554 3 Oral 0.30 protein_coding synonymous_variant LOW 207T>G Val69Val
M0136542 HALCJMND_00006 5560 3 Oral 0.30 protein_coding synonymous_variant LOW 213G>A Pro71Pro
M0136543 HALCJMND_00006 5626 4 Oral 0.40 protein_coding synonymous_variant LOW 279A>G Lys93Lys
M0136544 HALCJMND_00006 5630 4 Oral 0.40 protein_coding synonymous_variant LOW 283T>C Leu95Leu
M0136545 HALCJMND_00006 5632 3 Oral 0.30 protein_coding synonymous_variant LOW 285G>A Leu95Leu
M0136546 HALCJMND_00006 5719 3 Oral 0.30 protein_coding synonymous_variant LOW 372C>T His124His
M0136547 HALCJMND_00006 5888 3 Oral 0.30 protein_coding missense_variant MODERATE 541A>G Thr181Ala
M0136548 HALCJMND_00007 6013 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -176T>G None
M0136549 HALCJMND_00007 6032 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -157T>C None
M0136550 HALCJMND_00007 6046 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -143A>G None
M0136551 HALCJMND_00007 6047 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -142T>C None
M0136552 HALCJMND_00007 6464 3 Oral 0.30 protein_coding synonymous_variant LOW 276T>G Thr92Thr
M0136553 HALCJMND_00007 6510 4 Oral 0.40 protein_coding missense_variant MODERATE 322A>G Lys108Glu
M0136554 HALCJMND_00007 6890 3 Oral 0.30 protein_coding synonymous_variant LOW 702G>A Leu234Leu
M0136555 HALCJMND_00007 6901 3 Oral 0.30 protein_coding missense_variant MODERATE 713G>A Arg238Lys
M0136556 HALCJMND_00007 7052 4 Oral 0.40 protein_coding synonymous_variant LOW 864T>C Asn288Asn
M0136557 HALCJMND_00009 7342 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -921A>G None
M0136558 HALCJMND_00008 7450 4 Oral 0.40 protein_coding synonymous_variant LOW 642C>T Asp214Asp
M0136559 HALCJMND_00008 7467 4 Oral 0.40 protein_coding synonymous_variant LOW 625T>C Leu209Leu
M0136560 HALCJMND_00008 7531 3 Oral 0.30 protein_coding synonymous_variant LOW 561T>A Gly187Gly
M0136561 HALCJMND_00008 7759 4 Oral 0.40 protein_coding synonymous_variant LOW 333A>C Arg111Arg
M0136562 HALCJMND_00008 7774 4 Oral 0.40 protein_coding synonymous_variant LOW 318T>C Ile106Ile
M0136563 HALCJMND_00008 7968 4 Oral 0.40 protein_coding synonymous_variant LOW 124C>A Arg42Arg
M0136564 HALCJMND_00009 8577 3 Oral 0.30 protein_coding synonymous_variant LOW 315C>T Val105Val
M0136565 HALCJMND_00010 9784 3 Oral 0.30 protein_coding synonymous_variant LOW 30G>T Val10Val
M0136566 HALCJMND_00008 7969 3 Oral 0.30 protein_coding synonymous_variant LOW 123C>T Cys41Cys
M0136567 HALCJMND_00006 5323 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -25A>C None
M0136568 HALCJMND_00006 5326 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -22T>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





        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