Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2456
  Reference Plasmid   1111525849768046_bin.37__k141_55837
  Reference Plasmid Size   3617
  Reference Plasmid GC Content   0.37
  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
M0127465 DOICGAGD_00001 62 6 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -69T>C None
M0127466 DOICGAGD_00001 262 4 Oral 0.40 protein_coding synonymous_variant LOW 132T>A Val44Val
M0127467 DOICGAGD_00001 289 4 Oral 0.40 protein_coding missense_variant MODERATE 159G>T Gln53His
M0127468 DOICGAGD_00001 292 4 Oral 0.40 protein_coding synonymous_variant LOW 162A>G Gln54Gln
M0127469 DOICGAGD_00001 295 6 Oral 0.60 protein_coding synonymous_variant LOW 165G>A Thr55Thr
M0127470 DOICGAGD_00001 311 4 Oral 0.40 protein_coding missense_variant MODERATE 181T>C Ser61Pro
M0127471 DOICGAGD_00001 313 8 Oral 0.80 protein_coding synonymous_variant LOW 183T>A Ser61Ser
M0127472 DOICGAGD_00001 319 4 Oral 0.40 protein_coding synonymous_variant LOW 189T>C Tyr63Tyr
M0127473 DOICGAGD_00002 367 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -9C>T None
M0127474 DOICGAGD_00002 407 7 Oral 0.70 protein_coding missense_variant MODERATE 32A>G Asn11Ser
M0127475 DOICGAGD_00002 453 6 Oral 0.60 protein_coding synonymous_variant LOW 78C>T Ile26Ile
M0127476 DOICGAGD_00002 717 10 Oral 1.00 protein_coding synonymous_variant LOW 342T>C Phe114Phe
M0127477 DOICGAGD_00002 816 7 Oral 0.70 protein_coding synonymous_variant LOW 441C>T Thr147Thr
M0127478 DOICGAGD_00002 921 5 Oral 0.50 protein_coding synonymous_variant LOW 546A>G Ser182Ser
M0127479 DOICGAGD_00002 951 10 Oral 1.00 protein_coding synonymous_variant LOW 576A>T Ala192Ala
M0127480 DOICGAGD_00002 1035 4 Oral 0.40 protein_coding synonymous_variant LOW 660T>A Ile220Ile
M0127481 DOICGAGD_00002 1038 4 Oral 0.40 protein_coding synonymous_variant LOW 663G>A Lys221Lys
M0127482 DOICGAGD_00002 1092 10 Oral 1.00 protein_coding synonymous_variant LOW 717C>T Gly239Gly
M0127483 DOICGAGD_00002 1494 6 Oral 0.60 protein_coding synonymous_variant LOW 1119G>A Glu373Glu
M0127484 DOICGAGD_00002 1645 10 Oral 1.00 protein_coding missense_variant MODERATE 1270A>G Ile424Val
M0127485 DOICGAGD_00002 1671 3 Oral 0.30 protein_coding synonymous_variant LOW 1296G>A Lys432Lys
M0127486 DOICGAGD_00002 1776 10 Oral 1.00 protein_coding synonymous_variant LOW 1401G>A Gln467Gln
M0127487 DOICGAGD_00002 1815 9 Oral 0.90 protein_coding synonymous_variant LOW 1440C>T Ala480Ala
M0127488 DOICGAGD_00002 1869 9 Oral 0.90 protein_coding synonymous_variant LOW 1494A>G Val498Val
M0127489 DOICGAGD_00002 1944 3 Oral 0.30 protein_coding synonymous_variant LOW 1569T>A Ile523Ile
M0127490 DOICGAGD_00003 2142 7 Oral 0.70 protein_coding synonymous_variant LOW 159A>C Arg53Arg
M0127491 DOICGAGD_00003 2373 3 Oral 0.30 protein_coding synonymous_variant LOW 390C>T Val130Val
M0127492 DOICGAGD_00003 2385 3 Oral 0.30 protein_coding synonymous_variant LOW 402C>A Gly134Gly
M0127493 DOICGAGD_00003 2388 3 Oral 0.30 protein_coding synonymous_variant LOW 405A>T Ala135Ala
M0127494 DOICGAGD_00003 2394 3 Oral 0.30 protein_coding synonymous_variant LOW 411T>A Ala137Ala
M0127495 DOICGAGD_00003 2487 3 Oral 0.30 protein_coding synonymous_variant LOW 504T>C His168His
M0127496 DOICGAGD_00003 2508 6 Oral 0.60 protein_coding synonymous_variant LOW 525T>C Asp175Asp
M0127497 DOICGAGD_00003 2580 5 Oral 0.50 protein_coding synonymous_variant LOW 597C>T Asn199Asn
M0127498 DOICGAGD_00003 2586 5 Oral 0.50 protein_coding synonymous_variant LOW 603G>A Val201Val
M0127499 DOICGAGD_00003 2673 5 Oral 0.50 protein_coding synonymous_variant LOW 690T>C Ile230Ile
M0127500 DOICGAGD_00003 2760 5 Oral 0.50 protein_coding synonymous_variant LOW 777C>A Val259Val
M0127501 DOICGAGD_00003 2784 3 Oral 0.30 protein_coding synonymous_variant LOW 801G>A Val267Val
M0127502 DOICGAGD_00003 2838 10 Oral 1.00 protein_coding synonymous_variant LOW 855A>T Thr285Thr
M0127503 DOICGAGD_00003 2871 6 Oral 0.60 protein_coding synonymous_variant LOW 888C>A Gly296Gly
M0127504 DOICGAGD_00003 2892 8 Oral 0.80 protein_coding synonymous_variant LOW 909A>G Val303Val
M0127505 DOICGAGD_00003 2895 5 Oral 0.50 protein_coding synonymous_variant LOW 912G>A Leu304Leu
M0127506 DOICGAGD_00003 2961 3 Oral 0.30 protein_coding synonymous_variant LOW 978C>T Ser326Ser
M0127507 DOICGAGD_00003 2973 3 Oral 0.30 protein_coding synonymous_variant LOW 990C>A Ile330Ile
M0127508 DOICGAGD_00003 3093 7 Oral 0.70 protein_coding synonymous_variant LOW 1110C>T Asp370Asp
M0127509 DOICGAGD_00003 3118 5 Oral 0.50 protein_coding missense_variant MODERATE 1135C>G Leu379Val
M0127510 DOICGAGD_00001 3214 4 Oral 0.40 protein_coding downstream_gene_variant MODIFIER *2862C>T None
M0127511 DOICGAGD_00001 3340 9 Oral 0.90 protein_coding downstream_gene_variant MODIFIER *2988G>A None
M0127512 DOICGAGD_00001 3421 7 Oral 0.70 protein_coding downstream_gene_variant MODIFIER *3069C>T None
M0127513 DOICGAGD_00001 3449 5 Oral 0.50 protein_coding downstream_gene_variant MODIFIER *3097T>A None
M0127514 DOICGAGD_00001 3481 9 Oral 0.90 protein_coding downstream_gene_variant MODIFIER *3129A>G None
M0127515 DOICGAGD_00001 63 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -68G>T None
M0127516 DOICGAGD_00002 549 8 Oral 0.80 protein_coding synonymous_variant LOW 174A>G Lys58Lys
M0127517 DOICGAGD_00002 585 4 Oral 0.40 protein_coding synonymous_variant LOW 210T>C Ile70Ile
M0127518 DOICGAGD_00002 639 3 Oral 0.30 protein_coding synonymous_variant LOW 264T>C Thr88Thr
M0127519 DOICGAGD_00002 735 5 Oral 0.50 protein_coding synonymous_variant LOW 360G>A Val120Val
M0127520 DOICGAGD_00002 960 4 Oral 0.40 protein_coding synonymous_variant LOW 585A>G Lys195Lys
M0127521 DOICGAGD_00002 1581 8 Oral 0.80 protein_coding synonymous_variant LOW 1206T>A Pro402Pro
M0127522 DOICGAGD_00002 1603 7 Oral 0.70 protein_coding missense_variant MODERATE 1228C>T Leu410Phe
M0127523 DOICGAGD_00002 1699 4 Oral 0.40 protein_coding missense_variant MODERATE 1324A>G Ile442Val
M0127524 DOICGAGD_00003 2154 4 Oral 0.40 protein_coding synonymous_variant LOW 171C>T Ile57Ile
M0127525 DOICGAGD_00003 2791 3 Oral 0.30 protein_coding missense_variant MODERATE 808G>A Val270Ile
M0127526 DOICGAGD_00003 2844 3 Oral 0.30 protein_coding synonymous_variant LOW 861C>T Asn287Asn
M0127527 DOICGAGD_00001 3160 5 Oral 0.50 protein_coding downstream_gene_variant MODIFIER *2808T>C None
M0127528 DOICGAGD_00002 408 5 Oral 0.50 protein_coding synonymous_variant LOW 33C>T Asn11Asn
M0127529 DOICGAGD_00002 628 4 Oral 0.40 protein_coding missense_variant MODERATE 253C>G Gln85Glu
M0127530 DOICGAGD_00002 813 3 Oral 0.30 protein_coding synonymous_variant LOW 438A>T Ala146Ala
M0127531 DOICGAGD_00002 1077 3 Oral 0.30 protein_coding synonymous_variant LOW 702C>T Ile234Ile
M0127532 DOICGAGD_00002 1243 3 Oral 0.30 protein_coding stop_gained HIGH 868A>T Lys290*
M0127533 DOICGAGD_00002 1244 3 Oral 0.30 protein_coding missense_variant MODERATE 869A>C Lys290Thr
M0127534 DOICGAGD_00002 1263 3 Oral 0.30 protein_coding synonymous_variant LOW 888A>G Glu296Glu
M0127535 DOICGAGD_00002 1291 5 Oral 0.50 protein_coding missense_variant MODERATE 916G>A Val306Ile
M0127536 DOICGAGD_00002 1440 5 Oral 0.50 protein_coding synonymous_variant LOW 1065T>A Thr355Thr
M0127537 DOICGAGD_00002 1485 3 Oral 0.30 protein_coding synonymous_variant LOW 1110A>G Ala370Ala
M0127538 DOICGAGD_00001 3235 3 Oral 0.30 protein_coding downstream_gene_variant MODIFIER *2883G>A None
M0127539 DOICGAGD_00001 110 5 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -21C>T None
M0127540 DOICGAGD_00001 124 5 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -7T>C None
M0127541 DOICGAGD_00001 130 5 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -1G>A None
M0127542 DOICGAGD_00001 241 5 Oral 0.50 protein_coding synonymous_variant LOW 111A>C Ile37Ile
M0127543 DOICGAGD_00002 1341 3 Oral 0.30 protein_coding synonymous_variant LOW 966G>A Val322Val
M0127544 DOICGAGD_00002 1353 3 Oral 0.30 protein_coding synonymous_variant LOW 978C>T Asn326Asn
M0127545 DOICGAGD_00002 1386 4 Oral 0.40 protein_coding synonymous_variant LOW 1011C>T Gly337Gly
M0127546 DOICGAGD_00002 1426 4 Oral 0.40 protein_coding missense_variant MODERATE 1051A>C Lys351Gln
M0127547 DOICGAGD_00001 122 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -9A>G None
M0127548 DOICGAGD_00002 504 3 Oral 0.30 protein_coding synonymous_variant LOW 129C>A Gly43Gly
M0127549 DOICGAGD_00003 2535 3 Oral 0.30 protein_coding synonymous_variant LOW 552C>A Ala184Ala






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