Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C964
  Reference Plasmid   NZ_CP085105.1
  Reference Plasmid Size   122654
  Reference Plasmid GC Content   0.52
  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
M0191112 HMADONFM_00111 106746 3 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -3954T>C None
M0191113 HMADONFM_00121 113258 3 Gut 0.19 protein_coding stop_gained HIGH 155T>A Leu52*
M0191114 HMADONFM_00020 17827 3 Gut 0.19 protein_coding missense_variant MODERATE 377C>T Pro126Leu
M0191115 HMADONFM_00028 24728 3 Gut 0.19 protein_coding missense_variant MODERATE 698C>T Thr233Ile
M0191116 HMADONFM_00029 27931 3 Gut 0.19 protein_coding missense_variant MODERATE 2598T>G Asp866Glu
M0191117 HMADONFM_00031 31239 3 Gut 0.19 protein_coding synonymous_variant LOW 2106T>A Gly702Gly
M0191118 HMADONFM_00071 64801 3 Gut 0.19 protein_coding synonymous_variant LOW 642C>T Ala214Ala
M0191119 HMADONFM_00073 67038 3 Gut 0.19 protein_coding synonymous_variant LOW 1680C>T Ala560Ala
M0191120 HMADONFM_00075 69499 3 Gut 0.19 protein_coding missense_variant MODERATE 165T>G Asn55Lys
M0191121 HMADONFM_00087 76412 3 Gut 0.19 protein_coding missense_variant MODERATE 163G>A Glu55Lys
M0191122 HMADONFM_00087 76556 3 Gut 0.19 protein_coding missense_variant MODERATE 307C>T His103Tyr






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
HMADONFM_00007 VFG043627 Type 3 fimbriae 96 3e-103 1 202 1.0 1 Biofilm type 3 fimbrial major pilin subunit MrkA experiment
HMADONFM_00008 VFG043626 Type 3 fimbriae 92.3 1.4e-120 1 233 1.0 1 Biofilm fimbrial chaperone protein mrkB precursor experiment
HMADONFM_00009 VFG043625 Type 3 fimbriae 88.8 0 1 828 1.0 1 Biofilm fimbrial biogenesis outer membrane usher protein mrkC precursor experiment
HMADONFM_00011 VFG043623 Type 3 fimbriae 81.9 4.5e-97 18 216 0.9213 0.9431 Biofilm type 3 fimbrial minor pilin subunit MrkF experiment
HMADONFM_00012 VFG048348 Type 3 fimbriae 76.3 1.3e-108 1 236 0.9916 0.9916 Biofilm phosphodiesterase experiment
HMADONFM_00026 VFG034679 Ibes 71.9 4.8e-183 102 560 0.8167 0.9978 Invasion Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC experiment
HMADONFM_00007 VFG048392 Type 3 fimbriae 100 1.5e-106 1 202 1.0 1 Biofilm type 3 fimbrial major pilin subunit MrkA prediction
HMADONFM_00008 VFG048381 Type 3 fimbriae 100 1.4e-127 1 233 1.0 1 Biofilm fimbrial chaperone protein mrkB precursor prediction
HMADONFM_00009 VFG048371 Type 3 fimbriae 99.2 0 1 828 1.0 1 Biofilm fimbrial biogenesis outer membrane usher protein mrkC precursor prediction
HMADONFM_00011 VFG042692 Type 3 fimbriae 99.1 1.5e-123 1 216 1.0 0.9774 Adherence MrkF prediction
HMADONFM_00012 VFG048341 Type 3 fimbriae 91.1 4.5e-126 1 236 0.9916 0.9916 Biofilm phosphodiesterase prediction
HMADONFM_00013 VFG048330 Type 3 fimbriae 80.9 6.1e-81 1 194 1.0 1 Biofilm LuxR family regulatory protein prediction
HMADONFM_00026 VFG034652 Ibes 71.9 2.8e-182 102 560 0.8167 0.9978 Invasion Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC 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
HMADONFM_00023 Silver (Ag) 97.2 4.3e-75 1 143 1.0000 1.0000 experiment
HMADONFM_00024 Silver (Ag) 92.9 4.2e-255 1 491 1.0081 0.9960 experiment
HMADONFM_00025 Silver (Ag) 92.6 3.5e-93 1 186 1.0108 0.8246 experiment
HMADONFM_00026 Silver (Ag) 97.6 7.2e-251 102 562 0.8203 1.0000 experiment
HMADONFM_00027 Silver (Ag) 98.9 3.1e-47 28 117 0.7692 0.9375 experiment
HMADONFM_00028 Silver (Ag) 97.9 2.1e-242 1 430 1.0000 1.0000 experiment
HMADONFM_00029 Silver (Ag) 98.8 0 1 1048 1.0000 1.0000 experiment
HMADONFM_00031 Silver (Ag) 94.6 0 1 815 1.0012 0.9903 experiment
HMADONFM_00036 Copper (Cu) 100 0 1 605 1.0000 1.0000 experiment
HMADONFM_00037 Copper (Cu) 99.3 8.3e-174 1 296 1.0000 1.0000 experiment
HMADONFM_00038 Copper (Cu) 100 4.9e-67 1 126 1.0000 1.0000 experiment
HMADONFM_00039 Copper (Cu) 99.7 2.5e-165 1 309 1.0000 1.0000 experiment
HMADONFM_00040 Copper (Cu) 100 1.7e-126 1 226 1.0000 1.0000 experiment
HMADONFM_00041 Copper (Cu) 99.4 1.5e-262 1 466 1.0000 1.0000 experiment
HMADONFM_00042 Copper (Cu), Silver (Ag) 89.6 1e-63 1 144 1.0000 1.0000 experiment
HMADONFM_00048 Arsenic (As), Antimony (Sb) 96.5 2.5e-75 1 141 1.0000 1.0000 experiment
HMADONFM_00049 Arsenic (As), Antimony (Sb) 98.1 2.6e-229 1 429 1.0000 1.0000 experiment
HMADONFM_00050 Arsenic (As), Antimony (Sb) 93.8 2.30000000001574e-313 1 583 1.0000 1.0000 experiment
HMADONFM_00051 Arsenic (As), Antimony (Sb) 94.2 4.4e-65 1 120 1.0000 1.0000 experiment
HMADONFM_00052 Arsenic (As), Antimony (Sb), Bismuth (Bi) 100 8.1e-64 1 117 1.0000 1.0000 experiment
HMADONFM_00023 Silver (Ag) 100 4.7e-75 1 143 1.0000 1.0000 prediction
HMADONFM_00024 Silver (Ag) 100 1.4e-275 1 491 1.0000 1.0000 prediction
HMADONFM_00025 Silver (Ag) 100 8.5e-101 1 186 1.0000 0.8230 prediction
HMADONFM_00026 Silver (Ag) 99.6 0 1 562 1.0000 1.0000 prediction
HMADONFM_00027 Silver (Ag) 100 1.6e-60 1 117 1.0000 1.0000 prediction
HMADONFM_00028 Silver (Ag) 100 3.2e-244 1 430 1.0000 1.0000 prediction
HMADONFM_00029 Silver (Ag) 99.9 0 1 1048 1.0000 0.9905 prediction
HMADONFM_00031 Silver (Ag) 100 0 1 815 1.0000 1.0000 prediction
HMADONFM_00036 Copper (Cu) 100 0 1 605 1.0000 0.9967 prediction
HMADONFM_00037 Copper (Cu) 100 4.5e-173 1 296 1.0000 0.9933 prediction
HMADONFM_00038 Copper (Cu) 100 1.1e-64 1 126 1.0000 1.0000 prediction
HMADONFM_00039 Copper (Cu) 100 4.4e-163 1 309 1.0000 1.0000 prediction
HMADONFM_00040 Copper (Cu) 100 3.9e-124 1 226 1.0000 0.9741 prediction
HMADONFM_00041 Copper (Cu) 100 3.7e-262 1 466 1.0000 1.0000 prediction
HMADONFM_00042 Copper (Cu), Silver (Ag) 99.3 6e-70 1 144 1.0000 1.0000 prediction
HMADONFM_00048 Arsenic (As) 100 9.3e-76 1 141 1.0000 1.0000 prediction
HMADONFM_00049 Arsenic (As), Antimony (Sb) 100 2.4e-231 1 429 1.0000 1.0000 prediction
HMADONFM_00050 Arsenic (As), Antimony (Sb) 100 0 1 583 1.0000 1.0000 prediction
HMADONFM_00051 Arsenic (As) 100 1.2e-66 1 120 1.0000 1.0000 prediction
HMADONFM_00052 Arsenic (As) 100 1.9e-61 1 117 1.0000 1.0000 prediction






        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
HMADONFM_00102 ARO:3000165 99.7 7.17e-278 1 390 0.9774 0.9198 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux






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
HMADONFM_00007 PHI:6099 MrkA 95.5 3.9e-102 1 202 1.0000 1.0000 rodents pneumonia ferrous iron transporter unaffected pathogenicity
HMADONFM_00060 PHI:3847 tcpYI 82.5 6.2e-99 1 234 1.0000 1.0000 rodents Far East scarlet-like fever homology to members of the Toll/IL-1 receptor family reduced virulence
HMADONFM_00072 PHI:3531 pld1 96.9 2.1e-28 1 65 1.0000 1.0000 rodents urinary tract infection; nosocomial pneumonia; abdominal infection lipid metabolism loss of 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





        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
HMADONFM_00009 1.B.11.3.2 98.8 0 1 828 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family
HMADONFM_00026 1.B.17.3.4 97.6 2.7e-249 102 562 0.8203 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.17 The Outer Membrane Factor (OMF) Family
HMADONFM_00029 2.A.6.1.3 98.8 0 1 1048 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
HMADONFM_00031 3.A.3.5.4 94.6 0 1 815 1.0000 0.9879 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
HMADONFM_00034 1.A.34.1.3 100 1.1e-135 1 245 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.34 The <i>Bacillus</i> Gap Junction-like Channel-forming Complex (GJ-CC) Family
HMADONFM_00037 1.B.76.1.5 99.3 3.1e-172 1 296 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.76 The Copper Resistance Putative Porin (CopB) Family
HMADONFM_00039 9.B.62.1.1 99.7 9.5e-164 1 309 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.62 The Copper Resistance (CopD) Family
HMADONFM_00049 3.A.4.1.1 93 2.1e-217 1 429 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
HMADONFM_00050 3.A.4.1.1 84 3.1e-280 1 582 0.9983 1.3566 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
HMADONFM_00101 2.A.7.3.67 100 1.8e-159 1 294 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
HMADONFM_00102 2.A.1.2.4 100 2.4e-223 1 399 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)