Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C100
  Reference Plasmid   CP056497.1
  Reference Plasmid Size   164815
  Reference Plasmid GC Content   0.52
  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
M0144071 LIHCGALI_00002 6400 6 Gut 0.86 protein_coding upstream_gene_variant MODIFIER -3951G>A None
M0144072 LIHCGALI_00010 6456 3 Gut 0.43 protein_coding missense_variant MODERATE 55C>T His19Tyr
M0144073 LIHCGALI_00010 6504 3 Gut 0.43 protein_coding stop_gained HIGH 7G>T Glu3*
M0144074 LIHCGALI_00002 6518 5 Gut 0.71 protein_coding upstream_gene_variant MODIFIER -4069A>C None
M0144075 LIHCGALI_00011 6999 3 Gut 0.43 protein_coding missense_variant MODERATE 334G>T Ala112Ser
M0144076 LIHCGALI_00002 7297 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -4848G>A None
M0144077 LIHCGALI_00013 8504 3 Gut 0.43 protein_coding missense_variant MODERATE 324A>T Glu108Asp
M0144078 LIHCGALI_00013 8831 3 Gut 0.43 protein_coding synonymous_variant LOW 651C>T Asn217Asn
M0144079 LIHCGALI_00013 9581 5 Gut 0.71 protein_coding missense_variant MODERATE 1401A>T Lys467Asn
M0144080 LIHCGALI_00013 9794 5 Gut 0.71 protein_coding synonymous_variant LOW 1614T>C Asn538Asn
M0144081 LIHCGALI_00014 10901 5 Gut 0.71 protein_coding missense_variant MODERATE 244G>A Val82Ile
M0144082 LIHCGALI_00014 11105 5 Gut 0.71 protein_coding missense_variant MODERATE 448A>T Ile150Leu
M0144083 LIHCGALI_00015 11787 5 Gut 0.71 protein_coding synonymous_variant LOW 141C>A Thr47Thr
M0144084 LIHCGALI_00016 13195 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -120C>T None
M0144085 LIHCGALI_00016 13199 5 Gut 0.71 protein_coding upstream_gene_variant MODIFIER -124T>C None
M0144086 LIHCGALI_00018 14098 5 Gut 0.71 protein_coding missense_variant MODERATE 532T>G Phe178Val
M0144087 LIHCGALI_00018 14146 5 Gut 0.71 protein_coding missense_variant MODERATE 484G>A Glu162Lys
M0144088 LIHCGALI_00018 14284 5 Gut 0.71 protein_coding missense_variant MODERATE 346A>G Arg116Gly
M0144089 LIHCGALI_00016 14743 5 Gut 0.71 protein_coding upstream_gene_variant MODIFIER -1668A>G None






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
LIHCGALI_00011 VFG043627 Type 3 fimbriae 96 3e-103 1 202 1.0 1 Biofilm type 3 fimbrial major pilin subunit MrkA experiment
LIHCGALI_00012 VFG043626 Type 3 fimbriae 92.3 1.4e-120 1 233 1.0 1 Biofilm fimbrial chaperone protein mrkB precursor experiment
LIHCGALI_00013 VFG043625 Type 3 fimbriae 88.8 0 1 828 1.0 1 Biofilm fimbrial biogenesis outer membrane usher protein mrkC precursor experiment
LIHCGALI_00015 VFG043623 Type 3 fimbriae 81.9 4.5e-97 18 216 0.9213 0.9431 Biofilm type 3 fimbrial minor pilin subunit MrkF experiment
LIHCGALI_00016 VFG048348 Type 3 fimbriae 76.3 1.3e-108 1 236 0.9916 0.9916 Biofilm phosphodiesterase experiment
LIHCGALI_00053 VFG034679 Ibes 71.9 4.8e-183 102 560 0.8167 0.9978 Invasion Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC experiment
LIHCGALI_00011 VFG048392 Type 3 fimbriae 100 1.5e-106 1 202 1.0 1 Biofilm type 3 fimbrial major pilin subunit MrkA prediction
LIHCGALI_00012 VFG048381 Type 3 fimbriae 100 1.4e-127 1 233 1.0 1 Biofilm fimbrial chaperone protein mrkB precursor prediction
LIHCGALI_00013 VFG048371 Type 3 fimbriae 99.2 0 1 828 1.0 1 Biofilm fimbrial biogenesis outer membrane usher protein mrkC precursor prediction
LIHCGALI_00015 VFG042692 Type 3 fimbriae 99.1 1.5e-123 1 216 1.0 0.9774 Adherence MrkF prediction
LIHCGALI_00016 VFG048341 Type 3 fimbriae 91.1 4.5e-126 1 236 0.9916 0.9916 Biofilm phosphodiesterase prediction
LIHCGALI_00017 VFG048330 Type 3 fimbriae 82.5 6.6e-83 1 194 1.0 1 Biofilm LuxR family regulatory protein prediction
LIHCGALI_00053 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
LIHCGALI_00037 Arsenic (As), Antimony (Sb), Bismuth (Bi) 100 8.1e-64 1 117 1.0000 1.0000 experiment
LIHCGALI_00038 Arsenic (As), Antimony (Sb) 98.3 1.6e-67 1 120 1.0000 1.0000 experiment
LIHCGALI_00039 Arsenic (As), Antimony (Sb) 99.1 0 1 583 1.0000 1.0000 experiment
LIHCGALI_00040 Arsenic (As), Antimony (Sb) 99.5 2e-232 1 429 1.0000 1.0000 experiment
LIHCGALI_00041 Arsenic (As), Antimony (Sb) 99.3 3.5e-77 1 141 1.0000 1.0000 experiment
LIHCGALI_00050 Silver (Ag) 84.6 1.5e-64 1 143 1.0000 1.0000 experiment
LIHCGALI_00051 Silver (Ag) 92.7 9.3e-255 1 491 1.0081 0.9960 experiment
LIHCGALI_00052 Copper (Cu), Silver (Ag) 87.6 3.8e-92 1 185 0.9946 0.8150 experiment
LIHCGALI_00053 Silver (Ag) 97.6 7.2e-251 102 562 0.8203 1.0000 experiment
LIHCGALI_00054 Silver (Ag) 98.9 3.1e-47 28 117 0.7692 0.9375 experiment
LIHCGALI_00055 Silver (Ag) 98.4 3.2e-243 1 430 1.0000 1.0000 experiment
LIHCGALI_00056 Silver (Ag) 99.4 0 1 1048 1.0000 1.0000 experiment
LIHCGALI_00058 Silver (Ag) 95.8 0 1 815 1.0012 0.9903 experiment
LIHCGALI_00062 Copper (Cu) 100 0 1 605 1.0000 1.0000 experiment
LIHCGALI_00063 Copper (Cu) 100 1.5e-175 1 296 1.0000 1.0000 experiment
LIHCGALI_00064 Copper (Cu) 99.2 1.9e-66 1 126 1.0000 1.0000 experiment
LIHCGALI_00065 Copper (Cu) 99.7 2.5e-165 1 309 1.0000 1.0000 experiment
LIHCGALI_00066 Copper (Cu) 99.6 4.9e-126 1 226 1.0000 1.0000 experiment
LIHCGALI_00067 Copper (Cu) 99.4 1.5e-262 1 466 1.0000 1.0000 experiment
LIHCGALI_00068 Copper (Cu), Silver (Ag) 88.3 3.4e-43 1 103 0.9279 0.7153 experiment
LIHCGALI_00037 Arsenic (As) 100 1.9e-61 1 117 1.0000 1.0000 prediction
LIHCGALI_00038 Arsenic (As) 100 4.4e-66 1 120 1.0000 1.0000 prediction
LIHCGALI_00039 Arsenic (As), Antimony (Sb) 100 0 1 583 1.0000 1.0000 prediction
LIHCGALI_00040 Arsenic (As), Antimony (Sb) 99.8 6.9e-231 1 428 0.9977 1.0000 prediction
LIHCGALI_00041 Arsenic (As) 100 1.6e-75 1 141 1.0000 1.0000 prediction
LIHCGALI_00050 Silver (Ag) 87.4 9.8e-65 1 143 1.0000 1.0000 prediction
LIHCGALI_00051 Silver (Ag) 100 8.1e-276 1 491 1.0000 1.0000 prediction
LIHCGALI_00052 Silver (Ag) 100 1.9e-100 1 186 1.0000 0.8230 prediction
LIHCGALI_00053 Silver (Ag) 99.6 0 1 562 1.0000 1.0000 prediction
LIHCGALI_00054 Silver (Ag) 100 1.6e-60 1 117 1.0000 1.0000 prediction
LIHCGALI_00055 Silver (Ag) 100 3.2e-244 1 430 1.0000 1.0000 prediction
LIHCGALI_00056 Silver (Ag) 100 0 1 1048 1.0000 1.0000 prediction
LIHCGALI_00058 Silver (Ag) 100 0 1 815 1.0000 1.0000 prediction
LIHCGALI_00062 Copper (Cu) 100 0 1 605 1.0000 0.9967 prediction
LIHCGALI_00063 Copper (Cu) 100 3.5e-173 1 296 1.0000 0.9900 prediction
LIHCGALI_00064 Copper (Cu) 100 6.6e-65 1 126 1.0000 1.0000 prediction
LIHCGALI_00065 Copper (Cu) 100 4.4e-163 1 309 1.0000 1.0000 prediction
LIHCGALI_00066 Copper (Cu) 100 1.3e-124 1 226 1.0000 1.0000 prediction
LIHCGALI_00067 Copper (Cu) 100 3.7e-262 1 466 1.0000 1.0000 prediction
LIHCGALI_00068 Copper (Cu), Silver (Ag) 100 6.5e-48 1 103 0.9279 0.7153 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






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
LIHCGALI_00011 PHI:6099 MrkA 95.5 3.9e-102 1 202 1.0000 1.0000 rodents pneumonia ferrous iron transporter unaffected pathogenicity
LIHCGALI_00121 PHI:6268 lacZ 95.9 0 1 1024 1.0000 1.0000 rodents urinary tract infection beta-galactosidase reduced virulence
LIHCGALI_00130 PHI:3165 hopA1 73.7 8.3e-29 1 76 1.0000 0.9215 eudicots leaf spot (celery); leaf spot (eggplant); leaf spot (sweet pepper); wilt rot (muskmelon); stem rot (muskmelon); stem rot (chrysanthemum); leaf spot (soybean) effector (plant avirulence determinant) effector (plant avirulence determinant)






        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
LIHCGALI_00121 QLP24917.1|GH2 100 0 1 1024 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
LIHCGALI_00013 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
LIHCGALI_00039 3.A.4.1.1 85.7 5e-283 1 581 0.9966 1.3543 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
LIHCGALI_00040 3.A.4.1.1 93.9 1.5e-220 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
LIHCGALI_00053 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
LIHCGALI_00056 2.A.6.1.3 99.4 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
LIHCGALI_00058 3.A.3.5.4 95.8 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
LIHCGALI_00060 1.A.34.1.3 99.6 4.3e-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
LIHCGALI_00063 1.B.76.1.5 100 5.7e-174 1 296 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.76 The Copper Resistance Putative Porin (CopB) Family
LIHCGALI_00065 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
LIHCGALI_00122 2.A.1.5.1 99 1.8e-229 1 417 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)