Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C785
  Reference Plasmid   NZ_CP062703.1
  Reference Plasmid Size   95141
  Reference Plasmid GC Content   0.48
  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
M0183633 PAPLAPHB_00047 51110 3 Gut 1.00 protein_coding missense_variant MODERATE 374C>T Ser125Leu






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
PAPLAPHB_00012 VFG000844 EspP 99.9 0 1 1300 1.0 1 Effector delivery system autotransporter, serine protease experiment
PAPLAPHB_00016 VFG034721 Ibes 81.8 9e-286 1 572 0.9983 0.9913 Invasion phosphoethanolamine transferase CptA experiment
PAPLAPHB_00021 VFG000846 StcE 100 0 1 886 1.0 0.9866 Exoenzyme metalloprotease experiment
PAPLAPHB_00026 VFG038285 Exe T2SS 72.7 2.1e-58 1 143 0.9931 1 Effector delivery system general secretion pathway protein G experiment
PAPLAPHB_00037 VFG000842 Hemolysin 100 3.1e-101 1 171 1.0 1 Exotoxin Hemolysin C experiment
PAPLAPHB_00038 VFG000840 Hemolysin 100 0 1 998 1.0 1 Exotoxin Hemolysin A experiment
PAPLAPHB_00039 VFG000841 Hemolysin 100 0 1 706 1.0 1 Exotoxin Hemolysin B experiment
PAPLAPHB_00040 VFG000843 Hemolysin 100 1.2e-267 1 479 1.0 1 Exotoxin Hemolysin D experiment
PAPLAPHB_00080 VFG000845 ToxB 100 0 1 3169 1.0 1 Effector delivery system cytotoxin experiment
PAPLAPHB_00012 VFG000844 EspP 99.9 0 1 1300 1.0 1 Effector delivery system autotransporter, serine protease prediction
PAPLAPHB_00016 VFG034689 Ibes 100 0 1 573 1.0 1 Invasion phosphoethanolamine transferase CptA prediction
PAPLAPHB_00021 VFG000846 StcE 100 0 1 886 1.0 0.9866 Exoenzyme metalloprotease prediction
PAPLAPHB_00022 VFG040931 Etp 100 5.3e-161 1 291 1.0 1 Effector delivery system type II secretion system protein GspC prediction
PAPLAPHB_00023 VFG040932 Etp 100 0 1 655 1.0 1 Effector delivery system variant type II secretion system secretin EtpD prediction
PAPLAPHB_00024 VFG040933 Etp 100 2.7e-282 1 501 1.0 1 Effector delivery system type II secretion system ATPase GspE prediction
PAPLAPHB_00025 VFG040934 Etp 100 1.7e-218 1 407 1.0 1 Effector delivery system type II secretion system inner membrane protein GspF prediction
PAPLAPHB_00026 VFG040935 Etp 100 1.7e-80 1 144 1.0 1 Effector delivery system type II secretion system major pseudopilin GspG prediction
PAPLAPHB_00027 VFG040936 Etp 100 1.9e-103 1 184 1.0 1 Effector delivery system type II secretion system minor pseudopilin GspH prediction
PAPLAPHB_00028 VFG040937 Etp 100 1.2e-58 7 121 0.9504 1 Effector delivery system type II secretion system minor pseudopilin GspI prediction
PAPLAPHB_00029 VFG040938 Etp 100 6.9e-112 1 199 1.0 1 Effector delivery system type II secretion system minor pseudopilin GspJ prediction
PAPLAPHB_00030 VFG040939 Etp 100 4.8e-179 1 325 1.0 1 Effector delivery system type II secretion system minor pseudopilin GspK prediction
PAPLAPHB_00031 VFG040940 Etp 99.7 3.3e-213 1 365 1.0 0.9359 Effector delivery system type II secretion system protein GspL prediction
PAPLAPHB_00032 VFG040941 Etp 100 3e-92 1 170 1.0 1 Effector delivery system type II secretion system protein M prediction
PAPLAPHB_00033 VFG040942 Etp 100 1.1e-160 1 277 1.0 1 Effector delivery system A24 family peptidase prediction
PAPLAPHB_00034 VFG040943 Etp 100 4.7e-72 1 133 1.0 1 Effector delivery system GspS family T2SS pilot lipoprotein variant EptO prediction
PAPLAPHB_00037 VFG000842 Hemolysin 100 2.3e-100 1 171 1.0 1 Exotoxin Hemolysin C prediction
PAPLAPHB_00038 VFG000840 Hemolysin 100 0 1 998 1.0 1 Exotoxin Hemolysin A prediction
PAPLAPHB_00039 VFG000841 Hemolysin 100 0 1 706 1.0 1 Exotoxin Hemolysin B prediction
PAPLAPHB_00040 VFG000843 Hemolysin 100 9e-267 1 479 1.0 1 Exotoxin Hemolysin D prediction
PAPLAPHB_00080 VFG000845 ToxB 100 0 1 3169 1.0 1 Effector delivery system cytotoxin prediction







        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
PAPLAPHB_00042 PHI:6737 L7052 98.9 1.4e-46 1 94 1.0000 1.0000 nematodes urinary tract infection transcriptional regulator increased virulence (hypervirulence)






        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
PAPLAPHB_00015 AHY68449.1|GT4 100 9.25e-267 1 368 1 1
PAPLAPHB_00080 QDK10460.1|GT44 100 0 1 3169 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
PAPLAPHB_00012 1.B.12.4.3 99.9 0 1 1300 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family
PAPLAPHB_00023 1.B.22.1.1 73 8.8e-260 10 650 0.9786 0.9742 1 Channels/Pores 1.B β-Barrel Porins 1.B.22 The Outer Bacterial Membrane Secretin (Secretin) Family
PAPLAPHB_00024 3.A.15.1.1 72.3 2.1e-200 9 499 0.9800 2.1535 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.15 The Outer Membrane Protein Secreting Main Terminal Branch (MTB) Family
PAPLAPHB_00038 1.C.11.1.6 98 0 1 998 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.11 The Pore-forming RTX Toxin (RTX-toxin) Family
PAPLAPHB_00039 3.A.1.109.1 73.6 4.5e-302 11 706 0.9858 0.9844 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
PAPLAPHB_00080 1.C.57.2.1 99.9 0 1 3169 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.57 The Clostridial Cytotoxin (CCT) Family