Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2717
  Reference Plasmid   1111525849861727_bin.16__k141_120623
  Reference Plasmid Size   8551
  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
M0131516 HODCMFIL_00001 104 8 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -13T>C None
M0131517 HODCMFIL_00001 155 8 Oral 1.00 protein_coding synonymous_variant LOW 39C>T Leu13Leu
M0131518 HODCMFIL_00001 239 8 Oral 1.00 protein_coding synonymous_variant LOW 123C>T Asn41Asn
M0131519 HODCMFIL_00001 266 4 Oral 0.50 protein_coding synonymous_variant LOW 150A>T Ser50Ser
M0131520 HODCMFIL_00001 278 4 Oral 0.50 protein_coding synonymous_variant LOW 162G>A Lys54Lys
M0131521 HODCMFIL_00001 302 6 Oral 0.75 protein_coding synonymous_variant LOW 186C>T Asp62Asp
M0131522 HODCMFIL_00001 308 4 Oral 0.50 protein_coding synonymous_variant LOW 192C>T Tyr64Tyr
M0131523 HODCMFIL_00001 318 3 Oral 0.38 protein_coding missense_variant MODERATE 202A>C Ile68Leu
M0131524 HODCMFIL_00001 320 3 Oral 0.38 protein_coding synonymous_variant LOW 204C>T Ile68Ile
M0131525 HODCMFIL_00001 560 6 Oral 0.75 protein_coding synonymous_variant LOW 444A>G Leu148Leu
M0131526 HODCMFIL_00001 908 8 Oral 1.00 protein_coding synonymous_variant LOW 792A>T Val264Val
M0131527 HODCMFIL_00001 956 8 Oral 1.00 protein_coding synonymous_variant LOW 840C>T Gly280Gly
M0131528 HODCMFIL_00001 975 6 Oral 0.75 protein_coding missense_variant MODERATE 859A>G Asn287Asp
M0131529 HODCMFIL_00001 980 6 Oral 0.75 protein_coding synonymous_variant LOW 864G>A Glu288Glu
M0131530 HODCMFIL_00001 1060 8 Oral 1.00 protein_coding missense_variant MODERATE 944T>A Leu315His
M0131531 HODCMFIL_00001 1066 8 Oral 1.00 protein_coding missense_variant MODERATE 950T>G Val317Gly
M0131532 HODCMFIL_00001 1122 3 Oral 0.38 protein_coding missense_variant MODERATE 1006A>G Ile336Val
M0131533 HODCMFIL_00002 1586 8 Oral 1.00 protein_coding missense_variant MODERATE 255A>G Ile85Met
M0131534 HODCMFIL_00002 1775 3 Oral 0.38 protein_coding synonymous_variant LOW 444A>G Glu148Glu
M0131535 HODCMFIL_00002 1838 3 Oral 0.38 protein_coding synonymous_variant LOW 507C>T Ile169Ile
M0131536 HODCMFIL_00002 1888 8 Oral 1.00 protein_coding missense_variant MODERATE 557G>A Arg186Lys
M0131537 HODCMFIL_00002 1925 6 Oral 0.75 protein_coding synonymous_variant LOW 594T>A Val198Val
M0131538 HODCMFIL_00002 1946 6 Oral 0.75 protein_coding synonymous_variant LOW 615T>A Ala205Ala
M0131539 HODCMFIL_00002 1975 7 Oral 0.88 protein_coding missense_variant MODERATE 644G>A Arg215Lys
M0131540 HODCMFIL_00002 2015 8 Oral 1.00 protein_coding synonymous_variant LOW 684G>A Ala228Ala
M0131541 HODCMFIL_00002 2324 3 Oral 0.38 protein_coding synonymous_variant LOW 993C>A Thr331Thr
M0131542 HODCMFIL_00002 2326 3 Oral 0.38 protein_coding missense_variant MODERATE 995G>C Ser332Thr
M0131543 HODCMFIL_00002 2405 8 Oral 1.00 protein_coding synonymous_variant LOW 1074T>C Tyr358Tyr
M0131544 HODCMFIL_00002 2757 7 Oral 0.88 protein_coding missense_variant MODERATE 1426G>A Ala476Thr
M0131545 HODCMFIL_00003 3267 8 Oral 1.00 protein_coding missense_variant MODERATE 362A>G Lys121Arg
M0131546 HODCMFIL_00003 3304 8 Oral 1.00 protein_coding synonymous_variant LOW 399G>T Ser133Ser
M0131547 HODCMFIL_00003 3316 6 Oral 0.75 protein_coding synonymous_variant LOW 411T>C Ser137Ser
M0131548 HODCMFIL_00004 3757 5 Oral 0.63 protein_coding synonymous_variant LOW 210T>C Gly70Gly
M0131549 HODCMFIL_00004 3808 8 Oral 1.00 protein_coding synonymous_variant LOW 261T>A Ser87Ser
M0131550 HODCMFIL_00004 3901 4 Oral 0.50 protein_coding synonymous_variant LOW 354A>C Val118Val
M0131551 HODCMFIL_00004 3927 6 Oral 0.75 protein_coding missense_variant MODERATE 380C>A Ala127Asp
M0131552 HODCMFIL_00004 3934 4 Oral 0.50 protein_coding synonymous_variant LOW 387T>C Ser129Ser
M0131553 HODCMFIL_00004 3943 4 Oral 0.50 protein_coding synonymous_variant LOW 396A>G Val132Val
M0131554 HODCMFIL_00005 4152 8 Oral 1.00 protein_coding synonymous_variant LOW 75T>C Ser25Ser
M0131555 HODCMFIL_00005 4332 3 Oral 0.38 protein_coding synonymous_variant LOW 255C>T His85His
M0131556 HODCMFIL_00005 4545 3 Oral 0.38 protein_coding synonymous_variant LOW 468T>C Tyr156Tyr
M0131557 HODCMFIL_00005 4662 6 Oral 0.75 protein_coding synonymous_variant LOW 585A>T Ile195Ile
M0131558 HODCMFIL_00005 4797 7 Oral 0.88 protein_coding synonymous_variant LOW 720T>C Ile240Ile
M0131559 HODCMFIL_00005 4911 3 Oral 0.38 protein_coding synonymous_variant LOW 834C>T Val278Val
M0131560 HODCMFIL_00005 4941 8 Oral 1.00 protein_coding synonymous_variant LOW 864C>T Ala288Ala
M0131561 HODCMFIL_00005 5196 7 Oral 0.88 protein_coding synonymous_variant LOW 1119C>T Leu373Leu
M0131562 HODCMFIL_00006 5584 3 Oral 0.38 protein_coding missense_variant MODERATE 39G>T Leu13Phe
M0131563 HODCMFIL_00006 5794 5 Oral 0.63 protein_coding synonymous_variant LOW 249T>A Thr83Thr
M0131564 HODCMFIL_00006 5813 7 Oral 0.88 protein_coding missense_variant MODERATE 268G>A Val90Ile
M0131565 HODCMFIL_00006 5815 7 Oral 0.88 protein_coding synonymous_variant LOW 270A>C Val90Val
M0131566 HODCMFIL_00006 5956 5 Oral 0.63 protein_coding synonymous_variant LOW 411C>T Cys137Cys
M0131567 HODCMFIL_00006 6094 7 Oral 0.88 protein_coding synonymous_variant LOW 549C>A Ala183Ala
M0131568 HODCMFIL_00006 6184 5 Oral 0.63 protein_coding synonymous_variant LOW 639T>C Asn213Asn
M0131569 HODCMFIL_00006 6346 6 Oral 0.75 protein_coding synonymous_variant LOW 801T>C Asp267Asp
M0131570 HODCMFIL_00006 6379 7 Oral 0.88 protein_coding synonymous_variant LOW 834T>C Tyr278Tyr
M0131571 HODCMFIL_00006 6637 3 Oral 0.38 protein_coding synonymous_variant LOW 1092C>T Cys364Cys
M0131572 HODCMFIL_00006 6643 4 Oral 0.50 protein_coding synonymous_variant LOW 1098T>A Val366Val
M0131573 HODCMFIL_00006 6667 4 Oral 0.50 protein_coding synonymous_variant LOW 1122A>G Glu374Glu
M0131574 HODCMFIL_00006 6668 4 Oral 0.50 protein_coding missense_variant MODERATE 1123A>G Thr375Ala
M0131575 HODCMFIL_00006 6774 4 Oral 0.50 protein_coding missense_variant MODERATE 1229A>G Asp410Gly
M0131576 HODCMFIL_00006 6854 3 Oral 0.38 protein_coding missense_variant MODERATE 1309A>G Thr437Ala
M0131577 HODCMFIL_00006 7009 5 Oral 0.63 protein_coding synonymous_variant LOW 1464C>T Ile488Ile
M0131578 HODCMFIL_00006 7159 7 Oral 0.88 protein_coding synonymous_variant LOW 1614T>A Ala538Ala
M0131579 HODCMFIL_00006 7183 7 Oral 0.88 protein_coding synonymous_variant LOW 1638A>T Ser546Ser
M0131580 HODCMFIL_00006 7216 7 Oral 0.88 protein_coding synonymous_variant LOW 1671T>C Thr557Thr
M0131581 HODCMFIL_00006 7356 7 Oral 0.88 protein_coding missense_variant MODERATE 1811T>C Val604Ala
M0131582 HODCMFIL_00006 7531 4 Oral 0.50 protein_coding synonymous_variant LOW 1986C>T Ser662Ser
M0131583 HODCMFIL_00006 7600 7 Oral 0.88 protein_coding synonymous_variant LOW 2055T>C Phe685Phe
M0131584 HODCMFIL_00006 7771 3 Oral 0.38 protein_coding synonymous_variant LOW 2226C>T Ile742Ile
M0131585 HODCMFIL_00006 7846 7 Oral 0.88 protein_coding synonymous_variant LOW 2301T>C Leu767Leu
M0131586 HODCMFIL_00006 7854 4 Oral 0.50 protein_coding missense_variant MODERATE 2309G>A Arg770Lys
M0131587 HODCMFIL_00006 7882 6 Oral 0.75 protein_coding synonymous_variant LOW 2337C>T Arg779Arg
M0131588 HODCMFIL_00006 7942 6 Oral 0.75 protein_coding synonymous_variant LOW 2397T>A Thr799Thr
M0131589 HODCMFIL_00006 8038 6 Oral 0.75 protein_coding synonymous_variant LOW 2493A>G Leu831Leu
M0131590 HODCMFIL_00006 8171 7 Oral 0.88 protein_coding missense_variant MODERATE 2626G>C Val876Leu
M0131591 HODCMFIL_00006 8209 3 Oral 0.38 protein_coding synonymous_variant LOW 2664T>C Gly888Gly
M0131592 HODCMFIL_00006 8350 3 Oral 0.38 protein_coding missense_variant MODERATE 2805A>T Glu935Asp
M0131593 HODCMFIL_00006 8356 5 Oral 0.63 protein_coding synonymous_variant LOW 2811G>A Lys937Lys
M0131594 HODCMFIL_00003 8418 6 Oral 0.75 protein_coding downstream_gene_variant MODIFIER *4874G>A None
M0131595 HODCMFIL_00003 8438 7 Oral 0.88 protein_coding downstream_gene_variant MODIFIER *4894T>C None
M0131596 HODCMFIL_00001 62 5 Oral 0.63 protein_coding upstream_gene_variant MODIFIER -55A>G None
M0131597 HODCMFIL_00001 658 3 Oral 0.38 protein_coding missense_variant MODERATE 542C>A Ala181Glu
M0131598 HODCMFIL_00001 823 5 Oral 0.63 protein_coding missense_variant MODERATE 707T>C Val236Ala
M0131599 HODCMFIL_00001 1133 4 Oral 0.50 protein_coding synonymous_variant LOW 1017A>G Gln339Gln
M0131600 HODCMFIL_00002 1814 6 Oral 0.75 protein_coding synonymous_variant LOW 483A>G Gln161Gln
M0131601 HODCMFIL_00002 1865 3 Oral 0.38 protein_coding synonymous_variant LOW 534G>A Leu178Leu
M0131602 HODCMFIL_00003 3217 7 Oral 0.88 protein_coding synonymous_variant LOW 312T>C Ile104Ile
M0131603 HODCMFIL_00003 3430 7 Oral 0.88 protein_coding synonymous_variant LOW 525T>C Ile175Ile
M0131604 HODCMFIL_00005 4041 6 Oral 0.75 protein_coding upstream_gene_variant MODIFIER -37T>C None
M0131605 HODCMFIL_00005 4599 7 Oral 0.88 protein_coding synonymous_variant LOW 522A>C Pro174Pro
M0131606 HODCMFIL_00005 4623 4 Oral 0.50 protein_coding synonymous_variant LOW 546C>T Gly182Gly
M0131607 HODCMFIL_00005 4767 4 Oral 0.50 protein_coding synonymous_variant LOW 690G>A Leu230Leu
M0131608 HODCMFIL_00005 4851 3 Oral 0.38 protein_coding synonymous_variant LOW 774A>G Ala258Ala
M0131609 HODCMFIL_00006 5839 4 Oral 0.50 protein_coding synonymous_variant LOW 294T>C Asn98Asn
M0131610 HODCMFIL_00006 5939 6 Oral 0.75 protein_coding missense_variant MODERATE 394G>A Val132Met
M0131611 HODCMFIL_00006 6526 6 Oral 0.75 protein_coding synonymous_variant LOW 981C>T Ser327Ser
M0131612 HODCMFIL_00006 6985 3 Oral 0.38 protein_coding synonymous_variant LOW 1440C>T Gly480Gly
M0131613 HODCMFIL_00006 7046 4 Oral 0.50 protein_coding missense_variant MODERATE 1501A>G Ile501Val
M0131614 HODCMFIL_00006 7174 5 Oral 0.63 protein_coding synonymous_variant LOW 1629C>T Gly543Gly
M0131615 HODCMFIL_00006 7207 3 Oral 0.38 protein_coding synonymous_variant LOW 1662C>T Ala554Ala
M0131616 HODCMFIL_00006 7318 6 Oral 0.75 protein_coding synonymous_variant LOW 1773T>C Leu591Leu
M0131617 HODCMFIL_00006 7558 3 Oral 0.38 protein_coding synonymous_variant LOW 2013T>A Ala671Ala
M0131618 HODCMFIL_00006 7732 4 Oral 0.50 protein_coding synonymous_variant LOW 2187A>G Lys729Lys
M0131619 HODCMFIL_00006 7735 4 Oral 0.50 protein_coding synonymous_variant LOW 2190A>T Ile730Ile
M0131620 HODCMFIL_00006 8136 4 Oral 0.50 protein_coding missense_variant MODERATE 2591G>A Ser864Asn
M0131621 HODCMFIL_00001 330 3 Oral 0.38 protein_coding missense_variant MODERATE 214T>A Leu72Met
M0131622 HODCMFIL_00002 1577 4 Oral 0.50 protein_coding synonymous_variant LOW 246C>T Arg82Arg
M0131623 HODCMFIL_00002 1816 4 Oral 0.50 protein_coding missense_variant MODERATE 485C>G Thr162Ser
M0131624 HODCMFIL_00002 1904 5 Oral 0.63 protein_coding synonymous_variant LOW 573G>A Ala191Ala
M0131625 HODCMFIL_00004 3650 4 Oral 0.50 protein_coding missense_variant MODERATE 103A>G Thr35Ala
M0131626 HODCMFIL_00004 3688 4 Oral 0.50 protein_coding synonymous_variant LOW 141T>G Val47Val
M0131627 HODCMFIL_00004 3946 6 Oral 0.75 protein_coding synonymous_variant LOW 399C>T Tyr133Tyr
M0131628 HODCMFIL_00005 4042 3 Oral 0.38 protein_coding upstream_gene_variant MODIFIER -36C>T None
M0131629 HODCMFIL_00005 5235 4 Oral 0.50 protein_coding missense_variant MODERATE 1158T>G Ile386Met
M0131630 HODCMFIL_00006 7591 3 Oral 0.38 protein_coding synonymous_variant LOW 2046C>T Pro682Pro
M0131631 HODCMFIL_00006 7855 3 Oral 0.38 protein_coding missense_variant MODERATE 2310A>C Arg770Ser
M0131632 HODCMFIL_00003 8389 3 Oral 0.38 protein_coding downstream_gene_variant MODIFIER *4845T>C None
M0131633 HODCMFIL_00003 8456 4 Oral 0.50 protein_coding downstream_gene_variant MODIFIER *4912G>A None
M0131634 HODCMFIL_00003 8485 3 Oral 0.38 protein_coding downstream_gene_variant MODIFIER *4941T>C None
M0131635 HODCMFIL_00002 1964 3 Oral 0.38 protein_coding synonymous_variant LOW 633G>A Leu211Leu
M0131636 HODCMFIL_00002 2252 4 Oral 0.50 protein_coding synonymous_variant LOW 921A>G Gln307Gln
M0131637 HODCMFIL_00005 4512 3 Oral 0.38 protein_coding synonymous_variant LOW 435G>A Glu145Glu
M0131638 HODCMFIL_00005 4746 5 Oral 0.63 protein_coding missense_variant MODERATE 669T>A Asp223Glu
M0131639 HODCMFIL_00001 138 3 Oral 0.38 protein_coding synonymous_variant LOW 22C>T Leu8Leu
M0131640 HODCMFIL_00001 1088 3 Oral 0.38 protein_coding synonymous_variant LOW 972A>G Glu324Glu






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