Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1609
  Reference Plasmid   1111525849481321_bin.4__k141_87464
  Reference Plasmid Size   17029
  Reference Plasmid GC Content   0.41
  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
M0008468 DFKAHJCB_00003 513 5 Skin 0.83 protein_coding missense_variant MODERATE 187A>G Ile63Val
M0008469 DFKAHJCB_00003 827 4 Skin 0.67 protein_coding synonymous_variant LOW 501G>A Ser167Ser
M0008470 DFKAHJCB_00004 1154 4 Skin 0.67 protein_coding missense_variant MODERATE 278T>C Val93Ala
M0008471 DFKAHJCB_00004 1215 4 Skin 0.67 protein_coding synonymous_variant LOW 339A>G Ser113Ser
M0008472 DFKAHJCB_00005 1576 4 Skin 0.67 protein_coding upstream_gene_variant MODIFIER -285C>T None
M0008473 DFKAHJCB_00009 4161 4 Skin 0.67 protein_coding upstream_gene_variant MODIFIER -118A>G None
M0008474 DFKAHJCB_00009 5549 4 Skin 0.67 protein_coding missense_variant MODERATE 1271C>T Ala424Val
M0008475 DFKAHJCB_00009 5751 4 Skin 0.67 protein_coding synonymous_variant LOW 1473C>T Phe491Phe
M0008476 DFKAHJCB_00009 6024 4 Skin 0.67 protein_coding synonymous_variant LOW 1746T>C Tyr582Tyr
M0008477 DFKAHJCB_00009 6096 4 Skin 0.67 protein_coding synonymous_variant LOW 1818G>A Ala606Ala
M0008478 DFKAHJCB_00009 6372 4 Skin 0.67 protein_coding synonymous_variant LOW 2094A>G Leu698Leu
M0008479 DFKAHJCB_00009 6732 3 Skin 0.50 protein_coding synonymous_variant LOW 2454A>G Leu818Leu
M0008480 DFKAHJCB_00010 8819 4 Skin 0.67 protein_coding synonymous_variant LOW 330T>C Ala110Ala
M0008481 DFKAHJCB_00010 8918 3 Skin 0.50 protein_coding synonymous_variant LOW 429C>T Phe143Phe
M0008482 DFKAHJCB_00010 9231 4 Skin 0.67 protein_coding missense_variant MODERATE 742A>T Ile248Leu
M0008483 DFKAHJCB_00010 9287 4 Skin 0.67 protein_coding synonymous_variant LOW 798A>G Ser266Ser
M0008484 DFKAHJCB_00010 9308 4 Skin 0.67 protein_coding synonymous_variant LOW 819C>A Arg273Arg
M0008485 DFKAHJCB_00010 10199 5 Skin 0.83 protein_coding synonymous_variant LOW 1710A>G Val570Val
M0008486 DFKAHJCB_00010 10370 5 Skin 0.83 protein_coding synonymous_variant LOW 1881C>T His627His
M0008487 DFKAHJCB_00010 11843 4 Skin 0.67 protein_coding synonymous_variant LOW 3354G>A Glu1118Glu
M0008488 DFKAHJCB_00011 12681 4 Skin 0.67 protein_coding upstream_gene_variant MODIFIER -118G>A None
M0008489 DFKAHJCB_00012 13468 4 Skin 0.67 protein_coding synonymous_variant LOW 282T>C Thr94Thr
M0008490 DFKAHJCB_00013 14476 4 Skin 0.67 protein_coding synonymous_variant LOW 795C>T Leu265Leu
M0008491 DFKAHJCB_00013 14845 4 Skin 0.67 protein_coding synonymous_variant LOW 1164T>C Asp388Asp
M0008492 DFKAHJCB_00013 14956 3 Skin 0.50 protein_coding synonymous_variant LOW 1275C>T Asp425Asp
M0008493 DFKAHJCB_00013 14989 4 Skin 0.67 protein_coding synonymous_variant LOW 1308A>G Leu436Leu
M0008494 DFKAHJCB_00014 16891 4 Skin 0.67 protein_coding synonymous_variant LOW 1059C>G Val353Val
M0008495 DFKAHJCB_00004 894 3 Skin 0.50 protein_coding synonymous_variant LOW 18T>C Tyr6Tyr
M0008496 DFKAHJCB_00007 3323 5 Skin 0.83 protein_coding missense_variant MODERATE 118A>G Thr40Ala
M0008497 DFKAHJCB_00014 16360 4 Skin 0.67 protein_coding synonymous_variant LOW 528A>G Leu176Leu
M0008498 DFKAHJCB_00010 11960 3 Skin 0.50 protein_coding synonymous_variant LOW 3471C>T Pro1157Pro
M0008499 DFKAHJCB_00013 14851 3 Skin 0.50 protein_coding synonymous_variant LOW 1170C>T Ile390Ile
M0008500 DFKAHJCB_00013 15434 3 Skin 0.50 protein_coding synonymous_variant LOW 1753T>C Leu585Leu






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
DFKAHJCB_00014 VFG046465 EF-Tu 77.2 1.2e-183 1 395 0.9975 1.0025 Adherence elongation factor Tu experiment
DFKAHJCB_00014 VFG046467 EF-Tu 77.7 3e-183 1 395 0.9975 1.0025 Adherence elongation factor Tu 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
DFKAHJCB_00011 ARO:3003395 70.7 4.73e-56 1 123 1.0000 0.9919 aminoglycoside antibiotic antibiotic-resistant rpsL antibiotic target alteration
DFKAHJCB_00014 ARO:3003368 80.3 1.19e-238 1 395 0.9975 1.0025 elfamycin antibiotic elfamycin resistant EF-Tu antibiotic target alteration






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
DFKAHJCB_00001 PHI:10282 tufA 71.4 1.8e-12 1 42 0.9767 0.9975 primates skin infection; food poisoning; respiratory disease elongation factor Tu increased virulence (hypervirulence)
DFKAHJCB_00014 PHI:10282 tufA 74.7 7.3e-177 1 395 0.9975 0.9975 primates skin infection; food poisoning; respiratory disease elongation factor Tu increased virulence (hypervirulence)






        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