Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1037
  Reference Plasmid   NZ_CP099749.1
  Reference Plasmid Size   243395
  Reference Plasmid GC Content   0.51
  Reference Plasmid Mobility Type   conjugative





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
M0193365 ABDGEPIC_00017 18196 3 Gut 0.60 protein_coding synonymous_variant LOW 45T>C Thr15Thr
M0193366 ABDGEPIC_00017 18203 3 Gut 0.60 protein_coding missense_variant MODERATE 52G>C Val18Leu
M0193367 ABDGEPIC_00017 18211 3 Gut 0.60 protein_coding synonymous_variant LOW 60T>A Leu20Leu
M0193368 ABDGEPIC_00017 18241 3 Gut 0.60 protein_coding synonymous_variant LOW 90G>A Ala30Ala
M0193369 ABDGEPIC_00017 18295 3 Gut 0.60 protein_coding synonymous_variant LOW 144A>G Glu48Glu
M0193370 ABDGEPIC_00017 18328 3 Gut 0.60 protein_coding synonymous_variant LOW 177T>C His59His
M0193371 ABDGEPIC_00017 18379 3 Gut 0.60 protein_coding synonymous_variant LOW 228G>T Ala76Ala
M0193372 ABDGEPIC_00017 18436 3 Gut 0.60 protein_coding synonymous_variant LOW 285G>A Gln95Gln
M0193373 ABDGEPIC_00017 18877 3 Gut 0.60 protein_coding synonymous_variant LOW 726T>C Phe242Phe
M0193374 ABDGEPIC_00017 18928 3 Gut 0.60 protein_coding synonymous_variant LOW 777G>A Pro259Pro
M0193375 ABDGEPIC_00017 19028 3 Gut 0.60 protein_coding missense_variant MODERATE 877G>A Ala293Thr
M0193376 ABDGEPIC_00017 19120 3 Gut 0.60 protein_coding synonymous_variant LOW 969C>T Ile323Ile
M0193377 ABDGEPIC_00017 19122 3 Gut 0.60 protein_coding missense_variant MODERATE 971C>T Pro324Leu
M0193378 ABDGEPIC_00022 19146 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -2786G>C None
M0193379 ABDGEPIC_00018 19206 3 Gut 0.60 protein_coding synonymous_variant LOW 235C>A Arg79Arg
M0193380 ABDGEPIC_00018 19219 3 Gut 0.60 protein_coding synonymous_variant LOW 222T>C Val74Val
M0193381 ABDGEPIC_00018 19345 3 Gut 0.60 protein_coding synonymous_variant LOW 96C>T Gly32Gly
M0193382 ABDGEPIC_00018 19349 3 Gut 0.60 protein_coding missense_variant MODERATE 92C>T Ser31Phe
M0193383 ABDGEPIC_00018 19394 3 Gut 0.60 protein_coding missense_variant MODERATE 47A>G Asn16Ser
M0193384 ABDGEPIC_00018 19478 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -38A>C None
M0193385 ABDGEPIC_00018 19519 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -79C>T None
M0193386 ABDGEPIC_00018 19537 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -97T>G None
M0193387 ABDGEPIC_00018 19550 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -110G>A None
M0193388 ABDGEPIC_00018 19554 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -114T>C None
M0193389 ABDGEPIC_00019 19698 3 Gut 0.60 protein_coding missense_variant MODERATE 681T>A Asp227Glu
M0193390 ABDGEPIC_00019 19769 3 Gut 0.60 protein_coding missense_variant MODERATE 610A>G Ile204Val
M0193391 ABDGEPIC_00019 19919 3 Gut 0.60 protein_coding missense_variant MODERATE 460A>G Thr154Ala
M0193392 ABDGEPIC_00019 19975 3 Gut 0.60 protein_coding missense_variant MODERATE 404A>G Asp135Gly
M0193393 ABDGEPIC_00019 20010 3 Gut 0.60 protein_coding synonymous_variant LOW 369A>T Gly123Gly
M0193394 ABDGEPIC_00019 20133 3 Gut 0.60 protein_coding synonymous_variant LOW 246G>T Gly82Gly
M0193395 ABDGEPIC_00019 20136 3 Gut 0.60 protein_coding synonymous_variant LOW 243C>A Ala81Ala
M0193396 ABDGEPIC_00019 20373 3 Gut 0.60 protein_coding synonymous_variant LOW 6A>G Leu2Leu
M0193397 ABDGEPIC_00020 20403 3 Gut 0.60 protein_coding missense_variant MODERATE 489A>T Leu163Phe
M0193398 ABDGEPIC_00020 20405 3 Gut 0.60 protein_coding missense_variant MODERATE 487T>A Leu163Ile
M0193399 ABDGEPIC_00020 20417 3 Gut 0.60 protein_coding missense_variant MODERATE 475A>C Lys159Gln
M0193400 ABDGEPIC_00020 20650 3 Gut 0.60 protein_coding missense_variant MODERATE 242T>G Leu81Arg
M0193401 ABDGEPIC_00020 20669 3 Gut 0.60 protein_coding missense_variant MODERATE 223G>T Gly75Trp
M0193402 ABDGEPIC_00020 20742 3 Gut 0.60 protein_coding synonymous_variant LOW 150T>C Ile50Ile
M0193403 ABDGEPIC_00021 20938 3 Gut 0.60 protein_coding synonymous_variant LOW 264A>C Gly88Gly
M0193404 ABDGEPIC_00021 21012 3 Gut 0.60 protein_coding missense_variant MODERATE 190T>C Tyr64His
M0193405 ABDGEPIC_00018 21641 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -2201C>T None
M0193406 ABDGEPIC_00022 23034 3 Gut 0.60 protein_coding missense_variant MODERATE 1103T>C Val368Ala
M0193407 ABDGEPIC_00022 23353 3 Gut 0.60 protein_coding synonymous_variant LOW 1422G>A Leu474Leu
M0193408 ABDGEPIC_00023 23699 3 Gut 0.60 protein_coding synonymous_variant LOW 288C>T Ala96Ala
M0193409 ABDGEPIC_00024 25428 3 Gut 0.60 protein_coding missense_variant MODERATE 854T>C Ile285Thr
M0193410 ABDGEPIC_00024 26170 3 Gut 0.60 protein_coding synonymous_variant LOW 1596A>T Val532Val
M0193411 ABDGEPIC_00024 26181 3 Gut 0.60 protein_coding splice_region_variant&stop_retained_variant LOW 1607G>A Ter536Ter
M0193412 ABDGEPIC_00025 26284 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -295T>C None
M0193413 ABDGEPIC_00079 70094 3 Gut 0.60 protein_coding synonymous_variant LOW 36G>A Arg12Arg
M0193414 ABDGEPIC_00079 70169 3 Gut 0.60 protein_coding synonymous_variant LOW 111A>G Val37Val
M0193415 ABDGEPIC_00079 70310 3 Gut 0.60 protein_coding synonymous_variant LOW 252C>T Cys84Cys
M0193416 ABDGEPIC_00079 70408 3 Gut 0.60 protein_coding missense_variant MODERATE 350G>A Gly117Asp
M0193417 ABDGEPIC_00079 70469 3 Gut 0.60 protein_coding synonymous_variant LOW 411G>A Val137Val
M0193418 ABDGEPIC_00079 70597 3 Gut 0.60 protein_coding missense_variant MODERATE 539C>T Thr180Ile
M0193419 ABDGEPIC_00073 70644 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4849G>A None
M0193420 ABDGEPIC_00073 70646 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4851C>A 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
ABDGEPIC_00012 Iron (Fe), Cobalt (Co), Nickel (Ni), Gallium (Ga) 100 0 1 712 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
ABDGEPIC_00125 ARO:3005323 97 3.83e-193 85 352 0.7614 1.0000 penicillin beta-lactam OXA 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
ABDGEPIC_00077 PHI:11470 STM14_3563 77 1.8e-27 5 78 0.8605 0.8132 rodents salmonellosis putative transcriptional regulator 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
ABDGEPIC_00041 9.A.52.1.4 95.6 7.9e-19 1 45 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.A Recognized transporters of unknown biochemical mechanism 9.A.52 The Microcin J25 (Microsin J25) Family
ABDGEPIC_00147 9.A.52.1.4 95.6 7.9e-19 1 45 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.A Recognized transporters of unknown biochemical mechanism 9.A.52 The Microcin J25 (Microsin J25) Family