Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C489
  Reference Plasmid   NZ_CP023496.1
  Reference Plasmid Size   169687
  Reference Plasmid GC Content   0.32
  Reference Plasmid Mobility Type   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
M0089127 MKDAFBIG_00046 33868 4 Skin 0.13 protein_coding missense_variant MODERATE 1145C>A Thr382Lys
M0089128 MKDAFBIG_00046 33874 5 Skin 0.17 protein_coding missense_variant MODERATE 1139A>C Glu380Ala
M0089129 MKDAFBIG_00046 33890 4 Skin 0.13 protein_coding missense_variant MODERATE 1123C>T Leu375Phe
M0089130 MKDAFBIG_00046 34007 5 Skin 0.17 protein_coding missense_variant MODERATE 1006A>G Ile336Val
M0089131 MKDAFBIG_00046 34008 5 Skin 0.17 protein_coding synonymous_variant LOW 1005A>G Gly335Gly
M0089132 MKDAFBIG_00046 34094 5 Skin 0.17 protein_coding synonymous_variant LOW 919C>T Leu307Leu
M0089133 MKDAFBIG_00046 34117 5 Skin 0.17 protein_coding missense_variant MODERATE 896C>T Thr299Ile
M0089134 MKDAFBIG_00047 35068 5 Skin 0.17 protein_coding synonymous_variant LOW 438C>T Ile146Ile
M0089135 MKDAFBIG_00046 35612 5 Skin 0.17 protein_coding upstream_gene_variant MODIFIER -600G>A None
M0089136 MKDAFBIG_00046 35634 5 Skin 0.17 protein_coding upstream_gene_variant MODIFIER -622C>T None
M0089137 MKDAFBIG_00046 35644 5 Skin 0.17 protein_coding upstream_gene_variant MODIFIER -632T>A None
M0089138 MKDAFBIG_00048 35668 5 Skin 0.17 protein_coding missense_variant MODERATE 7A>G Asn3Asp
M0089139 MKDAFBIG_00130 116072 3 Skin 0.10 protein_coding missense_variant MODERATE 2446A>G Lys816Glu
M0089140 MKDAFBIG_00130 117384 3 Skin 0.10 protein_coding synonymous_variant LOW 1134G>A Ser378Ser
M0089141 MKDAFBIG_00095 71634 9 Skin 0.30 protein_coding synonymous_variant LOW 546A>G Thr182Thr
M0089142 MKDAFBIG_00095 71659 9 Skin 0.30 protein_coding missense_variant MODERATE 521A>T Glu174Val
M0089143 MKDAFBIG_00095 71708 9 Skin 0.30 protein_coding synonymous_variant LOW 472C>A Arg158Arg
M0089144 MKDAFBIG_00095 71723 9 Skin 0.30 protein_coding missense_variant MODERATE 457A>G Ile153Val
M0089145 MKDAFBIG_00095 71724 9 Skin 0.30 protein_coding synonymous_variant LOW 456T>C Gly152Gly
M0089146 MKDAFBIG_00095 71739 9 Skin 0.30 protein_coding synonymous_variant LOW 441C>T Asp147Asp
M0089147 MKDAFBIG_00095 71791 9 Skin 0.30 protein_coding missense_variant MODERATE 389A>C Asp130Ala
M0089148 MKDAFBIG_00095 71807 9 Skin 0.30 protein_coding missense_variant MODERATE 373T>C Ser125Pro
M0089149 MKDAFBIG_00095 71969 9 Skin 0.30 protein_coding missense_variant MODERATE 211G>A Gly71Ser
M0089150 MKDAFBIG_00095 72042 9 Skin 0.30 protein_coding synonymous_variant LOW 138C>T Tyr46Tyr
M0089151 MKDAFBIG_00095 72156 9 Skin 0.30 protein_coding synonymous_variant LOW 24C>T Arg8Arg
M0089152 MKDAFBIG_00091 72270 8 Skin 0.27 protein_coding upstream_gene_variant MODIFIER -3079A>G None
M0089153 MKDAFBIG_00091 72341 8 Skin 0.27 protein_coding upstream_gene_variant MODIFIER -3150C>T None
M0089154 MKDAFBIG_00091 72359 8 Skin 0.27 protein_coding upstream_gene_variant MODIFIER -3168C>T None
M0089155 MKDAFBIG_00091 72385 8 Skin 0.27 protein_coding upstream_gene_variant MODIFIER -3194G>A None
M0089156 MKDAFBIG_00091 72443 8 Skin 0.27 protein_coding upstream_gene_variant MODIFIER -3252T>C None
M0089157 MKDAFBIG_00091 72519 8 Skin 0.27 protein_coding upstream_gene_variant MODIFIER -3328T>A None
M0089158 MKDAFBIG_00096 72533 8 Skin 0.27 protein_coding missense_variant MODERATE 941A>T Asn314Ile
M0089159 MKDAFBIG_00096 72583 9 Skin 0.30 protein_coding synonymous_variant LOW 891A>G Val297Val
M0089160 MKDAFBIG_00096 72690 9 Skin 0.30 protein_coding missense_variant MODERATE 784A>G Ile262Val
M0089161 MKDAFBIG_00096 72993 9 Skin 0.30 protein_coding missense_variant MODERATE 481A>G Thr161Ala
M0089162 MKDAFBIG_00096 73066 9 Skin 0.30 protein_coding synonymous_variant LOW 408G>A Val136Val
M0089163 MKDAFBIG_00096 73141 9 Skin 0.30 protein_coding synonymous_variant LOW 333T>C Tyr111Tyr
M0089164 MKDAFBIG_00096 73168 8 Skin 0.27 protein_coding synonymous_variant LOW 306C>A Ile102Ile
M0089165 MKDAFBIG_00096 73178 9 Skin 0.30 protein_coding missense_variant MODERATE 296A>C Glu99Ala
M0089166 MKDAFBIG_00096 73326 9 Skin 0.30 protein_coding missense_variant MODERATE 148C>T Pro50Ser
M0089167 MKDAFBIG_00096 73383 9 Skin 0.30 protein_coding missense_variant MODERATE 91A>G Ser31Gly
M0089168 MKDAFBIG_00096 73385 9 Skin 0.30 protein_coding missense_variant MODERATE 89G>A Ser30Asn
M0089169 MKDAFBIG_00096 73432 9 Skin 0.30 protein_coding synonymous_variant LOW 42T>C Ala14Ala
M0089170 MKDAFBIG_00091 73485 8 Skin 0.27 protein_coding upstream_gene_variant MODIFIER -4294A>G None
M0089171 MKDAFBIG_00097 73509 9 Skin 0.30 protein_coding synonymous_variant LOW 2670G>A Glu890Glu
M0089172 MKDAFBIG_00097 73599 9 Skin 0.30 protein_coding synonymous_variant LOW 2580G>A Leu860Leu
M0089173 MKDAFBIG_00097 73659 9 Skin 0.30 protein_coding synonymous_variant LOW 2520C>T Phe840Phe
M0089174 MKDAFBIG_00097 73710 8 Skin 0.27 protein_coding synonymous_variant LOW 2469T>C His823His
M0089175 MKDAFBIG_00097 73725 8 Skin 0.27 protein_coding synonymous_variant LOW 2454C>T Asn818Asn
M0089176 MKDAFBIG_00097 73728 9 Skin 0.30 protein_coding missense_variant MODERATE 2451T>A Ser817Arg
M0089177 MKDAFBIG_00097 73845 9 Skin 0.30 protein_coding missense_variant MODERATE 2334T>A His778Gln
M0089178 MKDAFBIG_00097 73880 9 Skin 0.30 protein_coding missense_variant MODERATE 2299G>A Asp767Asn
M0089179 MKDAFBIG_00097 73928 9 Skin 0.30 protein_coding missense_variant MODERATE 2251C>T His751Tyr
M0089180 MKDAFBIG_00097 73976 9 Skin 0.30 protein_coding missense_variant MODERATE 2203G>T Ala735Ser
M0089181 MKDAFBIG_00097 73984 9 Skin 0.30 protein_coding missense_variant MODERATE 2195A>G Asn732Ser
M0089182 MKDAFBIG_00097 74031 9 Skin 0.30 protein_coding missense_variant MODERATE 2148A>T Lys716Asn
M0089183 MKDAFBIG_00097 74322 8 Skin 0.27 protein_coding synonymous_variant LOW 1857C>T Asp619Asp
M0089184 MKDAFBIG_00097 74504 9 Skin 0.30 protein_coding synonymous_variant LOW 1675C>T Leu559Leu
M0089185 MKDAFBIG_00097 74559 8 Skin 0.27 protein_coding synonymous_variant LOW 1620A>G Ser540Ser
M0089186 MKDAFBIG_00097 74568 9 Skin 0.30 protein_coding synonymous_variant LOW 1611A>G Val537Val
M0089187 MKDAFBIG_00097 74601 9 Skin 0.30 protein_coding synonymous_variant LOW 1578C>T Ile526Ile
M0089188 MKDAFBIG_00097 74811 9 Skin 0.30 protein_coding synonymous_variant LOW 1368C>T Thr456Thr
M0089189 MKDAFBIG_00097 74862 10 Skin 0.33 protein_coding synonymous_variant LOW 1317C>T Ser439Ser
M0089190 MKDAFBIG_00097 74880 9 Skin 0.30 protein_coding synonymous_variant LOW 1299C>T Asp433Asp
M0089191 MKDAFBIG_00097 75131 8 Skin 0.27 protein_coding missense_variant MODERATE 1048C>T Pro350Ser
M0089192 MKDAFBIG_00097 75158 8 Skin 0.27 protein_coding missense_variant MODERATE 1021T>A Ser341Thr
M0089193 MKDAFBIG_00097 75234 8 Skin 0.27 protein_coding synonymous_variant LOW 945G>A Ala315Ala
M0089194 MKDAFBIG_00097 75351 8 Skin 0.27 protein_coding synonymous_variant LOW 828T>C Gly276Gly
M0089195 MKDAFBIG_00097 75375 8 Skin 0.27 protein_coding synonymous_variant LOW 804C>T Ile268Ile
M0089196 MKDAFBIG_00097 75629 9 Skin 0.30 protein_coding missense_variant MODERATE 550G>A Val184Ile
M0089197 MKDAFBIG_00097 75630 9 Skin 0.30 protein_coding synonymous_variant LOW 549T>C Ile183Ile
M0089198 MKDAFBIG_00097 75663 9 Skin 0.30 protein_coding synonymous_variant LOW 516T>C Ala172Ala
M0089199 MKDAFBIG_00097 75665 9 Skin 0.30 protein_coding missense_variant MODERATE 514G>T Ala172Ser
M0089200 MKDAFBIG_00097 75705 9 Skin 0.30 protein_coding synonymous_variant LOW 474C>T His158His
M0089201 MKDAFBIG_00097 75792 9 Skin 0.30 protein_coding synonymous_variant LOW 387T>C Asn129Asn
M0089202 MKDAFBIG_00097 75912 9 Skin 0.30 protein_coding synonymous_variant LOW 267T>G Thr89Thr
M0089203 MKDAFBIG_00097 76002 9 Skin 0.30 protein_coding synonymous_variant LOW 177T>C Ile59Ile
M0089204 MKDAFBIG_00097 76092 9 Skin 0.30 protein_coding synonymous_variant LOW 87C>T Val29Val
M0089205 MKDAFBIG_00095 76231 9 Skin 0.30 protein_coding upstream_gene_variant MODIFIER -4052A>G None
M0089206 MKDAFBIG_00095 76237 9 Skin 0.30 protein_coding upstream_gene_variant MODIFIER -4058T>A None
M0089207 MKDAFBIG_00095 76380 9 Skin 0.30 protein_coding upstream_gene_variant MODIFIER -4201G>A None
M0089208 MKDAFBIG_00095 76384 9 Skin 0.30 protein_coding upstream_gene_variant MODIFIER -4205A>C None
M0089209 MKDAFBIG_00095 76404 9 Skin 0.30 protein_coding upstream_gene_variant MODIFIER -4225C>T None
M0089210 MKDAFBIG_00095 76496 7 Skin 0.23 protein_coding upstream_gene_variant MODIFIER -4317A>G None
M0089211 MKDAFBIG_00095 76500 7 Skin 0.23 protein_coding upstream_gene_variant MODIFIER -4321C>T None
M0089212 MKDAFBIG_00048 35984 3 Skin 0.10 protein_coding missense_variant MODERATE 323T>G Met108Arg
M0089213 MKDAFBIG_00048 36011 3 Skin 0.10 protein_coding missense_variant MODERATE 350A>C Tyr117Ser
M0089214 MKDAFBIG_00048 36252 3 Skin 0.10 protein_coding synonymous_variant LOW 591T>A Ala197Ala
M0089215 MKDAFBIG_00049 36853 3 Skin 0.10 protein_coding synonymous_variant LOW 504G>A Leu168Leu
M0089216 MKDAFBIG_00049 36930 3 Skin 0.10 protein_coding missense_variant MODERATE 581G>A Arg194Lys
M0089217 MKDAFBIG_00046 37618 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -2606G>A None
M0089218 MKDAFBIG_00046 37631 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -2619T>C None
M0089219 MKDAFBIG_00046 37646 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -2634T>A None
M0089220 MKDAFBIG_00046 37660 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -2648T>A None
M0089221 MKDAFBIG_00046 37665 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -2653A>T None
M0089222 MKDAFBIG_00046 37666 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -2654G>T None






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
MKDAFBIG_00074 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 74.1 2e-237 1 547 1.0110 0.8764 experiment
AGHFIBOF_00074 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 74.1 2e-237 1 547 1.0110 0.8764 experiment
MKDAFBIG_00070 Mercury (Hg) 100 5.3e-73 1 132 1.0000 1.0000 prediction
MKDAFBIG_00074 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 2.9e-306 1 547 1.0000 1.0000 prediction
AGHFIBOF_00070 Mercury (Hg) 100 5.3e-73 1 132 1.0000 1.0000 prediction
AGHFIBOF_00074 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 2.9e-306 1 547 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
MKDAFBIG_00124 ARO:3008823 100 1.9e-196 1 281 1.0000 1.0000 penicillin beta-lactam BlaZ beta-lactamase antibiotic inactivation
AGHFIBOF_00124 ARO:3008823 100 1.9e-196 1 281 1.0000 1.0000 penicillin beta-lactam BlaZ beta-lactamase antibiotic inactivation






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
MKDAFBIG_00105 PHI:6191 Lqo 81.7 1.3e-242 1 495 0.9920 0.9960 rodents skin infection; food poisoning; respiratory disease L-lactate-quinone oxidoreductases reduced virulence
AGHFIBOF_00105 PHI:6191 Lqo 81.7 1.3e-242 1 495 0.9920 0.9960 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
MKDAFBIG_00114 ATF29459.1|GH13_31 100 0 1 552 1 1
AGHFIBOF_00114 ATF29459.1|GH13_31 100 0 1 552 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
MKDAFBIG_00096 3.A.1.12.16 99.7 1.2e-174 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
AGHFIBOF_00096 3.A.1.12.16 99.7 1.2e-174 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