Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1176
  Reference Plasmid   NZ_CP128591.1
  Reference Plasmid Size   179123
  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
M0199203 IDHOFOKN_00128 117317 3 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -744A>T None
M0199204 IDHOFOKN_00131 120530 3 Gut 0.21 protein_coding synonymous_variant LOW 1233C>T Gly411Gly
M0199205 IDHOFOKN_00132 123185 3 Gut 0.21 protein_coding missense_variant MODERATE 74T>C Val25Ala
M0199206 IDHOFOKN_00113 98663 3 Gut 0.21 protein_coding missense_variant MODERATE 61C>T Pro21Ser
M0199207 IDHOFOKN_00117 106947 3 Gut 0.21 protein_coding missense_variant MODERATE 226A>G Ile76Val
M0199208 IDHOFOKN_00112 96990 3 Gut 0.21 protein_coding synonymous_variant LOW 858T>C Pro286Pro






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
IDHOFOKN_00113 VFG000905 Alpha-Hemolysin 95.3 1.9e-98 1 170 1.0 1 Exotoxin Hemolysin C experiment
IDHOFOKN_00114 VFG000906 Alpha-Hemolysin 97.2 0 1 1024 1.0 1 Exotoxin Hemolysin A experiment
IDHOFOKN_00115 VFG000907 Alpha-Hemolysin 99 0 1 707 1.0 1 Exotoxin Hemolysin B experiment
IDHOFOKN_00116 VFG000908 Alpha-Hemolysin 96.9 1e-250 1 478 1.0 1 Exotoxin Hemolysin D experiment
IDHOFOKN_00083 VFG035354 AAI/SCI-II T6SS 87.3 4.1e-75 1 158 1.0 1 Effector delivery system type VI secretion system contractile sheath small subunit prediction
IDHOFOKN_00084 VFG035359 AAI/SCI-II T6SS 93.3 1.3e-273 1 492 1.0 1 Effector delivery system type VI secretion system contractile sheath large subunit prediction
IDHOFOKN_00085 VFG035364 AAI/SCI-II T6SS 75.3 2.5e-70 1 170 1.0 1.0119 Effector delivery system type VI secretion system protein AaiC/Hcp2 prediction
IDHOFOKN_00086 VFG035369 AAI/SCI-II T6SS 82.1 1.3e-61 1 140 1.0 1 Effector delivery system hypothetical protein prediction
IDHOFOKN_00087 VFG035374 AAI/SCI-II T6SS 79.8 1.2e-289 1 600 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssF prediction
IDHOFOKN_00088 VFG035379 AAI/SCI-II T6SS 77.7 7.6e-145 10 319 0.9718 1 Effector delivery system type VI secretion system baseplate subunit TssG prediction
IDHOFOKN_00089 VFG035384 AAI/SCI-II T6SS 72.1 1.1e-291 3 658 0.997 0.9939 Effector delivery system type VI secretion system tip protein VgrG prediction
IDHOFOKN_00091 VFG035394 AAI/SCI-II T6SS 84.8 4.7e-45 1 99 1.0 1 Effector delivery system PAAR domain-containing protein prediction
IDHOFOKN_00092 VFG035399 AAI/SCI-II T6SS 78.3 2.8e-164 1 359 1.0 1.0028 Effector delivery system type VI secretion system protein TssA prediction
IDHOFOKN_00093 VFG035404 AAI/SCI-II T6SS 79.4 8.2e-80 1 178 0.9944 0.9727 Effector delivery system type VI secretion lipoprotein TssJ prediction
IDHOFOKN_00094 VFG035409 AAI/SCI-II T6SS 75.2 7.9e-204 1 451 0.9847 0.9596 Effector delivery system type VI secretion system baseplate subunit TssK prediction
IDHOFOKN_00100 VFG035432 AAI/SCI-II T6SS 78.1 0 1 841 0.9976 0.9906 Effector delivery system type VI secretion system ATPase TssH prediction
IDHOFOKN_00113 VFG033901 Hemolysin 99.4 1.4e-100 1 170 1.0 1 Exotoxin Hemolysin C prediction
IDHOFOKN_00114 VFG033893 Hemolysin 99.3 0 1 1024 1.0 1 Exotoxin Hemolysin A prediction
IDHOFOKN_00115 VFG033885 Hemolysin 99.9 0 1 707 1.0 1 Exotoxin Hemolysin B prediction
IDHOFOKN_00116 VFG033877 Hemolysin 99.6 6.5e-257 1 478 1.0 1 Exotoxin Hemolysin D prediction
IDHOFOKN_00134 VFG042570 Locus for diffuse adherence (lda), afimbrial adhesin 99.4 5.4e-180 1 309 1.0 1 Adherence LdaA prediction
IDHOFOKN_00135 VFG034595 Adhesive fimbriae 79.5 2.3e-69 25 184 0.8696 0.884 Adherence FaeC prediction
IDHOFOKN_00136 VFG042572 Locus for diffuse adherence (lda), afimbrial adhesin 99.2 0 21 810 0.9753 1 Adherence LdaD prediction
IDHOFOKN_00137 VFG042573 Locus for diffuse adherence (lda), afimbrial adhesin 96.1 4.3e-138 1 258 1.0 0.899 Adherence LdaE prediction
IDHOFOKN_00138 VFG042574 Locus for diffuse adherence (lda), afimbrial adhesin 94.5 2.8e-82 1 164 1.0 1.0061 Adherence LdaF prediction
IDHOFOKN_00140 VFG042576 Locus for diffuse adherence (lda), afimbrial adhesin 85 4.7e-124 4 263 0.9886 0.9701 Adherence LdaH prediction
IDHOFOKN_00141 VFG042577 Locus for diffuse adherence (lda), afimbrial adhesin 97.4 1.5e-151 1 265 1.0 1 Adherence LdaI prediction
IDHOFOKN_00144 VFG042578 Locus for diffuse adherence (lda), afimbrial adhesin 100 5.3e-58 1 108 1.0 1 Adherence LdaB 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
IDHOFOKN_00085 PHI:123579 Hcp2 75.3 8.8e-71 1 170 1.0000 1.0000 primates avian colibacillosis type VI secretion system protein effector (plant avirulence determinant)
IDHOFOKN_00114 PHI:4522 HlyA 99.3 0 1 1024 1.0000 1.0000 rodents urinary tract infection induces caspase-1/caspase-4-dependent inflammatory cell death in human urothelial cells 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
IDHOFOKN_00025 ARD54634.1|GH23 100 4.96e-124 1 169 1 1
IDHOFOKN_00130 QEG96644.1|GT112 100 5.51999999999825e-312 1 392 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
IDHOFOKN_00007 2.A.7.3.25 83.2 7.2e-135 1 303 0.9619 0.9967 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
IDHOFOKN_00073 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
IDHOFOKN_00114 1.C.11.1.3 97.5 0 1 1024 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
IDHOFOKN_00115 3.A.1.109.1 99.4 0 1 707 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
IDHOFOKN_00116 8.A.1.3.1 99.4 1.3e-255 1 478 1.0000 1.0000 8 Accessory Factors Involved in Transport 8.A Auxiliary transport proteins 8.A.1 The Membrane Fusion Protein (MFP) Family
IDHOFOKN_00136 1.B.11.1.1 85 0 14 810 0.9840 0.9828 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family