Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2140
  Reference Plasmid   1111525849743258_bin.25__k141_50502
  Reference Plasmid Size   14399
  Reference Plasmid GC Content   0.63
  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
M0027225 MDGJGNAJ_00007 7600 6 Skin 0.10 protein_coding synonymous_variant LOW 888G>T Val296Val
M0027226 MDGJGNAJ_00011 10623 3 Skin 0.05 protein_coding synonymous_variant LOW 258C>G Gly86Gly
M0027227 MDGJGNAJ_00008 10954 4 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -2757T>C None
M0027228 MDGJGNAJ_00012 11180 20 Skin 0.34 protein_coding missense_variant MODERATE 767G>A Ser256Asn
M0027229 MDGJGNAJ_00012 11190 20 Skin 0.34 protein_coding missense_variant MODERATE 757A>G Thr253Ala
M0027230 MDGJGNAJ_00012 11215 20 Skin 0.34 protein_coding synonymous_variant LOW 732T>C Arg244Arg
M0027231 MDGJGNAJ_00006 5612 6 Skin 0.10 protein_coding synonymous_variant LOW 744T>C Ser248Ser
M0027232 MDGJGNAJ_00006 5621 6 Skin 0.10 protein_coding synonymous_variant LOW 753G>A Glu251Glu
M0027233 MDGJGNAJ_00006 5624 6 Skin 0.10 protein_coding synonymous_variant LOW 756A>C Ile252Ile
M0027234 MDGJGNAJ_00011 10225 5 Skin 0.08 protein_coding missense_variant MODERATE 656C>G Thr219Ser
M0027235 MDGJGNAJ_00011 10521 4 Skin 0.07 protein_coding synonymous_variant LOW 360C>G Ala120Ala
M0027236 MDGJGNAJ_00011 10580 3 Skin 0.05 protein_coding missense_variant MODERATE 301G>A Glu101Lys
M0027237 MDGJGNAJ_00009 8554 3 Skin 0.05 protein_coding missense_variant MODERATE 385G>A Ala129Thr
M0027238 MDGJGNAJ_00009 8636 4 Skin 0.07 protein_coding missense_variant MODERATE 303C>G Asp101Glu
M0027239 MDGJGNAJ_00003 1851 3 Skin 0.05 protein_coding synonymous_variant LOW 702C>G Leu234Leu
M0027240 MDGJGNAJ_00004 7853 7 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -4459G>T None
M0027241 MDGJGNAJ_00004 7856 7 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -4462G>T None
M0027242 MDGJGNAJ_00004 7891 6 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4497A>G None
M0027243 MDGJGNAJ_00004 7895 6 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4501G>A None
M0027244 MDGJGNAJ_00003 2061 5 Skin 0.08 protein_coding synonymous_variant LOW 492A>G Lys164Lys
M0027245 MDGJGNAJ_00004 3371 3 Skin 0.05 protein_coding synonymous_variant LOW 24C>T Pro8Pro
M0027246 MDGJGNAJ_00007 7270 9 Skin 0.15 protein_coding synonymous_variant LOW 558T>C Arg186Arg
M0027247 MDGJGNAJ_00010 8986 6 Skin 0.10 protein_coding missense_variant MODERATE 929C>G Thr310Ser
M0027248 MDGJGNAJ_00010 9700 4 Skin 0.07 protein_coding missense_variant MODERATE 215A>C Lys72Thr
M0027249 MDGJGNAJ_00010 9717 4 Skin 0.07 protein_coding synonymous_variant LOW 198A>T Ala66Ala
M0027250 MDGJGNAJ_00010 9723 4 Skin 0.07 protein_coding synonymous_variant LOW 192G>A Glu64Glu
M0027251 MDGJGNAJ_00010 9724 4 Skin 0.07 protein_coding missense_variant MODERATE 191A>C Glu64Ala
M0027252 MDGJGNAJ_00010 9725 4 Skin 0.07 protein_coding missense_variant MODERATE 190G>C Glu64Gln
M0027253 MDGJGNAJ_00010 9726 4 Skin 0.07 protein_coding synonymous_variant LOW 189A>G Ala63Ala
M0027254 MDGJGNAJ_00010 9731 4 Skin 0.07 protein_coding synonymous_variant LOW 184C>T Leu62Leu
M0027255 MDGJGNAJ_00009 8669 4 Skin 0.07 protein_coding synonymous_variant LOW 270C>T His90His
M0027256 MDGJGNAJ_00010 9285 7 Skin 0.12 protein_coding synonymous_variant LOW 630C>G Val210Val
M0027257 MDGJGNAJ_00011 10839 4 Skin 0.07 protein_coding synonymous_variant LOW 42T>A Ala14Ala
M0027258 MDGJGNAJ_00006 5348 5 Skin 0.08 protein_coding synonymous_variant LOW 480C>T Gly160Gly
M0027259 MDGJGNAJ_00006 5378 5 Skin 0.08 protein_coding synonymous_variant LOW 510G>C Pro170Pro
M0027260 MDGJGNAJ_00008 7964 8 Skin 0.14 protein_coding synonymous_variant LOW 234G>C Leu78Leu
M0027261 MDGJGNAJ_00010 9591 6 Skin 0.10 protein_coding synonymous_variant LOW 324C>T Ala108Ala
M0027262 MDGJGNAJ_00010 9609 6 Skin 0.10 protein_coding synonymous_variant LOW 306T>C His102His
M0027263 MDGJGNAJ_00001 329 4 Skin 0.07 protein_coding synonymous_variant LOW 60T>C Gly20Gly
M0027264 MDGJGNAJ_00001 332 4 Skin 0.07 protein_coding synonymous_variant LOW 63C>T Gly21Gly
M0027265 MDGJGNAJ_00001 380 4 Skin 0.07 protein_coding synonymous_variant LOW 111T>G Pro37Pro
M0027266 MDGJGNAJ_00001 392 4 Skin 0.07 protein_coding synonymous_variant LOW 123T>C Gly41Gly
M0027267 MDGJGNAJ_00001 431 5 Skin 0.08 protein_coding synonymous_variant LOW 162C>T Asp54Asp
M0027268 MDGJGNAJ_00001 449 4 Skin 0.07 protein_coding synonymous_variant LOW 180C>T Ala60Ala
M0027269 MDGJGNAJ_00001 452 4 Skin 0.07 protein_coding synonymous_variant LOW 183C>T Phe61Phe
M0027270 MDGJGNAJ_00002 477 5 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -6A>C None
M0027271 MDGJGNAJ_00002 478 5 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -5C>T None
M0027272 MDGJGNAJ_00013 12237 4 Skin 0.07 protein_coding missense_variant MODERATE 145G>C Glu49Gln
M0027273 MDGJGNAJ_00013 12377 10 Skin 0.17 protein_coding synonymous_variant LOW 285C>T Asp95Asp
M0027274 MDGJGNAJ_00013 12416 10 Skin 0.17 protein_coding synonymous_variant LOW 324T>G Pro108Pro
M0027275 MDGJGNAJ_00008 13104 9 Skin 0.15 protein_coding upstream_gene_variant MODIFIER -4907G>A None
M0027276 MDGJGNAJ_00015 14347 6 Skin 0.10 protein_coding missense_variant MODERATE 35C>A Pro12His
M0027277 MDGJGNAJ_00015 14371 6 Skin 0.10 protein_coding missense_variant MODERATE 11C>T Ala4Val
M0027278 MDGJGNAJ_00006 5468 6 Skin 0.10 protein_coding synonymous_variant LOW 600A>C Val200Val
M0027279 MDGJGNAJ_00006 5477 7 Skin 0.12 protein_coding synonymous_variant LOW 609T>C Ser203Ser
M0027280 MDGJGNAJ_00015 14321 5 Skin 0.08 protein_coding missense_variant MODERATE 61G>A Ala21Thr
M0027281 MDGJGNAJ_00002 656 3 Skin 0.05 protein_coding synonymous_variant LOW 174C>T Asp58Asp
M0027282 MDGJGNAJ_00006 5685 3 Skin 0.05 protein_coding synonymous_variant LOW 817C>T Leu273Leu
M0027283 MDGJGNAJ_00006 5702 4 Skin 0.07 protein_coding synonymous_variant LOW 834G>A Glu278Glu
M0027284 MDGJGNAJ_00012 11849 3 Skin 0.05 protein_coding missense_variant MODERATE 98C>T Ala33Val






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
MDGJGNAJ_00002 PHI:10701 hisF (A1S_3245) 75.6 8.8e-107 3 256 0.9922 0.9921 rodents pneumonia imidazole glycerol phosphate synthase cyclase subunit 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
MDGJGNAJ_00003 3.A.1.12.12 75.3 8.6e-170 1 392 1.0000 1.3754 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
MDGJGNAJ_00004 3.A.1.12.12 81.9 6.9e-121 2 272 0.9644 0.9509 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily