Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1127
  Reference Plasmid   NZ_CP118846.1
  Reference Plasmid Size   41938
  Reference Plasmid GC Content   0.30
  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
M0109461 JCMBGFDL_00019 13423 4 Skin 0.10 protein_coding synonymous_variant LOW 462G>A Gln154Gln
M0109462 JCMBGFDL_00017 15244 5 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3728T>C None
M0109463 JCMBGFDL_00017 15301 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -3785C>A None
M0109464 JCMBGFDL_00017 15333 3 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -3817C>G None
M0109465 JCMBGFDL_00021 15388 3 Skin 0.07 protein_coding synonymous_variant LOW 36A>G Leu12Leu
M0109466 JCMBGFDL_00021 15468 3 Skin 0.07 protein_coding missense_variant MODERATE 116A>G Lys39Arg
M0109467 JCMBGFDL_00021 15733 3 Skin 0.07 protein_coding synonymous_variant LOW 381T>G Ala127Ala
M0109468 JCMBGFDL_00021 15802 3 Skin 0.07 protein_coding synonymous_variant LOW 450A>G Leu150Leu
M0109469 JCMBGFDL_00021 15804 3 Skin 0.07 protein_coding missense_variant MODERATE 452A>C Lys151Thr
M0109470 JCMBGFDL_00021 15805 3 Skin 0.07 protein_coding missense_variant MODERATE 453A>T Lys151Asn
M0109471 JCMBGFDL_00021 15835 3 Skin 0.07 protein_coding synonymous_variant LOW 483A>C Thr161Thr
M0109472 JCMBGFDL_00021 15838 3 Skin 0.07 protein_coding synonymous_variant LOW 486A>G Pro162Pro
M0109473 JCMBGFDL_00021 15856 3 Skin 0.07 protein_coding synonymous_variant LOW 504A>G Glu168Glu
M0109474 JCMBGFDL_00021 15877 3 Skin 0.07 protein_coding synonymous_variant LOW 525C>A Thr175Thr
M0109475 JCMBGFDL_00017 15939 3 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -4423T>C None
M0109476 JCMBGFDL_00017 15941 3 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -4425T>C None
M0109477 JCMBGFDL_00017 15959 3 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -4443T>C None
M0109478 JCMBGFDL_00049 39346 4 Skin 0.10 protein_coding missense_variant MODERATE 296T>A Phe99Tyr
M0109479 JCMBGFDL_00028 23827 4 Skin 0.10 protein_coding synonymous_variant LOW 118C>T Leu40Leu
M0109480 JCMBGFDL_00028 23855 5 Skin 0.12 protein_coding synonymous_variant LOW 90C>T Gly30Gly
M0109481 JCMBGFDL_00028 23878 3 Skin 0.07 protein_coding missense_variant MODERATE 67C>A Gln23Lys
M0109482 JCMBGFDL_00029 23987 6 Skin 0.14 protein_coding synonymous_variant LOW 894A>G Glu298Glu
M0109483 JCMBGFDL_00029 24032 6 Skin 0.14 protein_coding synonymous_variant LOW 849C>T Asp283Asp
M0109484 JCMBGFDL_00029 24056 6 Skin 0.14 protein_coding missense_variant MODERATE 825A>C Arg275Ser
M0109485 JCMBGFDL_00029 24093 7 Skin 0.17 protein_coding missense_variant MODERATE 788C>T Ala263Val
M0109486 JCMBGFDL_00029 24132 7 Skin 0.17 protein_coding missense_variant MODERATE 749A>G Asn250Ser
M0109487 JCMBGFDL_00029 24134 7 Skin 0.17 protein_coding missense_variant MODERATE 747C>G Asn249Lys
M0109488 JCMBGFDL_00029 24169 7 Skin 0.17 protein_coding missense_variant MODERATE 712G>A Glu238Lys
M0109489 JCMBGFDL_00029 24202 7 Skin 0.17 protein_coding missense_variant MODERATE 679G>A Glu227Lys
M0109490 JCMBGFDL_00029 24223 7 Skin 0.17 protein_coding missense_variant MODERATE 658C>T His220Tyr
M0109491 JCMBGFDL_00029 24261 7 Skin 0.17 protein_coding missense_variant MODERATE 620A>G Asn207Ser
M0109492 JCMBGFDL_00029 24340 7 Skin 0.17 protein_coding missense_variant MODERATE 541A>G Asn181Asp
M0109493 JCMBGFDL_00029 24373 4 Skin 0.10 protein_coding missense_variant MODERATE 508C>T His170Tyr
M0109494 JCMBGFDL_00029 24527 7 Skin 0.17 protein_coding missense_variant MODERATE 354A>T Leu118Phe
M0109495 JCMBGFDL_00029 24656 7 Skin 0.17 protein_coding missense_variant MODERATE 225C>A Asp75Glu
M0109496 JCMBGFDL_00029 24673 7 Skin 0.17 protein_coding missense_variant MODERATE 208A>G Ser70Gly
M0109497 JCMBGFDL_00029 24674 7 Skin 0.17 protein_coding missense_variant MODERATE 207C>A Asn69Lys
M0109498 JCMBGFDL_00029 24707 6 Skin 0.14 protein_coding synonymous_variant LOW 174C>T Asp58Asp
M0109499 JCMBGFDL_00029 24859 4 Skin 0.10 protein_coding missense_variant MODERATE 22G>T Val8Leu
M0109500 JCMBGFDL_00026 24881 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -3160T>G None
M0109501 JCMBGFDL_00026 24900 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -3179T>C None
M0109502 JCMBGFDL_00030 24939 5 Skin 0.12 protein_coding missense_variant MODERATE 290A>C Asn97Thr
M0109503 JCMBGFDL_00030 24993 5 Skin 0.12 protein_coding missense_variant MODERATE 236T>G Phe79Cys
M0109504 JCMBGFDL_00030 24994 5 Skin 0.12 protein_coding missense_variant MODERATE 235T>G Phe79Val
M0109505 JCMBGFDL_00030 25004 5 Skin 0.12 protein_coding missense_variant MODERATE 225G>C Met75Ile
M0109506 JCMBGFDL_00030 25006 5 Skin 0.12 protein_coding missense_variant MODERATE 223A>G Met75Val
M0109507 JCMBGFDL_00030 25027 5 Skin 0.12 protein_coding missense_variant MODERATE 202A>G Asn68Asp
M0109508 JCMBGFDL_00030 25088 5 Skin 0.12 protein_coding missense_variant MODERATE 141G>T Leu47Phe
M0109509 JCMBGFDL_00030 25097 5 Skin 0.12 protein_coding synonymous_variant LOW 132A>G Gly44Gly
M0109510 JCMBGFDL_00030 25111 5 Skin 0.12 protein_coding missense_variant MODERATE 118T>A Phe40Ile
M0109511 JCMBGFDL_00030 25116 5 Skin 0.12 protein_coding missense_variant MODERATE 113T>A Met38Lys
M0109512 JCMBGFDL_00030 25117 5 Skin 0.12 protein_coding missense_variant MODERATE 112A>G Met38Val
M0109513 JCMBGFDL_00030 25134 5 Skin 0.12 protein_coding missense_variant MODERATE 95G>A Ser32Asn
M0109514 JCMBGFDL_00030 25205 3 Skin 0.07 protein_coding synonymous_variant LOW 24G>A Leu8Leu
M0109515 JCMBGFDL_00031 25298 6 Skin 0.14 protein_coding missense_variant MODERATE 351A>C Glu117Asp
M0109516 JCMBGFDL_00031 25311 6 Skin 0.14 protein_coding missense_variant MODERATE 338T>C Ile113Thr
M0109517 JCMBGFDL_00031 25364 5 Skin 0.12 protein_coding synonymous_variant LOW 285G>C Ala95Ala
M0109518 JCMBGFDL_00031 25367 5 Skin 0.12 protein_coding synonymous_variant LOW 282C>T Asp94Asp
M0109519 JCMBGFDL_00031 25439 5 Skin 0.12 protein_coding synonymous_variant LOW 210A>G Lys70Lys
M0109520 JCMBGFDL_00031 25499 6 Skin 0.14 protein_coding missense_variant MODERATE 150A>T Glu50Asp
M0109521 JCMBGFDL_00026 25657 6 Skin 0.14 protein_coding upstream_gene_variant MODIFIER -3936A>G None
M0109522 JCMBGFDL_00026 25938 6 Skin 0.14 protein_coding upstream_gene_variant MODIFIER -4217G>A None
M0109523 JCMBGFDL_00026 26049 5 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -4328C>A None
M0109524 JCMBGFDL_00026 26050 5 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -4329C>A None
M0109525 JCMBGFDL_00026 26130 5 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -4409G>C None
M0109526 JCMBGFDL_00026 26177 5 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -4456A>C None
M0109527 JCMBGFDL_00026 26593 3 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -4872G>A None
M0109528 JCMBGFDL_00028 27006 5 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3062A>C None
M0109529 JCMBGFDL_00028 27059 5 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3115A>G None
M0109530 JCMBGFDL_00028 28673 3 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -4729T>C None
M0109531 JCMBGFDL_00031 25643 3 Skin 0.07 protein_coding synonymous_variant LOW 6A>T Ala2Ala






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
JCMBGFDL_00040 Copper (Cu) 100 1.6e-33 1 69 1.0000 1.0000 prediction
JCMBGFDL_00041 Copper (Cu), Silver (Ag) 75.6 0 1 795 1.0000 1.0013 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
JCMBGFDL_00001 ARO:3000178 100 3.12e-293 1 429 1.0000 0.9346 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
JCMBGFDL_00018 ARO:3008823 97.5 1.43e-191 1 281 1.0000 1.0000 penicillin beta-lactam BlaZ beta-lactamase antibiotic inactivation
JCMBGFDL_00023 ARO:3000251 97.5 0 1 488 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
JCMBGFDL_00049 ARO:3002865 80.4 1.35e-95 1 158 1.0000 0.9814 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement






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
JCMBGFDL_00024 PHI:6324 StpC 85.9 9.6e-108 1 227 0.9619 0.9827 birds skin infection; food poisoning; respiratory disease cysteine protease unaffected pathogenicity






        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
JCMBGFDL_00001 2.A.1.3.6 100 3.6e-230 1 429 1.0000 0.9346 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
JCMBGFDL_00023 3.A.1.121.1 99.8 2.5e-275 1 488 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
JCMBGFDL_00041 3.A.3.5.19 73.6 0 4 795 0.9962 0.9888 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily