Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1363
  Reference Plasmid   NZ_LT719075.1
  Reference Plasmid Size   121486
  Reference Plasmid GC Content   0.46
  Reference Plasmid Mobility Type   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
M0208049 OIDOMDIM_00044 28848 6 Gut 0.27 protein_coding synonymous_variant LOW 33A>G Leu11Leu
M0208050 OIDOMDIM_00045 29502 10 Gut 0.45 protein_coding missense_variant MODERATE 493C>A Leu165Met
M0208051 OIDOMDIM_00055 40018 5 Gut 0.23 protein_coding synonymous_variant LOW 324G>A Arg108Arg
M0208052 OIDOMDIM_00056 40123 4 Gut 0.18 protein_coding missense_variant MODERATE 530A>C Gln177Pro
M0208053 OIDOMDIM_00056 40172 5 Gut 0.23 protein_coding missense_variant MODERATE 481A>T Arg161Trp
M0208054 OIDOMDIM_00056 40203 5 Gut 0.23 protein_coding synonymous_variant LOW 450T>C Ser150Ser
M0208055 OIDOMDIM_00056 40475 5 Gut 0.23 protein_coding missense_variant MODERATE 178A>G Asn60Asp
M0208056 OIDOMDIM_00057 40817 5 Gut 0.23 protein_coding synonymous_variant LOW 93T>C Gly31Gly
M0208057 OIDOMDIM_00021 19888 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -4883T>A None
M0208058 OIDOMDIM_00022 20063 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -3506A>G None
M0208059 OIDOMDIM_00029 20293 3 Gut 0.14 protein_coding missense_variant MODERATE 196A>G Ile66Val






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
OIDOMDIM_00004 VFG034574 Dispersin 99.1 8.7e-63 1 116 1.0 1 Others dispersin experiment
OIDOMDIM_00046 VFG001827 ShET2 99.5 3e-224 1 391 1.0 1 Exotoxin enterotoxin experiment
OIDOMDIM_00061 VFG000861 Pic 99.6 0 1 1037 0.9981 0.7558 Effector delivery system Pic serine protease precursor, autotransporter experiment
OIDOMDIM_00081 VFG035902 Dispersin 98.9 2.3e-197 1 376 1.0 1 Others permease AatP experiment
OIDOMDIM_00082 VFG035909 Dispersin 98.5 1.3e-225 1 412 1.0 1 Others outer membrane protein AatA experiment
OIDOMDIM_00083 VFG035916 Dispersin 99.5 9.8e-113 1 212 1.0 0.7766 Others AatB experiment
OIDOMDIM_00084 VFG035923 Dispersin 99.5 9.1e-111 1 209 1.0 1 Others ATP-binding protein AatC experiment
OIDOMDIM_00085 VFG035929 Dispersin 99 7.1e-229 1 404 1.0 1 Others AatD experiment
OIDOMDIM_00152 VFG000862 Pet 98.9 0 1 1295 1.0 1 Effector delivery system Pet serine protease precursor, autotransporter experiment
OIDOMDIM_00004 VFG034574 Dispersin 99.1 6.5e-62 1 116 1.0 1 Others dispersin prediction
OIDOMDIM_00006 VFG036090 AggR 98.9 3.2e-141 1 265 1.0 1 Regulation aggregative adherence transcriptional regulator AggR prediction
OIDOMDIM_00030 VFG017870 Icm/dot type IVB locus 77.9 1e-89 1 208 0.9905 0.9952 Effector delivery system ParA family protein prediction
OIDOMDIM_00046 VFG036084 Enterotoxin SenB/TieB 99.7 4.5e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB prediction
OIDOMDIM_00061 VFG000861 Pic 99.6 0 1 1037 0.9981 0.7558 Effector delivery system Pic serine protease precursor, autotransporter prediction
OIDOMDIM_00081 VFG035902 Dispersin 98.9 1.7e-196 1 376 1.0 1 Others permease AatP prediction
OIDOMDIM_00082 VFG035909 Dispersin 98.5 9.6e-225 1 412 1.0 1 Others outer membrane protein AatA prediction
OIDOMDIM_00083 VFG035916 Dispersin 99.5 7.4e-112 1 212 1.0 0.7766 Others AatB prediction
OIDOMDIM_00084 VFG035923 Dispersin 99.5 6.8e-110 1 209 1.0 1 Others ATP-binding protein AatC prediction
OIDOMDIM_00085 VFG035929 Dispersin 99 5.3e-228 1 404 1.0 1 Others AatD prediction
OIDOMDIM_00090 VFG034586 AAFs 100 3e-80 1 145 1.0 0.9932 Adherence usher protein prediction
OIDOMDIM_00094 VFG034582 AAFs 93.4 2.4e-86 1 166 1.0 1 Adherence periplasmic chaperone prediction
OIDOMDIM_00095 VFG034586 AAFs 100 3e-80 1 145 1.0 0.9932 Adherence usher protein prediction
OIDOMDIM_00096 VFG034590 AAFs 98.7 0 1 849 1.0 1 Adherence invasin protein prediction
OIDOMDIM_00097 VFG034594 AAFs 98.4 3e-143 51 300 0.8333 1 Adherence adhesin protein prediction
OIDOMDIM_00104 VFG041000 AAI/SCI-II T6SS 95.7 1.2e-102 1 188 1.0 1 Effector delivery system hypothetical protein prediction
OIDOMDIM_00113 VFG035429 AAI/SCI-II T6SS 88.5 0 1 842 1.0 0.9918 Effector delivery system type VI secretion system ATPase TssH prediction
OIDOMDIM_00114 VFG035428 AAI/SCI-II T6SS 80.1 0 1 1134 1.0 1 Effector delivery system hypothetical protein prediction
OIDOMDIM_00115 VFG035422 AAI/SCI-II T6SS 75.5 2.2e-81 10 205 0.9561 1 Effector delivery system DotU family type IV/VI secretion system protein prediction
OIDOMDIM_00117 VFG035409 AAI/SCI-II T6SS 85.6 2.1e-233 1 451 0.9934 0.9596 Effector delivery system type VI secretion system baseplate subunit TssK prediction
OIDOMDIM_00118 VFG035404 AAI/SCI-II T6SS 86.3 5.2e-90 1 183 1.0 1 Effector delivery system type VI secretion lipoprotein TssJ prediction
OIDOMDIM_00119 VFG035399 AAI/SCI-II T6SS 85.5 2.4e-179 1 358 1.0 1 Effector delivery system type VI secretion system protein TssA prediction
OIDOMDIM_00120 VFG035394 AAI/SCI-II T6SS 89.9 6.6e-47 1 99 1.0 1 Effector delivery system PAAR domain-containing protein prediction
OIDOMDIM_00121 VFG035389 AAI/SCI-II T6SS 77.8 6.2e-68 1 153 0.9871 0.9871 Effector delivery system hypothetical protein prediction
OIDOMDIM_00122 VFG035384 AAI/SCI-II T6SS 79.4 2.4e-305 23 679 0.9676 0.9955 Effector delivery system type VI secretion system tip protein VgrG prediction
OIDOMDIM_00123 VFG035379 AAI/SCI-II T6SS 86.5 2.4e-159 10 319 0.9718 1 Effector delivery system type VI secretion system baseplate subunit TssG prediction
OIDOMDIM_00124 VFG035374 AAI/SCI-II T6SS 87.2 0 1 600 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssF prediction
OIDOMDIM_00125 VFG035369 AAI/SCI-II T6SS 89.3 7.3e-68 1 140 1.0 1 Effector delivery system hypothetical protein prediction
OIDOMDIM_00127 VFG035359 AAI/SCI-II T6SS 96.3 3.3e-280 1 492 1.0 1 Effector delivery system type VI secretion system contractile sheath large subunit prediction
OIDOMDIM_00128 VFG035354 AAI/SCI-II T6SS 93 1.6e-79 1 158 1.0 1 Effector delivery system type VI secretion system contractile sheath small subunit prediction
OIDOMDIM_00138 VFG020186 VirK 98.4 2.1e-187 1 316 1.0 1 Others virulence factor VirK prediction
OIDOMDIM_00139 VFG013087 MsbB2 97.5 4.1e-183 1 314 1.0 1 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase prediction
OIDOMDIM_00152 VFG000862 Pet 98.9 0 1 1295 1.0 1 Effector delivery system Pet serine protease precursor, autotransporter 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
OIDOMDIM_00006 PHI:9507 aggR 98.1 2.2e-140 1 265 1.0000 1.0000 moths diarrhea transcriptional activator reduced virulence
OIDOMDIM_00046 PHI:10795 senB 99.7 1.6e-224 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
OIDOMDIM_00047 PHI:10794 cjrC 99.5 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
OIDOMDIM_00048 PHI:10793 cjrB 99.6 1.1e-136 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
OIDOMDIM_00049 PHI:10792 cjrA 99.3 2.4e-161 1 283 1.0000 0.9725 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
OIDOMDIM_00061 PHI:3792 pic 99.6 0 1 1037 0.9981 0.7558 birds colibacillosis; cellulitis; swollen head syndrome serin protease aut o transporter reduced virulence
OIDOMDIM_00137 PHI:10400 Sfgtr4 (ORF186) 95.9 5.6e-208 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) 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
OIDOMDIM_00137 SJK83533.1|GT4 100 2.19e-271 1 362 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
OIDOMDIM_00047 1.B.14.7.1 99.5 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
OIDOMDIM_00048 2.C.1.1.3 99.6 2.4e-136 1 258 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.C Ion-gradient-driven energizers 2.C.1 The TonB-ExbB-ExbD/TolA-TolQ-TolR Outer Membrane Receptor Energizers and Stabilizers (TonB/TolA) Family
OIDOMDIM_00061 1.B.12.4.5 99.6 0 1 1037 0.9981 0.7558 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family
OIDOMDIM_00152 1.B.12.4.4 98.9 0 1 1295 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family