Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C925
  Reference Plasmid   NZ_CP080135.1
  Reference Plasmid Size   98016
  Reference Plasmid GC Content   0.50
  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
M0188548 GHBCHELO_00076 67877 3 Gut 0.75 protein_coding missense_variant MODERATE 932G>A Cys311Tyr
M0188549 GHBCHELO_00072 68019 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -3057T>C None
M0188550 GHBCHELO_00072 68676 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -3714T>A None
M0188551 GHBCHELO_00072 68936 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -3974A>G None
M0188552 GHBCHELO_00077 69497 3 Gut 0.75 protein_coding missense_variant MODERATE 109G>A Glu37Lys
M0188553 GHBCHELO_00077 69703 3 Gut 0.75 protein_coding synonymous_variant LOW 315C>A Gly105Gly
M0188554 GHBCHELO_00077 70152 3 Gut 0.75 protein_coding missense_variant MODERATE 764G>A Ser255Asn
M0188555 GHBCHELO_00077 70225 3 Gut 0.75 protein_coding synonymous_variant LOW 837T>C Gly279Gly
M0188556 GHBCHELO_00077 70254 3 Gut 0.75 protein_coding missense_variant MODERATE 866G>A Gly289Asp
M0188557 GHBCHELO_00077 70591 3 Gut 0.75 protein_coding synonymous_variant LOW 1203T>G Ala401Ala
M0188558 GHBCHELO_00077 70620 3 Gut 0.75 protein_coding missense_variant MODERATE 1232C>T Ala411Val
M0188559 GHBCHELO_00077 70861 3 Gut 0.75 protein_coding synonymous_variant LOW 1473T>A Ser491Ser
M0188560 GHBCHELO_00077 71126 3 Gut 0.75 protein_coding missense_variant MODERATE 1738A>G Met580Val
M0188561 GHBCHELO_00080 73423 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -1488T>C None
M0188562 GHBCHELO_00080 73462 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -1449G>A None
M0188563 GHBCHELO_00080 73587 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -1324A>G None
M0188564 GHBCHELO_00080 73703 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -1208C>T None
M0188565 GHBCHELO_00078 73856 3 Gut 0.75 protein_coding missense_variant MODERATE 196A>G Ile66Val
M0188566 GHBCHELO_00078 74396 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -345T>C None
M0188567 GHBCHELO_00078 74566 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -515T>C None
M0188568 GHBCHELO_00078 74596 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -545C>A None
M0188569 GHBCHELO_00078 74746 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -695G>A None
M0188570 GHBCHELO_00080 75023 3 Gut 0.75 protein_coding missense_variant MODERATE 113C>T Thr38Ile
M0188571 GHBCHELO_00080 76253 3 Gut 0.75 protein_coding missense_variant MODERATE 1343C>T Ala448Val
M0188572 GHBCHELO_00080 76274 3 Gut 0.75 protein_coding missense_variant MODERATE 1364A>T Lys455Met
M0188573 GHBCHELO_00080 76279 3 Gut 0.75 protein_coding missense_variant MODERATE 1369A>G Arg457Gly
M0188574 GHBCHELO_00080 76357 3 Gut 0.75 protein_coding synonymous_variant LOW 1447C>T Leu483Leu
M0188575 GHBCHELO_00080 76506 3 Gut 0.75 protein_coding synonymous_variant LOW 1596C>T Ile532Ile
M0188576 GHBCHELO_00080 76557 3 Gut 0.75 protein_coding synonymous_variant LOW 1647G>T Thr549Thr
M0188577 GHBCHELO_00080 76560 3 Gut 0.75 protein_coding synonymous_variant LOW 1650T>C Asp550Asp
M0188578 GHBCHELO_00080 76566 3 Gut 0.75 protein_coding synonymous_variant LOW 1656C>T His552His
M0188579 GHBCHELO_00080 76569 3 Gut 0.75 protein_coding synonymous_variant LOW 1659C>T His553His
M0188580 GHBCHELO_00080 76581 3 Gut 0.75 protein_coding synonymous_variant LOW 1671G>A Pro557Pro
M0188581 GHBCHELO_00080 76597 3 Gut 0.75 protein_coding missense_variant MODERATE 1687A>G Ile563Val
M0188582 GHBCHELO_00080 76605 3 Gut 0.75 protein_coding synonymous_variant LOW 1695A>G Gln565Gln
M0188583 GHBCHELO_00080 76623 3 Gut 0.75 protein_coding synonymous_variant LOW 1713A>C Ala571Ala
M0188584 GHBCHELO_00080 76659 3 Gut 0.75 protein_coding synonymous_variant LOW 1749C>T His583His
M0188585 GHBCHELO_00080 76677 3 Gut 0.75 protein_coding synonymous_variant LOW 1767G>T Gly589Gly
M0188586 GHBCHELO_00080 76779 3 Gut 0.75 protein_coding synonymous_variant LOW 1869T>C Asn623Asn
M0188587 GHBCHELO_00080 76782 3 Gut 0.75 protein_coding synonymous_variant LOW 1872C>T Asp624Asp
M0188588 GHBCHELO_00080 76809 3 Gut 0.75 protein_coding synonymous_variant LOW 1899G>T Ala633Ala
M0188589 GHBCHELO_00080 76818 3 Gut 0.75 protein_coding synonymous_variant LOW 1908C>T Asp636Asp
M0188590 GHBCHELO_00080 76866 3 Gut 0.75 protein_coding synonymous_variant LOW 1956T>C Ala652Ala
M0188591 GHBCHELO_00080 76870 3 Gut 0.75 protein_coding missense_variant MODERATE 1960A>C Lys654Gln
M0188592 GHBCHELO_00080 76878 3 Gut 0.75 protein_coding synonymous_variant LOW 1968T>C Ala656Ala
M0188593 GHBCHELO_00080 76896 3 Gut 0.75 protein_coding synonymous_variant LOW 1986T>C Ala662Ala
M0188594 GHBCHELO_00080 76897 3 Gut 0.75 protein_coding missense_variant MODERATE 1987A>G Thr663Ala
M0188595 GHBCHELO_00080 76929 3 Gut 0.75 protein_coding synonymous_variant LOW 2019G>A Gln673Gln
M0188596 GHBCHELO_00080 76932 3 Gut 0.75 protein_coding synonymous_variant LOW 2022C>T His674His
M0188597 GHBCHELO_00080 76950 3 Gut 0.75 protein_coding synonymous_variant LOW 2040G>T Val680Val
M0188598 GHBCHELO_00080 76952 3 Gut 0.75 protein_coding missense_variant MODERATE 2042A>C Glu681Ala
M0188599 GHBCHELO_00080 76955 3 Gut 0.75 protein_coding missense_variant MODERATE 2045T>C Val682Ala
M0188600 GHBCHELO_00080 76956 3 Gut 0.75 protein_coding synonymous_variant LOW 2046A>T Val682Val
M0188601 GHBCHELO_00080 76980 3 Gut 0.75 protein_coding synonymous_variant LOW 2070C>T Ser690Ser
M0188602 GHBCHELO_00080 77033 3 Gut 0.75 protein_coding missense_variant MODERATE 2123C>T Ala708Val
M0188603 GHBCHELO_00080 77043 3 Gut 0.75 protein_coding synonymous_variant LOW 2133G>A Lys711Lys
M0188604 GHBCHELO_00080 77049 3 Gut 0.75 protein_coding synonymous_variant LOW 2139G>T Ala713Ala
M0188605 GHBCHELO_00080 77055 3 Gut 0.75 protein_coding synonymous_variant LOW 2145C>T Asn715Asn
M0188606 GHBCHELO_00080 77079 3 Gut 0.75 protein_coding synonymous_variant LOW 2169G>T Gly723Gly
M0188607 GHBCHELO_00080 77082 3 Gut 0.75 protein_coding synonymous_variant LOW 2172T>C Ser724Ser
M0188608 GHBCHELO_00080 77102 3 Gut 0.75 protein_coding missense_variant MODERATE 2192T>C Met731Thr
M0188609 GHBCHELO_00080 77115 3 Gut 0.75 protein_coding missense_variant MODERATE 2205G>T Gln735His
M0188610 GHBCHELO_00080 77161 3 Gut 0.75 protein_coding missense_variant MODERATE 2251T>A Ser751Thr
M0188611 GHBCHELO_00080 77166 3 Gut 0.75 protein_coding synonymous_variant LOW 2256G>A Gln752Gln
M0188612 GHBCHELO_00080 77205 3 Gut 0.75 protein_coding missense_variant MODERATE 2295T>G His765Gln
M0188613 GHBCHELO_00081 79151 3 Gut 0.75 protein_coding missense_variant MODERATE 269T>C Val90Ala
M0188614 GHBCHELO_00082 80053 3 Gut 0.75 protein_coding missense_variant MODERATE 403G>A Asp135Asn
M0188615 GHBCHELO_00082 80452 3 Gut 0.75 protein_coding missense_variant MODERATE 802C>T His268Tyr






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
GHBCHELO_00077 VFG036043 AatA, AIDA-I type 96.6 0 1 1171 1.0 1.0052 Adherence autotransporter outer membrane beta-barrel domain-containing protein 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
GHBCHELO_00005 Mercury (Hg) 93.8 4e-73 1 144 1.0000 1.0000 experiment
GHBCHELO_00006 Mercury (Hg) 100 1.2e-62 1 116 1.0000 1.0000 experiment
GHBCHELO_00007 Mercury (Hg) 90.1 7e-39 1 91 1.0000 1.0000 experiment
GHBCHELO_00009 Mercury (Hg) 85.3 5e-268 1 564 1.0018 1.0071 experiment
GHBCHELO_00010 Mercury (Hg) 82.6 1.3e-48 1 120 1.0083 1.0000 experiment
GHBCHELO_00011 Mercury (Hg) 78.2 4.9e-33 1 78 1.0000 1.0000 experiment
GHBCHELO_00005 Mercury (Hg) 100 4.3e-76 1 144 1.0000 0.7619 prediction
GHBCHELO_00006 Mercury (Hg) 99.1 3.5e-60 1 116 1.0000 1.0000 prediction
GHBCHELO_00007 Mercury (Hg) 100 6.3e-41 1 91 1.0000 0.8835 prediction
GHBCHELO_00009 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 0 1 564 1.0000 1.0000 prediction
GHBCHELO_00010 Mercury (Hg) 91.7 5.5e-53 1 120 1.0000 1.0000 prediction
GHBCHELO_00011 Mercury (Hg) 83.3 2.7e-32 1 78 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
GHBCHELO_00002 ARO:3000165 99.5 1.02e-277 1 390 0.9774 0.9198 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux






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
GHBCHELO_00027 PHI:3317 hsdR 73.1 0 1 1038 1.0000 1.0000 rodents Glasser's disease involved in pathogenicity 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
GHBCHELO_00080 AYL89119.1|GH24 96.2 0 810 1312 0.3834 0.9031





        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
GHBCHELO_00001 2.A.7.3.67 100 1.8e-159 1 294 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
GHBCHELO_00002 2.A.1.2.4 99.7 5.2e-223 1 399 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
GHBCHELO_00006 1.A.72.3.1 87.9 3e-54 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GHBCHELO_00007 1.A.72.3.1 90.1 2.6e-37 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GHBCHELO_00011 1.A.72.5.1 100 1.8e-39 1 78 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GHBCHELO_00039 1.B.55.3.1 99.1 0 1 1156 0.9991 0.9991 1 Channels/Pores 1.B β-Barrel Porins 1.B.55 The Poly Acetyl Glucosamine Porin (PgaA) Family
GHBCHELO_00063 2.A.76.1.3 84.8 6e-101 1 210 1.0000 0.9417 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.76 The Resistance to Homoserine/Threonine (RhtB) Family