Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C221
  Reference Plasmid   CP146553.1
  Reference Plasmid Size   88982
  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
M0149013 AKMGNAON_00030 27604 4 Gut 0.07 protein_coding missense_variant MODERATE 1258G>A Ala420Thr
M0149014 AKMGNAON_00007 8879 4 Gut 0.07 protein_coding synonymous_variant LOW 2115G>A Gln705Gln
M0149015 AKMGNAON_00008 9814 5 Gut 0.09 protein_coding missense_variant MODERATE 908G>A Arg303Lys
M0149016 AKMGNAON_00019 18487 4 Gut 0.07 protein_coding missense_variant MODERATE 41T>C Val14Ala
M0149017 AKMGNAON_00016 18930 4 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -2191A>G None
M0149018 AKMGNAON_00023 25628 4 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -3005G>A None
M0149019 AKMGNAON_00023 26104 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -3481T>G None
M0149020 AKMGNAON_00030 26888 3 Gut 0.06 protein_coding synonymous_variant LOW 1974G>A Arg658Arg
M0149021 AKMGNAON_00030 27064 3 Gut 0.06 protein_coding missense_variant MODERATE 1798C>T Pro600Ser
M0149022 AKMGNAON_00030 27112 3 Gut 0.06 protein_coding missense_variant MODERATE 1750C>T Pro584Ser
M0149023 AKMGNAON_00030 27934 3 Gut 0.06 protein_coding missense_variant MODERATE 928C>T Arg310Trp
M0149024 AKMGNAON_00030 27960 3 Gut 0.06 protein_coding missense_variant MODERATE 902C>T Pro301Leu
M0149025 AKMGNAON_00030 27998 3 Gut 0.06 protein_coding synonymous_variant LOW 864T>C Asp288Asp
M0149026 AKMGNAON_00030 28003 3 Gut 0.06 protein_coding missense_variant MODERATE 859T>A Trp287Arg
M0149027 AKMGNAON_00030 28310 3 Gut 0.06 protein_coding synonymous_variant LOW 552A>C Ser184Ser
M0149028 AKMGNAON_00030 28721 3 Gut 0.06 protein_coding synonymous_variant LOW 141C>T Arg47Arg
M0149029 AKMGNAON_00030 28747 3 Gut 0.06 protein_coding missense_variant MODERATE 115A>G Lys39Glu
M0149030 AKMGNAON_00026 29206 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -4497C>T None
M0149031 AKMGNAON_00026 29270 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -4561A>G None
M0149032 AKMGNAON_00026 29386 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -4677A>G None
M0149033 AKMGNAON_00032 29575 3 Gut 0.06 protein_coding synonymous_variant LOW 138A>G Leu46Leu
M0149034 AKMGNAON_00032 29739 3 Gut 0.06 protein_coding missense_variant MODERATE 302G>A Gly101Asp
M0149035 AKMGNAON_00033 29890 3 Gut 0.06 protein_coding missense_variant MODERATE 820T>C Tyr274His
M0149036 AKMGNAON_00033 30053 3 Gut 0.06 protein_coding synonymous_variant LOW 657T>C Ser219Ser
M0149037 AKMGNAON_00033 30106 3 Gut 0.06 protein_coding synonymous_variant LOW 604T>C Leu202Leu
M0149038 AKMGNAON_00033 30518 3 Gut 0.06 protein_coding synonymous_variant LOW 192A>G Gly64Gly
M0149039 AKMGNAON_00033 30572 3 Gut 0.06 protein_coding synonymous_variant LOW 138A>G Leu46Leu
M0149040 AKMGNAON_00029 30876 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -4830C>T None
M0149041 AKMGNAON_00030 31088 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -2227G>A None
M0149042 AKMGNAON_00034 31218 3 Gut 0.06 protein_coding missense_variant MODERATE 20A>G Gln7Arg
M0149043 AKMGNAON_00034 31273 3 Gut 0.06 protein_coding synonymous_variant LOW 75A>C Gly25Gly
M0149044 AKMGNAON_00030 32700 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -3839C>T None
M0149045 AKMGNAON_00006 5484 6 Gut 0.11 protein_coding missense_variant MODERATE 1866T>G Asn622Lys
M0149046 AKMGNAON_00006 6139 7 Gut 0.13 protein_coding missense_variant MODERATE 2521T>C Phe841Leu
M0149047 AKMGNAON_00069 67265 8 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4824T>G None
M0149048 AKMGNAON_00080 68984 8 Gut 0.15 protein_coding synonymous_variant LOW 2445A>G Thr815Thr
M0149049 AKMGNAON_00080 70139 6 Gut 0.11 protein_coding synonymous_variant LOW 1290A>G Glu430Glu
M0149050 AKMGNAON_00080 71000 6 Gut 0.11 protein_coding synonymous_variant LOW 429C>T Phe143Phe
M0149051 AKMGNAON_00080 71411 6 Gut 0.11 protein_coding synonymous_variant LOW 18C>T Ser6Ser
M0149052 AKMGNAON_00080 71716 6 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -288T>C None
M0149053 AKMGNAON_00080 71757 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -329C>T None
M0149054 AKMGNAON_00062 49898 5 Gut 0.09 protein_coding synonymous_variant LOW 292T>C Leu98Leu
M0149055 AKMGNAON_00063 50514 5 Gut 0.09 protein_coding stop_lost&splice_region_variant HIGH 253T>C Ter85Argext*?
M0149056 AKMGNAON_00065 51612 3 Gut 0.06 protein_coding missense_variant MODERATE 174A>G Ile58Met
M0149057 AKMGNAON_00065 52252 5 Gut 0.09 protein_coding synonymous_variant LOW 814T>C Leu272Leu
M0149058 AKMGNAON_00065 54808 5 Gut 0.09 protein_coding missense_variant MODERATE 3370A>G Asn1124Asp
M0149059 AKMGNAON_00065 57423 5 Gut 0.09 protein_coding synonymous_variant LOW 5985G>A Val1995Val
M0149060 AKMGNAON_00065 58596 5 Gut 0.09 protein_coding synonymous_variant LOW 7158T>C Ile2386Ile
M0149061 AKMGNAON_00074 64560 5 Gut 0.09 protein_coding missense_variant MODERATE 29A>G His10Arg
M0149062 AKMGNAON_00074 64764 7 Gut 0.13 protein_coding missense_variant MODERATE 233C>A Thr78Lys
M0149063 AKMGNAON_00074 64845 4 Gut 0.07 protein_coding missense_variant MODERATE 314C>A Ala105Glu
M0149064 AKMGNAON_00075 64901 3 Gut 0.06 protein_coding missense_variant MODERATE 48A>C Leu16Phe
M0149065 AKMGNAON_00079 66924 4 Gut 0.07 protein_coding missense_variant MODERATE 403G>A Asp135Asn
M0149066 AKMGNAON_00106 87120 4 Gut 0.07 protein_coding synonymous_variant LOW 222C>T Gly74Gly
M0149067 AKMGNAON_00107 87672 4 Gut 0.07 protein_coding missense_variant MODERATE 92T>C Val31Ala
M0149068 AKMGNAON_00097 87809 4 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -4935G>A None
M0149069 AKMGNAON_00108 88187 4 Gut 0.07 protein_coding missense_variant MODERATE 34A>G Thr12Ala
M0149070 AKMGNAON_00099 88388 5 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -4490G>A None
M0149071 AKMGNAON_00006 5742 5 Gut 0.09 protein_coding synonymous_variant LOW 2124A>G Lys708Lys
M0149072 AKMGNAON_00007 6754 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -11T>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
AKMGNAON_00005 VFG000905 Alpha-Hemolysin 95.3 1.9e-98 1 170 1.0 1 Exotoxin Hemolysin C experiment
AKMGNAON_00006 VFG000906 Alpha-Hemolysin 96.4 0 1 1024 1.0 1 Exotoxin Hemolysin A experiment
AKMGNAON_00007 VFG000907 Alpha-Hemolysin 98.7 0 1 707 1.0 1 Exotoxin Hemolysin B experiment
AKMGNAON_00008 VFG000908 Alpha-Hemolysin 95.8 1.1e-247 1 478 1.0 1 Exotoxin Hemolysin D experiment
AKMGNAON_00065 VFG000845 ToxB 98.5 0 1 2629 1.0 0.8296 Effector delivery system cytotoxin experiment
AKMGNAON_00082 VFG034837 TTSS secreted effectors 93.5 8.8e-202 1 369 1.0 0.9179 Effector delivery system type III secretion system effector experiment
AKMGNAON_00005 VFG033901 Hemolysin 99.4 1.4e-100 1 170 1.0 1 Exotoxin Hemolysin C prediction
AKMGNAON_00006 VFG033893 Hemolysin 98.5 0 1 1024 1.0 1 Exotoxin Hemolysin A prediction
AKMGNAON_00007 VFG033885 Hemolysin 99.6 0 1 707 1.0 1 Exotoxin Hemolysin B prediction
AKMGNAON_00008 VFG033877 Hemolysin 98.5 6.7e-254 1 478 1.0 1 Exotoxin Hemolysin D prediction
AKMGNAON_00065 VFG000845 ToxB 98.5 0 1 2629 1.0 0.8296 Effector delivery system cytotoxin prediction
AKMGNAON_00080 VFG033809 Vat 92.4 0 1 1364 1.0 1 Effector delivery system vacuolating autotransporter toxin prediction
AKMGNAON_00082 VFG034837 TTSS secreted effectors 93.5 6.6e-201 1 369 1.0 0.9179 Effector delivery system type III secretion system effector 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
AKMGNAON_00020 Cadmium (Cd), Mercury (Hg), Tributyltin (TBT) [class: Organo-tin], Hydrogen Peroxide (H2O2) [class: Peroxides], Hydrochloric acid (HCl) [class: Acid] 96.9 3e-65 1 127 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






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
AKMGNAON_00006 PHI:4522 HlyA 98.5 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
AKMGNAON_00065 QKA18767.1|GT44 98.5 0 1 2629 1 0.8296
AKMGNAON_00099 QKB64535.1|GH24 99.4 3.28e-132 1 177 0.9267 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
AKMGNAON_00006 1.C.11.1.3 96.6 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
AKMGNAON_00007 3.A.1.109.1 99.2 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
AKMGNAON_00008 8.A.1.3.1 98.3 1.3e-252 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
AKMGNAON_00065 1.C.57.2.1 98.4 0 1 2629 1.0000 0.8296 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.57 The Clostridial Cytotoxin (CCT) Family
AKMGNAON_00101 1.E.1.1.3 97.1 1.6e-31 1 68 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.1 The P21 Holin S (P21 Holin) Family