Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1414
  Reference Plasmid   NZ_OR345929.1
  Reference Plasmid Size   60852
  Reference Plasmid GC Content   0.49
  Reference Plasmid Mobility Type   conjugative





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
M0209551 DBEGKALA_00036 37650 3 Gut 0.23 protein_coding synonymous_variant LOW 702C>T Thr234Thr
M0209552 DBEGKALA_00038 40514 4 Gut 0.31 protein_coding synonymous_variant LOW 936G>A Leu312Leu






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
DBEGKALA_00034 VFG000902 Sat 99.4 0 1 1295 1.0 1 Effector delivery system Aecreted auto transpoter toxin experiment
DBEGKALA_00036 VFG048621 Aerobactin 99.6 0 1 733 1.0 1 Nutritional/Metabolic factor ferric aerobactin receptor IutA experiment
DBEGKALA_00037 VFG000937 Aerobactin 97.9 1.3e-252 1 425 1.0 0.9551 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD experiment
DBEGKALA_00038 VFG000617 Aerobactin 99.3 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin synthesis protein IucC experiment
DBEGKALA_00039 VFG000616 Aerobactin 99.7 1.6e-196 1 315 1.0 1 Nutritional/Metabolic factor aerobactin synthesis protein IucB experiment
DBEGKALA_00040 VFG000615 Aerobactin 99.8 0 1 574 1.0 0.968 Nutritional/Metabolic factor aerobactin synthesis protein IucA experiment
DBEGKALA_00049 VFG000891 P fimbriae 94.5 1.7e-35 1 73 1.0 0.9481 Adherence regulatory protein PapI experiment
DBEGKALA_00054 VFG001713 P fimbriae 95.8 3.8e-88 1 166 1.0 0.9071 Adherence PapX protein regulates flagellum synthesis to repress motility experiment
DBEGKALA_00034 VFG033824 Sat 100 0 1 1295 1.0 1 Effector delivery system Aecreted auto transpoter toxin prediction
DBEGKALA_00036 VFG033945 Aerobactin 100 0 1 733 1.0 1 Nutritional/Metabolic factor ferric aerobactin receptor precusor IutA prediction
DBEGKALA_00037 VFG033958 Aerobactin 100 3.7e-256 1 425 1.0 1 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD prediction
DBEGKALA_00038 VFG033972 Aerobactin 100 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC prediction
DBEGKALA_00039 VFG033987 Aerobactin 100 2.5e-196 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB prediction
DBEGKALA_00040 VFG034000 Aerobactin 100 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD prediction
DBEGKALA_00049 VFG033155 P fimbriae 100 1e-36 1 73 1.0 0.9481 Adherence regulatory protein PapI prediction
DBEGKALA_00054 VFG033079 P fimbriae 100 1.9e-91 1 166 1.0 0.9071 Adherence PapX protein regulates flagellum synthesis to repress motility 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
DBEGKALA_00001 ARO:3001877 100 2.82e-203 1 291 1.0000 1.0000 cephalosporin CTX-M beta-lactamase 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
DBEGKALA_00034 PHI:5262 Sat 99.4 0 1 1295 1.0000 1.0000 rodents non-pathogenic: probiotic auto transporter unaffected pathogenicity
DBEGKALA_00036 PHI:6563 iucA 99.6 0 1 733 1.0000 1.0000 rodents pneumonia aerobactin reduced virulence
DBEGKALA_00037 PHI:3610 iucD 100 1.3e-256 1 425 1.0000 1.0000 birds colibacillosis aerobactin reduced virulence
DBEGKALA_00038 PHI:124069 iucC (PAGR_g3925) 84.1 3.7e-302 1 577 0.9948 0.9983 monocots None aerobactin siderophores unaffected pathogenicity
DBEGKALA_00039 PHI:124068 iucB (PAGR_g3926) 80 5.5e-159 1 315 1.0000 1.0000 monocots None aerobactin siderophores unaffected pathogenicity
DBEGKALA_00040 PHI:124067 iucA (PAGR_g3927) 79.9 2.3e-272 11 573 0.9808 0.9430 monocots None aerobactin siderophores 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
DBEGKALA_00004 3.A.7.10.1 73.3 1.9e-40 1 116 1.0000 1.1979 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
DBEGKALA_00006 3.A.7.10.1 74.6 4.2e-138 1 324 1.0000 3.4063 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
DBEGKALA_00020 1.E.53.1.10 100 2e-18 8 50 0.8600 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
DBEGKALA_00034 1.B.12.4.6 99.4 0 1 1295 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family