Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C921
  Reference Plasmid   NZ_CP078095.1
  Reference Plasmid Size   211593
  Reference Plasmid GC Content   0.36
  Reference Plasmid Mobility Type   conjugative





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
M0188503 KIDPJDNP_00013 11607 3 Gut 0.21 protein_coding synonymous_variant LOW 225C>T Asp75Asp
M0188504 KIDPJDNP_00015 12156 3 Gut 0.21 protein_coding synonymous_variant LOW 142C>T Leu48Leu
M0188505 KIDPJDNP_00015 12204 3 Gut 0.21 protein_coding missense_variant MODERATE 190T>C Phe64Leu
M0188506 KIDPJDNP_00015 13864 3 Gut 0.21 protein_coding missense_variant MODERATE 1850T>C Leu617Ser
M0188507 KIDPJDNP_00032 29118 3 Gut 0.21 protein_coding synonymous_variant LOW 406C>T Leu136Leu
M0188508 KIDPJDNP_00034 33942 3 Gut 0.21 protein_coding synonymous_variant LOW 1329T>A Leu443Leu
M0188509 KIDPJDNP_00036 35093 3 Gut 0.21 protein_coding synonymous_variant LOW 27G>A Leu9Leu
M0188510 KIDPJDNP_00036 35117 4 Gut 0.29 protein_coding synonymous_variant LOW 51A>G Leu17Leu
M0188511 KIDPJDNP_00040 38101 3 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -239G>T None
M0188512 KIDPJDNP_00070 71230 3 Gut 0.21 protein_coding synonymous_variant LOW 288T>C Arg96Arg
M0188513 KIDPJDNP_00070 71469 3 Gut 0.21 protein_coding missense_variant MODERATE 527C>T Ala176Val
M0188514 KIDPJDNP_00070 71481 3 Gut 0.21 protein_coding missense_variant MODERATE 539A>T His180Leu
M0188515 KIDPJDNP_00071 72700 3 Gut 0.21 protein_coding synonymous_variant LOW 591A>G Lys197Lys
M0188516 KIDPJDNP_00071 72754 3 Gut 0.21 protein_coding synonymous_variant LOW 645G>A Lys215Lys
M0188517 KIDPJDNP_00071 72766 3 Gut 0.21 protein_coding synonymous_variant LOW 657T>C Asn219Asn
M0188518 KIDPJDNP_00071 72769 3 Gut 0.21 protein_coding synonymous_variant LOW 660G>A Gln220Gln
M0188519 KIDPJDNP_00071 72775 3 Gut 0.21 protein_coding synonymous_variant LOW 666A>T Gly222Gly
M0188520 KIDPJDNP_00071 72778 3 Gut 0.21 protein_coding synonymous_variant LOW 669T>C Ile223Ile
M0188521 KIDPJDNP_00071 72784 3 Gut 0.21 protein_coding synonymous_variant LOW 675C>T Ser225Ser
M0188522 KIDPJDNP_00071 72789 3 Gut 0.21 protein_coding missense_variant MODERATE 680G>A Arg227Lys
M0188523 KIDPJDNP_00071 72793 3 Gut 0.21 protein_coding synonymous_variant LOW 684T>C Asp228Asp
M0188524 KIDPJDNP_00071 72794 3 Gut 0.21 protein_coding missense_variant MODERATE 685C>T Leu229Phe
M0188525 KIDPJDNP_00071 72796 3 Gut 0.21 protein_coding synonymous_variant LOW 687T>A Leu229Leu
M0188526 KIDPJDNP_00071 72802 3 Gut 0.21 protein_coding synonymous_variant LOW 693C>T Asn231Asn
M0188527 KIDPJDNP_00071 72817 3 Gut 0.21 protein_coding synonymous_variant LOW 708C>T Thr236Thr
M0188528 KIDPJDNP_00071 72853 3 Gut 0.21 protein_coding synonymous_variant LOW 744A>G Leu248Leu
M0188529 KIDPJDNP_00071 72859 3 Gut 0.21 protein_coding synonymous_variant LOW 750T>C Phe250Phe
M0188530 KIDPJDNP_00071 72865 3 Gut 0.21 protein_coding synonymous_variant LOW 756A>T Ala252Ala
M0188531 KIDPJDNP_00071 72868 3 Gut 0.21 protein_coding synonymous_variant LOW 759T>C Asn253Asn
M0188532 KIDPJDNP_00071 72871 3 Gut 0.21 protein_coding synonymous_variant LOW 762T>G Gly254Gly
M0188533 KIDPJDNP_00071 72874 3 Gut 0.21 protein_coding synonymous_variant LOW 765T>C Ile255Ile
M0188534 KIDPJDNP_00071 72883 3 Gut 0.21 protein_coding synonymous_variant LOW 774T>A Thr258Thr
M0188535 KIDPJDNP_00071 72892 3 Gut 0.21 protein_coding synonymous_variant LOW 783A>G Ala261Ala
M0188536 KIDPJDNP_00071 72895 3 Gut 0.21 protein_coding synonymous_variant LOW 786C>A Ile262Ile
M0188537 KIDPJDNP_00071 72907 3 Gut 0.21 protein_coding synonymous_variant LOW 798G>A Pro266Pro
M0188538 KIDPJDNP_00071 72910 3 Gut 0.21 protein_coding synonymous_variant LOW 801A>C Thr267Thr
M0188539 KIDPJDNP_00071 72919 3 Gut 0.21 protein_coding synonymous_variant LOW 810G>A Lys270Lys
M0188540 KIDPJDNP_00071 73036 3 Gut 0.21 protein_coding synonymous_variant LOW 927A>G Lys309Lys
M0188541 KIDPJDNP_00072 73521 3 Gut 0.21 protein_coding missense_variant MODERATE 121A>G Thr41Ala
M0188542 KIDPJDNP_00072 73527 3 Gut 0.21 protein_coding missense_variant MODERATE 127C>T His43Tyr
M0188543 KIDPJDNP_00072 73569 3 Gut 0.21 protein_coding missense_variant MODERATE 169A>G Lys57Glu
M0188544 KIDPJDNP_00072 73613 3 Gut 0.21 protein_coding synonymous_variant LOW 213C>T Ile71Ile
M0188545 KIDPJDNP_00072 73698 3 Gut 0.21 protein_coding missense_variant MODERATE 298G>A Val100Ile
M0188546 KIDPJDNP_00073 73948 3 Gut 0.21 protein_coding synonymous_variant LOW 30A>G Leu10Leu






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
KIDPJDNP_00007 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 98.2 7.5e-123 1 223 1.0 1 Adherence putative housekeeping sortase prediction
KIDPJDNP_00008 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 99.5 0 1 658 1.0 1 Adherence PilA prediction
KIDPJDNP_00009 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 99.2 1.4e-138 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
KIDPJDNP_00010 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 99.2 3.4e-132 1 251 1.0 1 Adherence cell wall-associated LPXTG-like protein prediction
KIDPJDNP_00011 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 0 1 696 1.0 1 Adherence minor pilin subunit prediction
KIDPJDNP_00054 VFG042995 Bee (biofilm enhancer in enterococci) 98.8 5.1e-133 1 243 1.0 1 Adherence Bee2 prediction
KIDPJDNP_00055 VFG042996 Bee (biofilm enhancer in enterococci) 98.6 3.4e-277 1 495 1.0 1 Adherence Bee3 prediction
KIDPJDNP_00056 VFG042997 Bee (biofilm enhancer in enterococci) 98.7 1.1e-222 1 397 0.99 0.9975 Adherence Srt1 prediction
KIDPJDNP_00057 VFG042998 Bee (biofilm enhancer in enterococci) 98.4 3.7e-207 1 373 1.0 1 Adherence Srt2 prediction







        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
KIDPJDNP_00064 PHI:5205 HMPREF0351_10118 (WxL locusC) 75.7 7.8e-80 1 185 0.3799 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
KIDPJDNP_00095 PHI:5205 HMPREF0351_10118 (WxL locusC) 74.5 2.9e-173 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
KIDPJDNP_00099 PHI:5205 HMPREF0351_10118 (WxL locusC) 99.7 5e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
KIDPJDNP_00129 PHI:5205 HMPREF0351_10118 (WxL locusC) 74.5 2.9e-173 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis 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
KIDPJDNP_00022 QXM04986.1|GH73 100 2.13e-275 1 401 1 1
KIDPJDNP_00067 QXM05028.1|GH32 100 0 1 486 1 1
KIDPJDNP_00104 QAA21152.1|GH36 100 0 1 727 1 1
KIDPJDNP_00105 QQJ93880.1|GH13_31 100 1.79e-306 1 406 1 1
KIDPJDNP_00106 AOM14759.1|GH13_18 100 0 1 486 1 1
KIDPJDNP_00136 QXM04906.1|GT4 100 0 1 1183 1 1
KIDPJDNP_00137 QXM04907.1|GT2 100 0 1 495 1 1
KIDPJDNP_00150 QXM05064.1|GH1 100 0 105 572 0.8182 1
KIDPJDNP_00210 QAT24339.1|GH36 100 0 1 749 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
KIDPJDNP_00085 1.C.24.1.10 100 7.8e-37 1 71 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.24 The Pediocin (Pediocin) Family
KIDPJDNP_00102 3.A.1.1.28 73.8 8.2e-125 1 290 1.0000 0.7692 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
KIDPJDNP_00103 3.A.1.1.28 74.9 1.2e-117 5 276 0.9855 0.7294 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily