Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3402
  Reference Plasmid   MGYG000303922__MGYG000303922_79
  Reference Plasmid Size   5777
  Reference Plasmid GC Content   0.53
  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
M0142190 CLJMLJPG_00001 209 3 Vaginal 1.00 protein_coding synonymous_variant LOW 1107A>G Ser369Ser
M0142191 CLJMLJPG_00001 258 3 Vaginal 1.00 protein_coding missense_variant MODERATE 1058G>C Gly353Ala
M0142192 CLJMLJPG_00001 297 3 Vaginal 1.00 protein_coding missense_variant MODERATE 1019T>C Met340Thr
M0142193 CLJMLJPG_00001 365 3 Vaginal 1.00 protein_coding synonymous_variant LOW 951T>C Val317Val
M0142194 CLJMLJPG_00001 458 3 Vaginal 1.00 protein_coding synonymous_variant LOW 858A>G Gly286Gly
M0142195 CLJMLJPG_00001 461 3 Vaginal 1.00 protein_coding synonymous_variant LOW 855T>C Asp285Asp
M0142196 CLJMLJPG_00001 479 3 Vaginal 1.00 protein_coding missense_variant MODERATE 837G>T Glu279Asp
M0142197 CLJMLJPG_00001 527 3 Vaginal 1.00 protein_coding synonymous_variant LOW 789G>A Lys263Lys
M0142198 CLJMLJPG_00001 530 3 Vaginal 1.00 protein_coding synonymous_variant LOW 786C>A Gly262Gly
M0142199 CLJMLJPG_00001 568 3 Vaginal 1.00 protein_coding missense_variant MODERATE 748C>A Leu250Met
M0142200 CLJMLJPG_00001 590 3 Vaginal 1.00 protein_coding synonymous_variant LOW 726T>C Ile242Ile
M0142201 CLJMLJPG_00001 626 3 Vaginal 1.00 protein_coding synonymous_variant LOW 690T>A Ala230Ala
M0142202 CLJMLJPG_00001 641 3 Vaginal 1.00 protein_coding synonymous_variant LOW 675T>C Thr225Thr
M0142203 CLJMLJPG_00001 668 3 Vaginal 1.00 protein_coding synonymous_variant LOW 648A>G Glu216Glu
M0142204 CLJMLJPG_00001 674 3 Vaginal 1.00 protein_coding synonymous_variant LOW 642A>G Ser214Ser
M0142205 CLJMLJPG_00001 690 3 Vaginal 1.00 protein_coding missense_variant MODERATE 626T>C Met209Thr
M0142206 CLJMLJPG_00001 1225 3 Vaginal 1.00 protein_coding missense_variant MODERATE 91C>A Gln31Lys
M0142207 CLJMLJPG_00002 1819 3 Vaginal 1.00 protein_coding missense_variant MODERATE 3766C>G Leu1256Val
M0142208 CLJMLJPG_00002 1829 3 Vaginal 1.00 protein_coding synonymous_variant LOW 3756C>T Ser1252Ser
M0142209 CLJMLJPG_00002 1836 3 Vaginal 1.00 protein_coding missense_variant MODERATE 3749T>C Val1250Ala
M0142210 CLJMLJPG_00002 1859 3 Vaginal 1.00 protein_coding synonymous_variant LOW 3726T>A Pro1242Pro
M0142211 CLJMLJPG_00002 1912 3 Vaginal 1.00 protein_coding missense_variant MODERATE 3673C>A Gln1225Lys
M0142212 CLJMLJPG_00002 2288 3 Vaginal 1.00 protein_coding synonymous_variant LOW 3297C>G Gly1099Gly
M0142213 CLJMLJPG_00002 2381 3 Vaginal 1.00 protein_coding synonymous_variant LOW 3204C>T His1068His
M0142214 CLJMLJPG_00002 2531 3 Vaginal 1.00 protein_coding synonymous_variant LOW 3054T>C Tyr1018Tyr
M0142215 CLJMLJPG_00002 2852 3 Vaginal 1.00 protein_coding synonymous_variant LOW 2733G>C Arg911Arg
M0142216 CLJMLJPG_00002 2864 3 Vaginal 1.00 protein_coding synonymous_variant LOW 2721A>C Ala907Ala
M0142217 CLJMLJPG_00002 3152 3 Vaginal 1.00 protein_coding synonymous_variant LOW 2433T>C Thr811Thr
M0142218 CLJMLJPG_00002 3200 3 Vaginal 1.00 protein_coding synonymous_variant LOW 2385G>A Ala795Ala
M0142219 CLJMLJPG_00002 3611 3 Vaginal 1.00 protein_coding synonymous_variant LOW 1974A>G Pro658Pro
M0142220 CLJMLJPG_00002 3635 3 Vaginal 1.00 protein_coding synonymous_variant LOW 1950A>G Gly650Gly
M0142221 CLJMLJPG_00002 3731 3 Vaginal 1.00 protein_coding synonymous_variant LOW 1854T>C Phe618Phe
M0142222 CLJMLJPG_00002 3950 3 Vaginal 1.00 protein_coding synonymous_variant LOW 1635A>G Thr545Thr
M0142223 CLJMLJPG_00002 4463 3 Vaginal 1.00 protein_coding synonymous_variant LOW 1122T>C Ser374Ser
M0142224 CLJMLJPG_00002 4478 3 Vaginal 1.00 protein_coding synonymous_variant LOW 1107T>C Ser369Ser
M0142225 CLJMLJPG_00002 4487 3 Vaginal 1.00 protein_coding synonymous_variant LOW 1098T>C Phe366Phe
M0142226 CLJMLJPG_00002 4544 3 Vaginal 1.00 protein_coding synonymous_variant LOW 1041T>C Ile347Ile
M0142227 CLJMLJPG_00002 4559 3 Vaginal 1.00 protein_coding synonymous_variant LOW 1026A>G Leu342Leu
M0142228 CLJMLJPG_00002 4655 3 Vaginal 1.00 protein_coding synonymous_variant LOW 930A>T Ser310Ser
M0142229 CLJMLJPG_00002 4697 3 Vaginal 1.00 protein_coding synonymous_variant LOW 888A>G Ser296Ser
M0142230 CLJMLJPG_00002 4757 3 Vaginal 1.00 protein_coding synonymous_variant LOW 828A>T Gly276Gly
M0142231 CLJMLJPG_00002 4913 3 Vaginal 1.00 protein_coding synonymous_variant LOW 672T>C Arg224Arg
M0142232 CLJMLJPG_00002 4914 3 Vaginal 1.00 protein_coding missense_variant MODERATE 671G>A Arg224His
M0142233 CLJMLJPG_00002 4915 3 Vaginal 1.00 protein_coding missense_variant MODERATE 670C>A Arg224Ser
M0142234 CLJMLJPG_00002 4979 3 Vaginal 1.00 protein_coding synonymous_variant LOW 606T>C Gly202Gly






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






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






        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