Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C60
  Reference Plasmid   CP020439.2
  Reference Plasmid Size   236564
  Reference Plasmid GC Content   0.34
  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
M0143176 IPDBAGDM_00089 82692 3 Gut 0.08 protein_coding synonymous_variant LOW 1797A>T Ile599Ile
M0143177 IPDBAGDM_00089 82737 3 Gut 0.08 protein_coding synonymous_variant LOW 1752T>C Ile584Ile
M0143178 IPDBAGDM_00089 82749 3 Gut 0.08 protein_coding synonymous_variant LOW 1740A>G Glu580Glu
M0143179 IPDBAGDM_00089 82758 3 Gut 0.08 protein_coding synonymous_variant LOW 1731T>C Val577Val
M0143180 IPDBAGDM_00089 82773 3 Gut 0.08 protein_coding synonymous_variant LOW 1716A>T Gly572Gly
M0143181 IPDBAGDM_00089 82782 3 Gut 0.08 protein_coding synonymous_variant LOW 1707T>A Val569Val
M0143182 IPDBAGDM_00089 82788 3 Gut 0.08 protein_coding synonymous_variant LOW 1701C>T Tyr567Tyr
M0143183 IPDBAGDM_00089 82794 3 Gut 0.08 protein_coding synonymous_variant LOW 1695T>A Pro565Pro
M0143184 IPDBAGDM_00089 83007 3 Gut 0.08 protein_coding synonymous_variant LOW 1482G>A Pro494Pro
M0143185 IPDBAGDM_00089 83223 3 Gut 0.08 protein_coding synonymous_variant LOW 1266A>G Ser422Ser
M0143186 IPDBAGDM_00089 83244 3 Gut 0.08 protein_coding synonymous_variant LOW 1245G>A Leu415Leu
M0143187 IPDBAGDM_00089 83247 3 Gut 0.08 protein_coding synonymous_variant LOW 1242A>G Glu414Glu
M0143188 IPDBAGDM_00091 85175 3 Gut 0.08 protein_coding synonymous_variant LOW 456C>T Ala152Ala
M0143189 IPDBAGDM_00091 85386 3 Gut 0.08 protein_coding missense_variant MODERATE 245G>A Arg82Lys
M0143190 IPDBAGDM_00087 85962 3 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -4009A>G None
M0143191 IPDBAGDM_00093 86206 3 Gut 0.08 protein_coding synonymous_variant LOW 1719T>C Phe573Phe
M0143192 IPDBAGDM_00093 86251 3 Gut 0.08 protein_coding synonymous_variant LOW 1674T>C Asn558Asn
M0143193 IPDBAGDM_00093 86263 3 Gut 0.08 protein_coding synonymous_variant LOW 1662T>C Leu554Leu
M0143194 IPDBAGDM_00093 86278 3 Gut 0.08 protein_coding synonymous_variant LOW 1647A>G Ser549Ser
M0143195 IPDBAGDM_00093 86293 3 Gut 0.08 protein_coding synonymous_variant LOW 1632C>T Ile544Ile
M0143196 IPDBAGDM_00093 86299 3 Gut 0.08 protein_coding synonymous_variant LOW 1626G>A Ala542Ala
M0143197 IPDBAGDM_00093 86371 3 Gut 0.08 protein_coding synonymous_variant LOW 1554T>C Phe518Phe
M0143198 IPDBAGDM_00093 86410 3 Gut 0.08 protein_coding synonymous_variant LOW 1515A>T Pro505Pro
M0143199 IPDBAGDM_00132 126357 3 Gut 0.08 protein_coding synonymous_variant LOW 558C>T Asn186Asn
M0143200 IPDBAGDM_00132 126519 3 Gut 0.08 protein_coding synonymous_variant LOW 396G>A Lys132Lys
M0143201 IPDBAGDM_00132 126846 3 Gut 0.08 protein_coding synonymous_variant LOW 69G>T Val23Val
M0143202 IPDBAGDM_00059 52609 3 Gut 0.08 protein_coding missense_variant MODERATE 589G>A Ala197Thr
M0143203 IPDBAGDM_00059 52746 3 Gut 0.08 protein_coding synonymous_variant LOW 726C>T Ile242Ile
M0143204 IPDBAGDM_00059 52761 3 Gut 0.08 protein_coding synonymous_variant LOW 741T>C Val247Val
M0143205 IPDBAGDM_00059 52770 3 Gut 0.08 protein_coding synonymous_variant LOW 750T>C Ala250Ala
M0143206 IPDBAGDM_00059 53016 3 Gut 0.08 protein_coding synonymous_variant LOW 996C>T Asp332Asp
M0143207 IPDBAGDM_00059 53179 3 Gut 0.08 protein_coding missense_variant MODERATE 1159A>G Asn387Asp
M0143208 IPDBAGDM_00060 53545 3 Gut 0.08 protein_coding synonymous_variant LOW 102C>A Val34Val
M0143209 IPDBAGDM_00060 53551 3 Gut 0.08 protein_coding synonymous_variant LOW 108C>T Ile36Ile
M0143210 IPDBAGDM_00060 53557 3 Gut 0.08 protein_coding synonymous_variant LOW 114A>G Gly38Gly
M0143211 IPDBAGDM_00060 53884 3 Gut 0.08 protein_coding synonymous_variant LOW 441C>T Asn147Asn
M0143212 IPDBAGDM_00060 53887 3 Gut 0.08 protein_coding synonymous_variant LOW 444T>C Thr148Thr
M0143213 IPDBAGDM_00060 54028 3 Gut 0.08 protein_coding synonymous_variant LOW 585A>T Gly195Gly
M0143214 IPDBAGDM_00060 54058 3 Gut 0.08 protein_coding synonymous_variant LOW 615A>G Lys205Lys
M0143215 IPDBAGDM_00060 54123 3 Gut 0.08 protein_coding missense_variant MODERATE 680A>T Glu227Val
M0143216 IPDBAGDM_00060 54139 3 Gut 0.08 protein_coding missense_variant MODERATE 696C>A Asp232Glu
M0143217 IPDBAGDM_00060 54161 3 Gut 0.08 protein_coding synonymous_variant LOW 718T>C Leu240Leu
M0143218 IPDBAGDM_00060 54190 3 Gut 0.08 protein_coding synonymous_variant LOW 747T>A Leu249Leu
M0143219 IPDBAGDM_00165 161844 3 Gut 0.08 protein_coding synonymous_variant LOW 249T>C Ile83Ile
M0143220 IPDBAGDM_00165 161886 3 Gut 0.08 protein_coding synonymous_variant LOW 291A>G Leu97Leu
M0143221 IPDBAGDM_00165 161993 3 Gut 0.08 protein_coding missense_variant MODERATE 398T>A Leu133Gln
M0143222 IPDBAGDM_00165 162045 3 Gut 0.08 protein_coding synonymous_variant LOW 450T>C Leu150Leu
M0143223 IPDBAGDM_00165 162201 3 Gut 0.08 protein_coding synonymous_variant LOW 606C>T Leu202Leu
M0143224 IPDBAGDM_00165 162237 3 Gut 0.08 protein_coding synonymous_variant LOW 642T>C Ala214Ala
M0143225 IPDBAGDM_00165 162327 3 Gut 0.08 protein_coding synonymous_variant LOW 732G>A Ser244Ser
M0143226 IPDBAGDM_00166 163245 3 Gut 0.08 protein_coding missense_variant MODERATE 278T>C Val93Ala
M0143227 IPDBAGDM_00166 163252 3 Gut 0.08 protein_coding synonymous_variant LOW 285A>G Gly95Gly
M0143228 IPDBAGDM_00166 163253 3 Gut 0.08 protein_coding missense_variant MODERATE 286C>T His96Tyr
M0143229 IPDBAGDM_00166 163284 3 Gut 0.08 protein_coding missense_variant MODERATE 317A>T Tyr106Phe
M0143230 IPDBAGDM_00166 163295 3 Gut 0.08 protein_coding missense_variant MODERATE 328A>G Ile110Val
M0143231 IPDBAGDM_00166 163478 3 Gut 0.08 protein_coding missense_variant MODERATE 511G>A Val171Ile
M0143232 IPDBAGDM_00167 164331 3 Gut 0.08 protein_coding missense_variant MODERATE 653G>A Arg218Gln
M0143233 IPDBAGDM_00137 128696 3 Gut 0.08 protein_coding synonymous_variant LOW 144A>G Lys48Lys
M0143234 IPDBAGDM_00137 128799 3 Gut 0.08 protein_coding missense_variant MODERATE 41T>C Leu14Ser
M0143235 IPDBAGDM_00137 128810 3 Gut 0.08 protein_coding synonymous_variant LOW 30T>C Asp10Asp
M0143236 IPDBAGDM_00137 128813 3 Gut 0.08 protein_coding synonymous_variant LOW 27C>A Ala9Ala






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
IPDBAGDM_00045 VFG005324 Autolysin 76.7 1.5e-120 1 315 0.2244 0.9783 Exoenzyme choline binding protein D prediction
IPDBAGDM_00219 VFG005324 Autolysin 76.7 1.5e-120 1 315 0.2244 0.9783 Exoenzyme choline binding protein D 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
IPDBAGDM_00055 PHI:4040 NisR 93.4 2.2e-117 1 227 1.0000 1.0000 rodents pneumonia; endocarditis; meningitis; arthritis two-component signal-transduction systems reduced virulence
IPDBAGDM_00056 PHI:4039 NisK 91.1 5.1e-116 1 235 0.6438 1.0000 rodents pneumonia; endocarditis; meningitis; arthritis two-component signal-transduction systems reduced virulence
IPDBAGDM_00104 PHI:8562 srtA 82.6 5.2e-18 1 46 1.0000 1.0000 primates infection sortase reduced virulence
IPDBAGDM_00224 PHI:4040 NisR 94.1 6.7e-87 1 170 1.0000 1.0000 rodents pneumonia; endocarditis; meningitis; arthritis two-component signal-transduction systems reduced virulence
IPDBAGDM_00225 PHI:4039 NisK 91.1 3.9e-116 1 235 0.8363 1.0000 rodents pneumonia; endocarditis; meningitis; arthritis two-component signal-transduction systems 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





        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
IPDBAGDM_00176 3.A.1.134.1 100 1.6e-134 1 245 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
IPDBAGDM_00177 3.A.1.134.1 99.7 0 1 635 1.0000 2.5918 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
IPDBAGDM_00185 1.C.21.1.7 100 8.3e-26 1 56 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.21 The Lacticin 481 (Lacticin 481) Family
IPDBAGDM_00187 3.A.1.111.6 95.2 0 1 692 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