Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C386
  Reference Plasmid   NZ_AP025752.1
  Reference Plasmid Size   220055
  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
M0163711 PANOMIFI_00264 213372 7 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4799G>T None
M0163712 PANOMIFI_00264 213535 7 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4962T>C None
M0163713 PANOMIFI_00267 213546 7 Gut 1.00 protein_coding stop_lost&splice_region_variant HIGH 193T>G Ter65Gluext*?
M0163714 PANOMIFI_00267 213548 7 Gut 1.00 protein_coding stop_gained HIGH 191C>A Ser64*
M0163715 PANOMIFI_00268 213935 7 Gut 1.00 protein_coding missense_variant MODERATE 205G>A Ala69Thr
M0163716 PANOMIFI_00268 214019 7 Gut 1.00 protein_coding missense_variant MODERATE 121G>A Gly41Ser






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
PANOMIFI_00157 VFG001445 TraJ 77.9 1.9e-85 1 195 0.8553 0.9701 Invasion unknown protein experiment
PANOMIFI_00218 VFG000842 Hemolysin 94.2 6.1e-97 1 171 1.0 1 Exotoxin Hemolysin C experiment
PANOMIFI_00266 VFG000844 EspP 91.5 0 1 1301 1.0 1.0008 Effector delivery system autotransporter, serine protease experiment
PANOMIFI_00016 VFG035429 AAI/SCI-II T6SS 83.8 0 1 842 0.9988 0.9918 Effector delivery system type VI secretion system ATPase TssH prediction
PANOMIFI_00019 VFG035419 AAI/SCI-II T6SS 77.8 9.4e-67 1 153 0.9387 0.7806 Effector delivery system DotU family type IV/VI secretion system protein prediction
PANOMIFI_00025 VFG035404 AAI/SCI-II T6SS 80.3 3e-85 1 183 1.0 1 Effector delivery system type VI secretion lipoprotein TssJ prediction
PANOMIFI_00026 VFG035399 AAI/SCI-II T6SS 85.2 6.5e-177 1 358 1.0 1 Effector delivery system type VI secretion system protein TssA prediction
PANOMIFI_00027 VFG035394 AAI/SCI-II T6SS 90.9 1.3e-47 1 99 1.0 1 Effector delivery system PAAR domain-containing protein prediction
PANOMIFI_00028 VFG035389 AAI/SCI-II T6SS 74.5 4.1e-64 1 153 1.0 0.9871 Effector delivery system hypothetical protein prediction
PANOMIFI_00029 VFG035384 AAI/SCI-II T6SS 78 6.9e-306 330 983 0.6653 0.9909 Effector delivery system type VI secretion system tip protein VgrG prediction
PANOMIFI_00030 VFG035374 AAI/SCI-II T6SS 84.5 4.7e-305 1 600 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssF prediction
PANOMIFI_00031 VFG035369 AAI/SCI-II T6SS 85 1e-61 1 140 1.0 1 Effector delivery system hypothetical protein prediction
PANOMIFI_00032 VFG035364 AAI/SCI-II T6SS 73.1 1.8e-65 7 166 0.9639 0.9524 Effector delivery system type VI secretion system protein AaiC/Hcp2 prediction
PANOMIFI_00033 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
PANOMIFI_00034 VFG035354 AAI/SCI-II T6SS 90.5 2.6e-77 1 158 1.0 1 Effector delivery system type VI secretion system contractile sheath small subunit prediction
PANOMIFI_00035 VFG041000 AAI/SCI-II T6SS 73.2 7.3e-67 1 164 1.0 0.8723 Effector delivery system hypothetical protein prediction
PANOMIFI_00157 VFG001445 TraJ 77.9 1.4e-84 1 195 0.8553 0.9701 Invasion unknown protein prediction
PANOMIFI_00218 VFG000842 Hemolysin 94.2 4.6e-96 1 171 1.0 1 Exotoxin Hemolysin C prediction
PANOMIFI_00250 VFG034602 Adhesive fimbriae 87.9 5.4e-133 1 257 1.0 1 Adherence fimbrial protein FaeJ prediction
PANOMIFI_00251 VFG043644 CS31A capsule-like antigen 85.8 1.3e-126 1 254 1.0 1 Adherence CS31A minor subunit prediction
PANOMIFI_00252 VFG043647 CS31A capsule-like antigen 84.8 7e-123 17 272 0.9412 0.9624 Adherence fimbrial protein prediction
PANOMIFI_00254 VFG042496 Adhesive fimbriae 90.7 6.1e-74 1 162 0.9939 0.9939 Adherence unknown protein prediction
PANOMIFI_00255 VFG042553 Adhesive fimbriae 92.9 9e-133 1 253 1.0 0.9806 Adherence F4 (K88) fimbrial chaperone FaeE prediction
PANOMIFI_00256 VFG042494 Adhesive fimbriae 93.1 0 15 814 0.9828 1 Adherence cshB porin (usher) prediction
PANOMIFI_00257 VFG042533 CS31A capsule-like antigen 93.1 3.5e-81 28 186 0.8548 0.8833 Adherence ClpC prediction
PANOMIFI_00266 VFG000844 EspP 91.5 0 1 1301 1.0 1.0008 Effector delivery system autotransporter, serine protease prediction
PANOMIFI_00273 VFG017870 Icm/dot type IVB locus 77.4 1.7e-89 1 208 0.9905 0.9952 Effector delivery system ParA family protein 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
PANOMIFI_00032 PHI:123579 Hcp2 73.1 6.4e-66 7 166 0.9639 0.9524 primates avian colibacillosis type VI secretion system protein effector (plant avirulence determinant)
PANOMIFI_00232 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
PANOMIFI_00159 QIC02838.1|GH23 99.1 1.93e-155 1 215 1 1
PANOMIFI_00242 ANO92402.1|GT4 100 5.58e-290 1 389 1 1
PANOMIFI_00243 ANP05419.1|GT4 99.8 9.5e-300 1 411 1 1
PANOMIFI_00244 ANP16064.1|GT1 100 1.43e-270 1 386 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
PANOMIFI_00111 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
PANOMIFI_00232 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
PANOMIFI_00238 1.B.13.1.6 100 3.1e-224 59 439 0.8679 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.13 The Alginate Export Porin (AEP) Family
PANOMIFI_00256 1.B.11.1.1 92 0 5 814 0.9951 0.9975 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family
PANOMIFI_00266 1.B.12.4.3 91.5 0 1 1301 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family