Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C429
  Reference Plasmid   NZ_CP012501.1
  Reference Plasmid Size   242187
  Reference Plasmid GC Content   0.47
  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
M0164811 BPHGHIBC_00114 82534 5 Gut 0.71 protein_coding missense_variant MODERATE 121G>A Gly41Ser
M0164812 BPHGHIBC_00114 82618 5 Gut 0.71 protein_coding missense_variant MODERATE 205G>A Ala69Thr
M0164813 BPHGHIBC_00114 82886 7 Gut 1.00 protein_coding missense_variant MODERATE 473C>A Ala158Asp
M0164814 BPHGHIBC_00114 83018 6 Gut 0.86 protein_coding stop_gained HIGH 605C>A Ser202*
M0164815 BPHGHIBC_00114 83031 6 Gut 0.86 protein_coding synonymous_variant LOW 618T>C Tyr206Tyr






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
BPHGHIBC_00105 VFG002039 Heat-stable toxin (ST) 76.4 4.5e-25 1 72 1.0 1 Exotoxin heat stable enterotoxin I experiment
BPHGHIBC_00142 VFG000846 StcE 78.5 0 1 883 0.9977 0.9833 Exoenzyme metalloprotease experiment
BPHGHIBC_00147 VFG038285 Exe T2SS 76.3 5.6e-59 1 139 0.9653 0.972 Effector delivery system general secretion pathway protein G experiment
BPHGHIBC_00170 VFG000843 Hemolysin 96 1.3e-258 1 479 1.0 1 Exotoxin Hemolysin D experiment
BPHGHIBC_00171 VFG000841 Hemolysin 97.3 0 1 705 1.0 0.9986 Exotoxin Hemolysin B experiment
BPHGHIBC_00172 VFG000840 Hemolysin 95.4 0 1 997 1.0 0.999 Exotoxin Hemolysin A experiment
BPHGHIBC_00173 VFG000842 Hemolysin 94.2 6.1e-97 1 171 1.0 1 Exotoxin Hemolysin C experiment
BPHGHIBC_00178 VFG002039 Heat-stable toxin (ST) 93.1 1.5e-33 1 72 1.0 1 Exotoxin heat stable enterotoxin I experiment
BPHGHIBC_00196 VFG002039 Heat-stable toxin (ST) 93.1 1.5e-33 1 72 1.0 1 Exotoxin heat stable enterotoxin I experiment
BPHGHIBC_00070 VFG041000 AAI/SCI-II T6SS 72 4e-77 1 189 1.0 1.0053 Effector delivery system hypothetical protein prediction
BPHGHIBC_00071 VFG035354 AAI/SCI-II T6SS 89.9 9.8e-77 1 158 1.0 1 Effector delivery system type VI secretion system contractile sheath small subunit prediction
BPHGHIBC_00072 VFG035359 AAI/SCI-II T6SS 95.9 1.6e-279 1 492 1.0 1 Effector delivery system type VI secretion system contractile sheath large subunit prediction
BPHGHIBC_00074 VFG035369 AAI/SCI-II T6SS 85 1.2e-62 1 140 1.0 1 Effector delivery system hypothetical protein prediction
BPHGHIBC_00075 VFG035374 AAI/SCI-II T6SS 84.7 2.7e-305 1 600 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssF prediction
BPHGHIBC_00076 VFG035379 AAI/SCI-II T6SS 83.8 1.6e-158 10 318 0.9656 0.9968 Effector delivery system type VI secretion system baseplate subunit TssG prediction
BPHGHIBC_00077 VFG035384 AAI/SCI-II T6SS 78 6.1e-306 7 660 0.9909 0.9909 Effector delivery system type VI secretion system tip protein VgrG prediction
BPHGHIBC_00078 VFG035389 AAI/SCI-II T6SS 74.5 4.1e-64 1 153 1.0 0.9871 Effector delivery system hypothetical protein prediction
BPHGHIBC_00079 VFG035394 AAI/SCI-II T6SS 90.9 1.3e-47 1 99 1.0 1 Effector delivery system PAAR domain-containing protein prediction
BPHGHIBC_00080 VFG035399 AAI/SCI-II T6SS 84.6 3.2e-176 1 358 1.0 1 Effector delivery system type VI secretion system protein TssA prediction
BPHGHIBC_00081 VFG035404 AAI/SCI-II T6SS 80.3 3e-85 1 183 1.0 1 Effector delivery system type VI secretion lipoprotein TssJ prediction
BPHGHIBC_00082 VFG035409 AAI/SCI-II T6SS 76.7 2e-212 1 450 1.0 0.9574 Effector delivery system type VI secretion system baseplate subunit TssK prediction
BPHGHIBC_00088 VFG035422 AAI/SCI-II T6SS 71.9 4.2e-77 1 196 1.0 1 Effector delivery system DotU family type IV/VI secretion system protein prediction
BPHGHIBC_00089 VFG035424 AAI/SCI-II T6SS 75.3 0 1 1134 1.0 1 Effector delivery system type VI secretion protein prediction
BPHGHIBC_00090 VFG035429 AAI/SCI-II T6SS 84.1 0 1 842 0.9988 0.9918 Effector delivery system type VI secretion system ATPase TssH prediction
BPHGHIBC_00105 VFG002039 Heat-stable toxin (ST) 76.4 3.3e-24 1 72 1.0 1 Exotoxin heat stable enterotoxin I prediction
BPHGHIBC_00111 VFG017870 Icm/dot type IVB locus 77.4 1.7e-89 1 208 0.9905 0.9952 Effector delivery system ParA family protein prediction
BPHGHIBC_00132 VFG042533 CS31A capsule-like antigen 93.7 1.5e-81 28 186 0.8548 0.8833 Adherence ClpC prediction
BPHGHIBC_00133 VFG042494 Adhesive fimbriae 94.6 0 16 813 0.9815 0.9975 Adherence cshB porin (usher) prediction
BPHGHIBC_00134 VFG043643 CS31A capsule-like antigen 94.7 6.1e-140 1 263 1.0 1 Adherence unknown protein prediction
BPHGHIBC_00135 VFG043645 CS31A capsule-like antigen 90.8 2.1e-74 1 163 1.0 1 Adherence unknown protein prediction
BPHGHIBC_00136 VFG042560 Adhesive fimbriae 90.6 4.1e-139 1 277 1.0 1 Adherence unknown protein prediction
BPHGHIBC_00137 VFG043647 CS31A capsule-like antigen 90.2 2.2e-134 1 265 1.0 0.9962 Adherence fimbrial protein prediction
BPHGHIBC_00138 VFG043644 CS31A capsule-like antigen 84.3 2.4e-125 1 254 1.0 1 Adherence CS31A minor subunit prediction
BPHGHIBC_00139 VFG034602 Adhesive fimbriae 89.5 5.4e-133 1 257 1.0 1 Adherence fimbrial protein FaeJ prediction
BPHGHIBC_00142 VFG000846 StcE 78.5 0 1 883 0.9977 0.9833 Exoenzyme metalloprotease prediction
BPHGHIBC_00144 VFG040932 Etp 82 4.1e-302 1 654 0.997 0.9985 Effector delivery system variant type II secretion system secretin EtpD prediction
BPHGHIBC_00145 VFG040933 Etp 84.1 5.7e-232 1 496 0.998 0.99 Effector delivery system type II secretion system ATPase GspE prediction
BPHGHIBC_00146 VFG040934 Etp 77.1 4.6e-163 1 407 1.0 1 Effector delivery system type II secretion system inner membrane protein GspF prediction
BPHGHIBC_00147 VFG040935 Etp 86.5 4e-69 1 141 0.9792 0.9792 Effector delivery system type II secretion system major pseudopilin GspG prediction
BPHGHIBC_00149 VFG040937 Etp 74.8 8.3e-44 7 121 0.9504 1 Effector delivery system type II secretion system minor pseudopilin GspI prediction
BPHGHIBC_00170 VFG000843 Hemolysin 96 1e-257 1 479 1.0 1 Exotoxin Hemolysin D prediction
BPHGHIBC_00171 VFG033882 Hemolysin 97.4 0 1 705 1.0 0.9986 Exotoxin Hemolysin B prediction
BPHGHIBC_00172 VFG033890 Hemolysin 95.5 0 1 997 1.0 0.999 Exotoxin Hemolysin A prediction
BPHGHIBC_00173 VFG000842 Hemolysin 94.2 4.6e-96 1 171 1.0 1 Exotoxin Hemolysin C prediction
BPHGHIBC_00178 VFG002039 Heat-stable toxin (ST) 93.1 1.1e-32 1 72 1.0 1 Exotoxin heat stable enterotoxin I prediction
BPHGHIBC_00196 VFG002039 Heat-stable toxin (ST) 93.1 1.1e-32 1 72 1.0 1 Exotoxin heat stable enterotoxin I 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
BPHGHIBC_00168 PHI:6737 L7052 86.1 1.4e-32 1 79 0.9186 0.8404 nematodes urinary tract infection transcriptional regulator increased virulence (hypervirulence)
BPHGHIBC_00191 PHI:11267 vrpB (STM2180) 89 3.7e-152 1 299 0.9708 0.9901 rodents infection putative LysR family transcriptional regulator reduced virulence
BPHGHIBC_00213 PHI:10997 fdnG 70.3 0 1 1016 1.0000 1.0000 rodents infection formate dehydrogenase, nitrate-inducible, major subunit 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
BPHGHIBC_00201 ANP16064.1|GT1 99.7 5.83e-270 1 386 1 1
BPHGHIBC_00202 ANP05419.1|GT4 100 2.33e-300 1 411 1 1
BPHGHIBC_00203 ANP05420.1|GT4 100 4.59e-289 1 389 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
BPHGHIBC_00006 1.E.53.1.11 100 1.1e-21 1 49 1.0000 0.7206 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
BPHGHIBC_00028 2.A.14.1.1 97.8 4.1e-303 1 551 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.14 The Lactate Permease (LctP) Family
BPHGHIBC_00133 1.B.11.1.1 94.6 0 15 813 0.9828 0.9840 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family
BPHGHIBC_00144 1.B.22.1.1 73.8 1.3e-263 10 650 0.9771 0.9742 1 Channels/Pores 1.B β-Barrel Porins 1.B.22 The Outer Bacterial Membrane Secretin (Secretin) Family
BPHGHIBC_00145 3.A.15.1.1 73.2 6.6e-199 10 494 0.9759 2.1272 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
BPHGHIBC_00171 3.A.1.109.1 73 1.6e-299 10 705 0.9872 0.9844 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
BPHGHIBC_00172 1.C.11.1.6 95.8 0 1 997 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
BPHGHIBC_00207 1.B.13.1.6 99.5 2.6e-223 59 439 0.8679 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.13 The Alginate Export Porin (AEP) Family
BPHGHIBC_00213 5.A.3.2.1 70.3 0 1 1016 1.0000 1.0000 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family