Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C321
  Reference Plasmid   NC_015432.1
  Reference Plasmid Size   66104
  Reference Plasmid GC Content   0.32
  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
M0152964 LOCIIDNE_00008 11595 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -284C>T None
M0152965 LOCIIDNE_00008 11600 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -289T>C None
M0152966 LOCIIDNE_00008 11606 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -295T>C None
M0152967 LOCIIDNE_00008 11676 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -365A>T None
M0152968 LOCIIDNE_00009 11684 3 Gut 1.00 protein_coding missense_variant MODERATE 8A>G Lys3Arg
M0152969 LOCIIDNE_00009 11694 3 Gut 1.00 protein_coding missense_variant MODERATE 18A>T Glu6Asp
M0152970 LOCIIDNE_00009 11697 3 Gut 1.00 protein_coding synonymous_variant LOW 21C>T Phe7Phe
M0152971 LOCIIDNE_00009 11715 3 Gut 1.00 protein_coding synonymous_variant LOW 39A>G Arg13Arg
M0152972 LOCIIDNE_00009 11734 3 Gut 1.00 protein_coding missense_variant MODERATE 58A>G Ile20Val
M0152973 LOCIIDNE_00009 11748 3 Gut 1.00 protein_coding synonymous_variant LOW 72T>C Tyr24Tyr
M0152974 LOCIIDNE_00009 11752 3 Gut 1.00 protein_coding missense_variant MODERATE 76C>T Leu26Phe
M0152975 LOCIIDNE_00009 11794 3 Gut 1.00 protein_coding missense_variant MODERATE 118T>A Ser40Thr
M0152976 LOCIIDNE_00009 11798 3 Gut 1.00 protein_coding missense_variant MODERATE 122A>G Asn41Ser
M0152977 LOCIIDNE_00009 11860 3 Gut 1.00 protein_coding missense_variant MODERATE 184A>G Ile62Val
M0152978 LOCIIDNE_00009 11869 3 Gut 1.00 protein_coding synonymous_variant LOW 193T>C Leu65Leu
M0152979 LOCIIDNE_00009 11874 3 Gut 1.00 protein_coding synonymous_variant LOW 198G>A Gly66Gly
M0152980 LOCIIDNE_00009 11887 3 Gut 1.00 protein_coding synonymous_variant LOW 211C>T Leu71Leu
M0152981 LOCIIDNE_00009 11903 3 Gut 1.00 protein_coding missense_variant MODERATE 227T>G Ile76Ser
M0152982 LOCIIDNE_00009 11938 3 Gut 1.00 protein_coding missense_variant MODERATE 262A>G Ile88Val
M0152983 LOCIIDNE_00009 11941 3 Gut 1.00 protein_coding missense_variant MODERATE 265G>A Val89Ile
M0152984 LOCIIDNE_00009 11958 3 Gut 1.00 protein_coding synonymous_variant LOW 282G>A Ser94Ser
M0152985 LOCIIDNE_00009 11989 3 Gut 1.00 protein_coding missense_variant MODERATE 313A>T Ile105Leu
M0152986 LOCIIDNE_00009 11994 3 Gut 1.00 protein_coding synonymous_variant LOW 318T>C Leu106Leu
M0152987 LOCIIDNE_00009 12002 3 Gut 1.00 protein_coding missense_variant MODERATE 326T>C Met109Thr
M0152988 LOCIIDNE_00009 12034 3 Gut 1.00 protein_coding missense_variant MODERATE 358A>G Ile120Val
M0152989 LOCIIDNE_00009 12056 3 Gut 1.00 protein_coding missense_variant MODERATE 380G>A Ser127Asn
M0152990 LOCIIDNE_00009 12123 3 Gut 1.00 protein_coding synonymous_variant LOW 447T>C Asp149Asp
M0152991 LOCIIDNE_00009 12131 3 Gut 1.00 protein_coding missense_variant MODERATE 455T>C Ile152Thr
M0152992 LOCIIDNE_00009 12134 3 Gut 1.00 protein_coding missense_variant MODERATE 458A>C Asn153Thr
M0152993 LOCIIDNE_00009 12141 3 Gut 1.00 protein_coding synonymous_variant LOW 465A>C Gly155Gly
M0152994 LOCIIDNE_00009 12147 3 Gut 1.00 protein_coding synonymous_variant LOW 471T>A Gly157Gly
M0152995 LOCIIDNE_00009 12177 3 Gut 1.00 protein_coding synonymous_variant LOW 501G>A Leu167Leu
M0152996 LOCIIDNE_00009 12202 3 Gut 1.00 protein_coding synonymous_variant LOW 526C>T Leu176Leu
M0152997 LOCIIDNE_00009 12204 3 Gut 1.00 protein_coding synonymous_variant LOW 528A>G Leu176Leu
M0152998 LOCIIDNE_00009 12243 3 Gut 1.00 protein_coding synonymous_variant LOW 567T>C Ile189Ile
M0152999 LOCIIDNE_00009 12262 3 Gut 1.00 protein_coding missense_variant MODERATE 586A>G Met196Val
M0153000 LOCIIDNE_00009 12269 3 Gut 1.00 protein_coding missense_variant MODERATE 593T>C Ile198Thr
M0153001 LOCIIDNE_00009 12279 3 Gut 1.00 protein_coding synonymous_variant LOW 603T>C Tyr201Tyr
M0153002 LOCIIDNE_00009 12286 3 Gut 1.00 protein_coding synonymous_variant LOW 610C>T Leu204Leu
M0153003 LOCIIDNE_00009 12352 3 Gut 1.00 protein_coding missense_variant MODERATE 676C>A Leu226Ile
M0153004 LOCIIDNE_00009 12357 3 Gut 1.00 protein_coding synonymous_variant LOW 681C>T Ala227Ala
M0153005 LOCIIDNE_00009 12378 3 Gut 1.00 protein_coding synonymous_variant LOW 702G>A Gly234Gly
M0153006 LOCIIDNE_00009 12476 3 Gut 1.00 protein_coding missense_variant MODERATE 800C>A Ala267Asp
M0153007 LOCIIDNE_00009 12483 3 Gut 1.00 protein_coding synonymous_variant LOW 807T>C Phe269Phe
M0153008 LOCIIDNE_00009 12533 3 Gut 1.00 protein_coding missense_variant MODERATE 857T>G Ile286Ser
M0153009 LOCIIDNE_00009 12561 3 Gut 1.00 protein_coding synonymous_variant LOW 885G>A Leu295Leu
M0153010 LOCIIDNE_00009 12576 3 Gut 1.00 protein_coding synonymous_variant LOW 900A>G Arg300Arg
M0153011 LOCIIDNE_00009 12614 3 Gut 1.00 protein_coding missense_variant MODERATE 938C>T Ala313Val
M0153012 LOCIIDNE_00009 12630 3 Gut 1.00 protein_coding synonymous_variant LOW 954C>T Gly318Gly
M0153013 LOCIIDNE_00009 12631 3 Gut 1.00 protein_coding missense_variant MODERATE 955G>A Glu319Lys
M0153014 LOCIIDNE_00009 12656 3 Gut 1.00 protein_coding missense_variant MODERATE 980T>A Ile327Lys
M0153015 LOCIIDNE_00009 12663 3 Gut 1.00 protein_coding synonymous_variant LOW 987A>G Ala329Ala
M0153016 LOCIIDNE_00009 12693 3 Gut 1.00 protein_coding synonymous_variant LOW 1017T>A Thr339Thr
M0153017 LOCIIDNE_00009 12696 3 Gut 1.00 protein_coding synonymous_variant LOW 1020G>T Val340Val
M0153018 LOCIIDNE_00009 12712 3 Gut 1.00 protein_coding missense_variant MODERATE 1036A>G Ile346Val
M0153019 LOCIIDNE_00009 12714 3 Gut 1.00 protein_coding missense_variant MODERATE 1038A>G Ile346Met
M0153020 LOCIIDNE_00009 12744 3 Gut 1.00 protein_coding synonymous_variant LOW 1068A>G Glu356Glu
M0153021 LOCIIDNE_00009 12783 3 Gut 1.00 protein_coding missense_variant MODERATE 1107A>G Ile369Met
M0153022 LOCIIDNE_00009 12784 3 Gut 1.00 protein_coding missense_variant MODERATE 1108G>T Val370Leu
M0153023 LOCIIDNE_00009 12796 3 Gut 1.00 protein_coding missense_variant MODERATE 1120A>G Ser374Gly
M0153024 LOCIIDNE_00009 12822 3 Gut 1.00 protein_coding synonymous_variant LOW 1146A>G Arg382Arg
M0153025 LOCIIDNE_00009 12825 3 Gut 1.00 protein_coding synonymous_variant LOW 1149A>C Ala383Ala
M0153026 LOCIIDNE_00009 12838 3 Gut 1.00 protein_coding missense_variant MODERATE 1162A>G Asn388Asp
M0153027 LOCIIDNE_00008 12882 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -1571A>G None
M0153028 LOCIIDNE_00010 12902 3 Gut 1.00 protein_coding missense_variant MODERATE 19T>G Ser7Ala
M0153029 LOCIIDNE_00010 12916 3 Gut 1.00 protein_coding synonymous_variant LOW 33A>G Gly11Gly
M0153030 LOCIIDNE_00010 12949 3 Gut 1.00 protein_coding synonymous_variant LOW 66T>C Phe22Phe
M0153031 LOCIIDNE_00010 12973 3 Gut 1.00 protein_coding missense_variant MODERATE 90T>G Asp30Glu
M0153032 LOCIIDNE_00010 13207 3 Gut 1.00 protein_coding synonymous_variant LOW 324G>A Pro108Pro
M0153033 LOCIIDNE_00010 13223 3 Gut 1.00 protein_coding missense_variant MODERATE 340G>A Val114Ile
M0153034 LOCIIDNE_00010 13239 3 Gut 1.00 protein_coding missense_variant MODERATE 356C>T Thr119Met
M0153035 LOCIIDNE_00010 13370 3 Gut 1.00 protein_coding missense_variant MODERATE 487A>G Asn163Asp
M0153036 LOCIIDNE_00010 13405 3 Gut 1.00 protein_coding synonymous_variant LOW 522A>G Leu174Leu
M0153037 LOCIIDNE_00010 13414 3 Gut 1.00 protein_coding missense_variant MODERATE 531G>T Lys177Asn
M0153038 LOCIIDNE_00010 13429 3 Gut 1.00 protein_coding synonymous_variant LOW 546C>T Asn182Asn
M0153039 LOCIIDNE_00010 13459 3 Gut 1.00 protein_coding synonymous_variant LOW 576T>C Asn192Asn
M0153040 LOCIIDNE_00010 13470 3 Gut 1.00 protein_coding missense_variant MODERATE 587G>A Gly196Asp






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
LOCIIDNE_00043 Cadmium (Cd), Bismuth (Bi), Zinc (Zn), Lead (Pb) 96.7 3.4e-65 1 122 1.0000 1.0000 experiment
LOCIIDNE_00045 Arsenic (As) 89.8 1.6e-68 1 128 0.9771 0.9771 experiment
LOCIIDNE_00046 Arsenic (As), Antimony (Sb) 91.1 1.5e-211 1 429 1.0000 1.0000 experiment
LOCIIDNE_00043 Cadmium (Cd), Bismuth (Bi), Zinc (Zn), Lead (Pb) 100 6.4e-65 1 122 1.0000 1.0000 prediction
LOCIIDNE_00045 Arsenic (As) 94.5 9.3e-70 1 128 0.9771 0.9771 prediction
LOCIIDNE_00046 Arsenic (As), Antimony (Sb) 100 1.3e-224 1 429 1.0000 1.0000 prediction






        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
LOCIIDNE_00025 PHI:6191 Lqo 82.3 5.9e-248 1 497 0.9960 1.0000 rodents skin infection; food poisoning; respiratory disease L-lactate-quinone oxidoreductases 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
LOCIIDNE_00014 CBW54928.1|GT4 100 0 1 503 1 1
LOCIIDNE_00015 CBW54929.1|GT8 100 0 1 446 1 1





        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
LOCIIDNE_00030 3.A.1.12.16 97.8 1.1e-170 1 314 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
LOCIIDNE_00042 3.A.3.6.1 98 0 89 805 0.8907 0.9862 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
LOCIIDNE_00046 2.A.45.1.1 90.9 7.9e-209 1 429 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.45 The Arsenite-Antimonite (ArsB) Efflux Family