Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1204
  Reference Plasmid   NZ_CP134465.1
  Reference Plasmid Size   71637
  Reference Plasmid GC Content   0.30
  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
M0199449 IFJCJMIA_00068 66474 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4811C>A None
M0199450 IFJCJMIA_00068 66523 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4860C>T None
M0199451 IFJCJMIA_00068 66580 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4917C>A None
M0199452 IFJCJMIA_00068 66589 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4926G>A None
M0199453 IFJCJMIA_00068 66621 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4958C>T None
M0199454 IFJCJMIA_00068 66637 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4974G>A None
M0199455 IFJCJMIA_00068 66638 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4975T>C None
M0199456 IFJCJMIA_00074 66670 3 Gut 1.00 protein_coding stop_lost&splice_region_variant HIGH 220T>C Ter74Glnext*?
M0199457 IFJCJMIA_00074 66688 3 Gut 1.00 protein_coding missense_variant MODERATE 202C>T His68Tyr
M0199458 IFJCJMIA_00074 66689 3 Gut 1.00 protein_coding missense_variant MODERATE 201A>T Lys67Asn
M0199459 IFJCJMIA_00074 66695 3 Gut 1.00 protein_coding missense_variant MODERATE 195T>G Asn65Lys
M0199460 IFJCJMIA_00074 66737 3 Gut 1.00 protein_coding synonymous_variant LOW 153G>A Arg51Arg
M0199461 IFJCJMIA_00074 66761 3 Gut 1.00 protein_coding synonymous_variant LOW 129A>C Gly43Gly
M0199462 IFJCJMIA_00074 66783 3 Gut 1.00 protein_coding missense_variant MODERATE 107T>C Ile36Thr
M0199463 IFJCJMIA_00074 66784 3 Gut 1.00 protein_coding missense_variant MODERATE 106A>G Ile36Val
M0199464 IFJCJMIA_00074 66797 3 Gut 1.00 protein_coding missense_variant MODERATE 93A>T Glu31Asp
M0199465 IFJCJMIA_00074 66818 3 Gut 1.00 protein_coding synonymous_variant LOW 72A>G Lys24Lys
M0199466 IFJCJMIA_00074 66825 3 Gut 1.00 protein_coding missense_variant MODERATE 65A>C Asn22Thr
M0199467 IFJCJMIA_00070 66900 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4186A>G None
M0199468 IFJCJMIA_00070 66901 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4187G>A None
M0199469 IFJCJMIA_00070 66948 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4234G>A None
M0199470 IFJCJMIA_00070 66987 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4273T>A None
M0199471 IFJCJMIA_00070 66994 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4280A>G None
M0199472 IFJCJMIA_00070 66996 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4282A>G None
M0199473 IFJCJMIA_00070 66998 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4284A>G None
M0199474 IFJCJMIA_00070 66999 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4285T>G None
M0199475 IFJCJMIA_00070 67018 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4304G>T None
M0199476 IFJCJMIA_00070 67029 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4315C>T None
M0199477 IFJCJMIA_00070 67041 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4327C>T None
M0199478 IFJCJMIA_00070 67045 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4331T>A None
M0199479 IFJCJMIA_00070 67058 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4344A>G None
M0199480 IFJCJMIA_00075 67072 3 Gut 1.00 protein_coding synonymous_variant LOW 12A>C Ile4Ile
M0199481 IFJCJMIA_00075 67084 3 Gut 1.00 protein_coding synonymous_variant LOW 24C>T Ala8Ala
M0199482 IFJCJMIA_00075 67129 3 Gut 1.00 protein_coding synonymous_variant LOW 69C>T Ser23Ser
M0199483 IFJCJMIA_00075 67131 3 Gut 1.00 protein_coding missense_variant MODERATE 71C>G Ala24Gly
M0199484 IFJCJMIA_00075 67150 3 Gut 1.00 protein_coding synonymous_variant LOW 90G>A Gly30Gly
M0199485 IFJCJMIA_00075 67180 3 Gut 1.00 protein_coding synonymous_variant LOW 120T>C His40His
M0199486 IFJCJMIA_00075 67222 3 Gut 1.00 protein_coding synonymous_variant LOW 162A>G Lys54Lys
M0199487 IFJCJMIA_00075 67231 3 Gut 1.00 protein_coding synonymous_variant LOW 171T>C Val57Val
M0199488 IFJCJMIA_00075 67290 3 Gut 1.00 protein_coding missense_variant MODERATE 230A>G His77Arg
M0199489 IFJCJMIA_00075 67327 3 Gut 1.00 protein_coding synonymous_variant LOW 267G>A Leu89Leu
M0199490 IFJCJMIA_00075 67396 3 Gut 1.00 protein_coding synonymous_variant LOW 336G>A Leu112Leu
M0199491 IFJCJMIA_00075 67492 3 Gut 1.00 protein_coding synonymous_variant LOW 432T>G Val144Val
M0199492 IFJCJMIA_00075 67531 3 Gut 1.00 protein_coding synonymous_variant LOW 471A>C Gly157Gly
M0199493 IFJCJMIA_00075 67546 3 Gut 1.00 protein_coding synonymous_variant LOW 486G>A Ser162Ser
M0199494 IFJCJMIA_00075 67709 3 Gut 1.00 protein_coding missense_variant MODERATE 649A>G Asn217Asp






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
IFJCJMIA_00038 Cadmium (Cd), Zinc (Zn) 88.3 2.8e-96 1 205 1.0000 1.0000 experiment
IFJCJMIA_00015 Copper (Cu) 97.8 0 1 687 1.0000 1.0000 prediction
IFJCJMIA_00038 Cadmium (Cd), Zinc (Zn) 97.6 7.2e-101 1 205 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






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
IFJCJMIA_00036 PHI:11807 ohyA 74.5 2.2e-270 1 591 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease oleate hydratase reduced virulence
IFJCJMIA_00064 PHI:6191 Lqo 82.1 2e-248 1 497 0.9960 1.0000 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
IFJCJMIA_00023 QKQ09233.1|GT2 99.5 7.53e-261 1 367 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
IFJCJMIA_00038 2.A.77.1.1 87.8 2.4e-94 1 205 1.0000 0.9809 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.77 The Cadmium Resistance (CadD) Family