Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2673
  Reference Plasmid   1111525849859858_bin.38__k141_434439
  Reference Plasmid Size   15396
  Reference Plasmid GC Content   0.57
  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
M0052730 OPHIJLDE_00001 141 7 Skin 0.18 protein_coding synonymous_variant LOW 75A>C Ala25Ala
M0052731 OPHIJLDE_00001 147 7 Skin 0.18 protein_coding synonymous_variant LOW 81G>T Pro27Pro
M0052732 OPHIJLDE_00001 156 7 Skin 0.18 protein_coding synonymous_variant LOW 90C>T Ile30Ile
M0052733 OPHIJLDE_00001 162 7 Skin 0.18 protein_coding synonymous_variant LOW 96C>A Ser32Ser
M0052734 OPHIJLDE_00001 180 7 Skin 0.18 protein_coding synonymous_variant LOW 114C>T Gly38Gly
M0052735 OPHIJLDE_00001 181 7 Skin 0.18 protein_coding synonymous_variant LOW 115C>T Leu39Leu
M0052736 OPHIJLDE_00001 189 7 Skin 0.18 protein_coding synonymous_variant LOW 123T>C Asp41Asp
M0052737 OPHIJLDE_00001 204 7 Skin 0.18 protein_coding synonymous_variant LOW 138C>T Tyr46Tyr
M0052738 OPHIJLDE_00001 213 7 Skin 0.18 protein_coding synonymous_variant LOW 147T>C Cys49Cys
M0052739 OPHIJLDE_00001 249 7 Skin 0.18 protein_coding synonymous_variant LOW 183T>C Thr61Thr
M0052740 OPHIJLDE_00001 252 7 Skin 0.18 protein_coding synonymous_variant LOW 186C>T Leu62Leu
M0052741 OPHIJLDE_00001 268 7 Skin 0.18 protein_coding synonymous_variant LOW 202C>T Leu68Leu
M0052742 OPHIJLDE_00001 279 7 Skin 0.18 protein_coding synonymous_variant LOW 213C>T Asp71Asp
M0052743 OPHIJLDE_00001 306 7 Skin 0.18 protein_coding synonymous_variant LOW 240A>G Glu80Glu
M0052744 OPHIJLDE_00001 327 7 Skin 0.18 protein_coding synonymous_variant LOW 261G>A Pro87Pro
M0052745 OPHIJLDE_00001 333 7 Skin 0.18 protein_coding synonymous_variant LOW 267C>T Ile89Ile
M0052746 OPHIJLDE_00001 477 3 Skin 0.08 protein_coding synonymous_variant LOW 411A>C Gly137Gly
M0052747 OPHIJLDE_00001 483 3 Skin 0.08 protein_coding synonymous_variant LOW 417A>G Pro139Pro
M0052748 OPHIJLDE_00001 498 3 Skin 0.08 protein_coding synonymous_variant LOW 432C>T Ser144Ser
M0052749 OPHIJLDE_00002 1547 7 Skin 0.18 protein_coding synonymous_variant LOW 660C>T Arg220Arg
M0052750 OPHIJLDE_00002 1637 7 Skin 0.18 protein_coding synonymous_variant LOW 750A>T Ile250Ile
M0052751 OPHIJLDE_00004 3240 7 Skin 0.18 protein_coding synonymous_variant LOW 72T>C Ser24Ser
M0052752 OPHIJLDE_00004 3309 5 Skin 0.13 protein_coding synonymous_variant LOW 141T>C Gly47Gly
M0052753 OPHIJLDE_00004 3463 6 Skin 0.15 protein_coding missense_variant MODERATE 295T>G Leu99Val
M0052754 OPHIJLDE_00007 4698 17 Skin 0.43 protein_coding upstream_gene_variant MODIFIER -20T>C None
M0052755 OPHIJLDE_00007 5642 3 Skin 0.08 protein_coding missense_variant MODERATE 925A>G Asn309Asp
M0052756 OPHIJLDE_00008 6003 13 Skin 0.33 protein_coding synonymous_variant LOW 279T>C Ala93Ala
M0052757 OPHIJLDE_00009 7327 11 Skin 0.28 protein_coding synonymous_variant LOW 594C>A Ile198Ile
M0052758 OPHIJLDE_00009 7361 10 Skin 0.25 protein_coding synonymous_variant LOW 628T>C Leu210Leu
M0052759 OPHIJLDE_00010 8067 14 Skin 0.35 protein_coding synonymous_variant LOW 531C>T Thr177Thr
M0052760 OPHIJLDE_00010 8082 14 Skin 0.35 protein_coding synonymous_variant LOW 546A>G Arg182Arg
M0052761 OPHIJLDE_00010 8097 13 Skin 0.33 protein_coding synonymous_variant LOW 561G>A Ala187Ala
M0052762 OPHIJLDE_00010 8652 5 Skin 0.13 protein_coding synonymous_variant LOW 1116C>T Ile372Ile
M0052763 OPHIJLDE_00010 8670 5 Skin 0.13 protein_coding synonymous_variant LOW 1134T>C Ala378Ala
M0052764 OPHIJLDE_00010 8674 5 Skin 0.13 protein_coding synonymous_variant LOW 1138T>C Leu380Leu
M0052765 OPHIJLDE_00011 8960 14 Skin 0.35 protein_coding synonymous_variant LOW 144T>C Ser48Ser
M0052766 OPHIJLDE_00011 9356 6 Skin 0.15 protein_coding synonymous_variant LOW 540T>A Ala180Ala
M0052767 OPHIJLDE_00011 9383 5 Skin 0.13 protein_coding synonymous_variant LOW 567G>A Val189Val
M0052768 OPHIJLDE_00011 9402 5 Skin 0.13 protein_coding missense_variant MODERATE 586G>A Val196Met
M0052769 OPHIJLDE_00011 9404 5 Skin 0.13 protein_coding synonymous_variant LOW 588G>A Val196Val
M0052770 OPHIJLDE_00012 10117 6 Skin 0.15 protein_coding missense_variant MODERATE 684G>T Glu228Asp
M0052771 OPHIJLDE_00012 10447 11 Skin 0.28 protein_coding synonymous_variant LOW 1014C>T Leu338Leu
M0052772 OPHIJLDE_00013 10718 6 Skin 0.15 protein_coding synonymous_variant LOW 159T>C Cys53Cys
M0052773 OPHIJLDE_00013 10748 5 Skin 0.13 protein_coding synonymous_variant LOW 189A>G Gln63Gln
M0052774 OPHIJLDE_00013 10764 5 Skin 0.13 protein_coding missense_variant MODERATE 205T>C Phe69Leu
M0052775 OPHIJLDE_00013 10856 4 Skin 0.10 protein_coding synonymous_variant LOW 297C>T Pro99Pro
M0052776 OPHIJLDE_00003 2728 7 Skin 0.18 protein_coding missense_variant MODERATE 300C>A Asp100Glu
M0052777 OPHIJLDE_00006 4491 7 Skin 0.18 protein_coding missense_variant MODERATE 263A>G Lys88Arg
M0052778 OPHIJLDE_00002 1031 5 Skin 0.13 protein_coding synonymous_variant LOW 144C>T Pro48Pro
M0052779 OPHIJLDE_00007 4919 8 Skin 0.20 protein_coding missense_variant MODERATE 202G>A Ala68Thr
M0052780 OPHIJLDE_00010 8196 6 Skin 0.15 protein_coding synonymous_variant LOW 660G>T Val220Val
M0052781 OPHIJLDE_00010 8532 10 Skin 0.25 protein_coding synonymous_variant LOW 996T>C Asn332Asn
M0052782 OPHIJLDE_00010 8733 10 Skin 0.25 protein_coding synonymous_variant LOW 1197G>C Ala399Ala
M0052783 OPHIJLDE_00011 8829 3 Skin 0.08 protein_coding missense_variant MODERATE 13G>A Val5Met
M0052784 OPHIJLDE_00011 8831 3 Skin 0.08 protein_coding synonymous_variant LOW 15G>T Val5Val
M0052785 OPHIJLDE_00011 8849 3 Skin 0.08 protein_coding synonymous_variant LOW 33A>G Gln11Gln
M0052786 OPHIJLDE_00011 9197 3 Skin 0.08 protein_coding synonymous_variant LOW 381G>T Leu127Leu
M0052787 OPHIJLDE_00014 12099 13 Skin 0.33 protein_coding missense_variant MODERATE 461C>A Pro154His
M0052788 OPHIJLDE_00010 12746 18 Skin 0.45 protein_coding downstream_gene_variant MODIFIER *3926T>C None
M0052789 OPHIJLDE_00015 12861 11 Skin 0.28 protein_coding synonymous_variant LOW 57G>C Val19Val
M0052790 OPHIJLDE_00015 12891 11 Skin 0.28 protein_coding synonymous_variant LOW 27A>T Pro9Pro
M0052791 OPHIJLDE_00016 13028 8 Skin 0.20 protein_coding synonymous_variant LOW 912G>A Val304Val
M0052792 OPHIJLDE_00016 13520 3 Skin 0.08 protein_coding synonymous_variant LOW 420C>T Gly140Gly
M0052793 OPHIJLDE_00016 13538 19 Skin 0.48 protein_coding synonymous_variant LOW 402T>C Val134Val
M0052794 OPHIJLDE_00016 13547 3 Skin 0.08 protein_coding synonymous_variant LOW 393A>G Gly131Gly
M0052795 OPHIJLDE_00007 5344 3 Skin 0.08 protein_coding synonymous_variant LOW 627C>T Thr209Thr
M0052796 OPHIJLDE_00009 6738 5 Skin 0.13 protein_coding missense_variant MODERATE 5T>C Val2Ala
M0052797 OPHIJLDE_00009 6913 7 Skin 0.18 protein_coding synonymous_variant LOW 180T>C Ser60Ser
M0052798 OPHIJLDE_00005 3985 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -23T>C None
M0052799 OPHIJLDE_00013 11525 4 Skin 0.10 protein_coding synonymous_variant LOW 966G>A Ala322Ala
M0052800 OPHIJLDE_00013 11531 4 Skin 0.10 protein_coding synonymous_variant LOW 972C>G Ala324Ala
M0052801 OPHIJLDE_00014 11932 9 Skin 0.23 protein_coding synonymous_variant LOW 294G>A Gln98Gln
M0052802 OPHIJLDE_00014 11935 9 Skin 0.23 protein_coding synonymous_variant LOW 297G>A Pro99Pro
M0052803 OPHIJLDE_00016 13366 4 Skin 0.10 protein_coding missense_variant MODERATE 574T>C Tyr192His
M0052804 OPHIJLDE_00016 13385 5 Skin 0.13 protein_coding synonymous_variant LOW 555T>C Gly185Gly
M0052805 OPHIJLDE_00016 13391 4 Skin 0.10 protein_coding synonymous_variant LOW 549G>A Thr183Thr
M0052806 OPHIJLDE_00016 13432 4 Skin 0.10 protein_coding missense_variant MODERATE 508A>G Thr170Ala
M0052807 OPHIJLDE_00017 14926 11 Skin 0.28 protein_coding synonymous_variant LOW 375A>G Thr125Thr
M0052808 OPHIJLDE_00007 5107 3 Skin 0.08 protein_coding synonymous_variant LOW 390T>G Ala130Ala
M0052809 OPHIJLDE_00007 5140 3 Skin 0.08 protein_coding synonymous_variant LOW 423C>T Gly141Gly
M0052810 OPHIJLDE_00008 6589 8 Skin 0.20 protein_coding missense_variant MODERATE 865G>C Gly289Arg
M0052811 OPHIJLDE_00010 8397 8 Skin 0.20 protein_coding synonymous_variant LOW 861T>C Arg287Arg
M0052812 OPHIJLDE_00010 8415 8 Skin 0.20 protein_coding synonymous_variant LOW 879T>G Val293Val
M0052813 OPHIJLDE_00010 8427 8 Skin 0.20 protein_coding synonymous_variant LOW 891G>C Leu297Leu
M0052814 OPHIJLDE_00010 8449 8 Skin 0.20 protein_coding missense_variant MODERATE 913A>G Thr305Ala
M0052815 OPHIJLDE_00013 11069 7 Skin 0.18 protein_coding synonymous_variant LOW 510C>T Ala170Ala
M0052816 OPHIJLDE_00014 12240 7 Skin 0.18 protein_coding missense_variant MODERATE 602T>C Ile201Thr
M0052817 OPHIJLDE_00008 6098 3 Skin 0.08 protein_coding missense_variant MODERATE 374A>T Gln125Leu
M0052818 OPHIJLDE_00012 9638 3 Skin 0.08 protein_coding synonymous_variant LOW 205T>C Leu69Leu
M0052819 OPHIJLDE_00014 12662 3 Skin 0.08 protein_coding synonymous_variant LOW 1024T>C Leu342Leu
M0052820 OPHIJLDE_00007 4945 7 Skin 0.18 protein_coding synonymous_variant LOW 228T>G Arg76Arg
M0052821 OPHIJLDE_00007 4946 7 Skin 0.18 protein_coding missense_variant MODERATE 229T>G Cys77Gly
M0052822 OPHIJLDE_00007 4949 7 Skin 0.18 protein_coding missense_variant MODERATE 232G>A Asp78Asn
M0052823 OPHIJLDE_00013 10907 3 Skin 0.08 protein_coding synonymous_variant LOW 348T>C Asp116Asp
M0052824 OPHIJLDE_00017 14685 6 Skin 0.15 protein_coding synonymous_variant LOW 616C>T Leu206Leu
M0052825 OPHIJLDE_00017 14713 6 Skin 0.15 protein_coding synonymous_variant LOW 588T>C Gly196Gly
M0052826 OPHIJLDE_00017 14734 6 Skin 0.15 protein_coding synonymous_variant LOW 567C>A Ala189Ala
M0052827 OPHIJLDE_00013 10601 4 Skin 0.10 protein_coding synonymous_variant LOW 42A>C Gly14Gly
M0052828 OPHIJLDE_00008 6395 3 Skin 0.08 protein_coding missense_variant MODERATE 671A>G His224Arg






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
OPHIJLDE_00002 PHI:10513 narH 86.4 6.4e-274 1 507 0.9864 0.9922 rodents urinary tract infection respiratory nitrate reductase 1 beta chain reduced virulence
OPHIJLDE_00004 PHI:10515 narI 82.1 6.6e-106 1 224 0.9956 0.9956 rodents urinary tract infection respiratory nitrate reductase 1 gamma chain reduced virulence






        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
OPHIJLDE_00001 5.A.3.1.1 87.6 4.1e-142 2 268 0.9745 1.1867 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
OPHIJLDE_00002 5.A.3.1.1 86.4 1.4e-273 1 507 0.9864 2.2578 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
OPHIJLDE_00004 5.A.3.1.1 82.1 1.5e-105 1 224 0.9956 0.9956 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family