Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C984
  Reference Plasmid   NZ_CP090012.1
  Reference Plasmid Size   35196
  Reference Plasmid GC Content   0.29
  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
M0105326 JIOAFOCJ_00026 26625 5 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -4068T>C None
M0105327 JIOAFOCJ_00035 26922 4 Skin 0.07 protein_coding synonymous_variant LOW 111G>A Pro37Pro
M0105328 JIOAFOCJ_00035 27321 4 Skin 0.07 protein_coding synonymous_variant LOW 510G>A Ser170Ser
M0105329 JIOAFOCJ_00035 27429 4 Skin 0.07 protein_coding synonymous_variant LOW 618A>G Lys206Lys
M0105330 JIOAFOCJ_00035 27468 4 Skin 0.07 protein_coding synonymous_variant LOW 657G>A Gln219Gln
M0105331 JIOAFOCJ_00035 27552 4 Skin 0.07 protein_coding synonymous_variant LOW 741G>A Thr247Thr
M0105332 JIOAFOCJ_00035 27585 4 Skin 0.07 protein_coding synonymous_variant LOW 774A>C Gly258Gly
M0105333 JIOAFOCJ_00035 27639 4 Skin 0.07 protein_coding synonymous_variant LOW 828T>C Asp276Asp
M0105334 JIOAFOCJ_00035 27681 4 Skin 0.07 protein_coding synonymous_variant LOW 870A>T Gly290Gly
M0105335 JIOAFOCJ_00035 27687 4 Skin 0.07 protein_coding synonymous_variant LOW 876C>T Val292Val
M0105336 JIOAFOCJ_00035 27740 4 Skin 0.07 protein_coding missense_variant MODERATE 929G>A Ser310Asn
M0105337 JIOAFOCJ_00035 27824 4 Skin 0.07 protein_coding missense_variant MODERATE 1013G>A Arg338His
M0105338 JIOAFOCJ_00035 27875 5 Skin 0.09 protein_coding missense_variant MODERATE 1064G>A Arg355Lys
M0105339 JIOAFOCJ_00034 27909 4 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -1358G>A None
M0105340 JIOAFOCJ_00034 27939 4 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -1388T>C None
M0105341 JIOAFOCJ_00034 27964 4 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -1413T>C None
M0105342 JIOAFOCJ_00001 515 7 Skin 0.13 protein_coding upstream_gene_variant MODIFIER -502A>T None
M0105343 JIOAFOCJ_00005 9804 4 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -4424A>T None
M0105344 JIOAFOCJ_00010 10277 4 Skin 0.07 protein_coding missense_variant MODERATE 421T>A Phe141Ile
M0105345 JIOAFOCJ_00010 10278 4 Skin 0.07 protein_coding missense_variant MODERATE 422T>A Phe141Tyr
M0105346 JIOAFOCJ_00010 10279 4 Skin 0.07 protein_coding missense_variant MODERATE 423T>A Phe141Leu
M0105347 JIOAFOCJ_00003 2321 5 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -52T>G None
M0105348 JIOAFOCJ_00003 2353 5 Skin 0.09 protein_coding upstream_gene_variant MODIFIER -20C>G None
M0105349 JIOAFOCJ_00003 2762 3 Skin 0.06 protein_coding missense_variant MODERATE 390G>T Met130Ile
M0105350 JIOAFOCJ_00002 1319 4 Skin 0.07 protein_coding start_lost HIGH 2T>C Met1?
M0105351 JIOAFOCJ_00008 11590 3 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -3367T>C None
M0105352 JIOAFOCJ_00011 11499 3 Skin 0.06 protein_coding missense_variant MODERATE 620C>A Thr207Lys
M0105353 JIOAFOCJ_00008 12039 3 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -3816G>A None
M0105354 JIOAFOCJ_00015 14416 3 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -731T>A None
M0105355 JIOAFOCJ_00001 680 3 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -337A>G None
M0105356 JIOAFOCJ_00001 946 4 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -71G>T None
M0105357 JIOAFOCJ_00001 1001 3 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -16T>C None
M0105358 JIOAFOCJ_00003 2408 4 Skin 0.07 protein_coding synonymous_variant LOW 36G>A Leu12Leu
M0105359 JIOAFOCJ_00003 2488 4 Skin 0.07 protein_coding missense_variant MODERATE 116G>A Arg39Lys
M0105360 JIOAFOCJ_00002 1446 3 Skin 0.06 protein_coding synonymous_variant LOW 129T>C Asn43Asn
M0105361 JIOAFOCJ_00002 1863 3 Skin 0.06 protein_coding synonymous_variant LOW 546C>A Thr182Thr
M0105362 JIOAFOCJ_00010 10567 3 Skin 0.06 protein_coding missense_variant MODERATE 711A>C Lys237Asn
M0105363 JIOAFOCJ_00010 10825 3 Skin 0.06 protein_coding missense_variant MODERATE 969G>T Arg323Ser






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







        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
JIOAFOCJ_00005 ARO:3000251 97.5 0 1 488 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
JIOAFOCJ_00033 ARO:3004671 98.6 9.49e-102 1 139 1.0000 1.0000 phosphonic acid antibiotic fosfomycin thiol transferase antibiotic inactivation






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
JIOAFOCJ_00006 PHI:6324 StpC 85.7 2.9e-109 1 231 1.0000 1.0000 birds skin infection; food poisoning; respiratory disease cysteine protease 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





        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
JIOAFOCJ_00005 3.A.1.121.1 99.8 2.5e-275 1 488 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
JIOAFOCJ_00020 9.B.351.1.1 97.8 2.4e-38 1 92 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.351 The Lantibiotic Immunity Protein (LIP) Family
JIOAFOCJ_00021 3.A.1.124.3 95.9 8.4e-123 1 245 1.0000 0.8419 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
JIOAFOCJ_00022 3.A.1.124.3 98.4 4.9e-126 1 250 1.0000 0.8591 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
JIOAFOCJ_00023 3.A.1.124.3 97.9 1.3e-154 1 289 0.9570 0.9931 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily