Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1331
  Reference Plasmid   NZ_KT754161.1
  Reference Plasmid Size   83692
  Reference Plasmid GC Content   0.53
  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
M0206530 IGKEHAEF_00060 55972 10 Gut 0.33 protein_coding missense_variant MODERATE 125A>T Lys42Met
M0206531 IGKEHAEF_00077 69668 4 Gut 0.13 protein_coding missense_variant MODERATE 320T>A Leu107Gln
M0206532 IGKEHAEF_00008 12344 4 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -3602C>G None
M0206533 IGKEHAEF_00008 12401 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3659T>A None
M0206534 IGKEHAEF_00058 55035 3 Gut 0.10 protein_coding missense_variant MODERATE 171A>T Leu57Phe
M0206535 IGKEHAEF_00058 55037 3 Gut 0.10 protein_coding synonymous_variant LOW 169T>C Leu57Leu
M0206536 IGKEHAEF_00058 55041 3 Gut 0.10 protein_coding synonymous_variant LOW 165C>T Tyr55Tyr
M0206537 IGKEHAEF_00062 57633 3 Gut 0.10 protein_coding synonymous_variant LOW 126C>T Ala42Ala
M0206538 IGKEHAEF_00060 55734 3 Gut 0.10 protein_coding synonymous_variant LOW 363A>G Ala121Ala
M0206539 IGKEHAEF_00060 55758 3 Gut 0.10 protein_coding synonymous_variant LOW 339A>T Thr113Thr
M0206540 IGKEHAEF_00060 55763 3 Gut 0.10 protein_coding synonymous_variant LOW 334T>C Leu112Leu
M0206541 IGKEHAEF_00060 55770 3 Gut 0.10 protein_coding synonymous_variant LOW 327T>C Asp109Asp
M0206542 IGKEHAEF_00060 55772 3 Gut 0.10 protein_coding missense_variant MODERATE 325G>A Asp109Asn
M0206543 IGKEHAEF_00060 55773 3 Gut 0.10 protein_coding synonymous_variant LOW 324G>T Gly108Gly
M0206544 IGKEHAEF_00060 55821 3 Gut 0.10 protein_coding synonymous_variant LOW 276T>G Leu92Leu
M0206545 IGKEHAEF_00060 55902 3 Gut 0.10 protein_coding synonymous_variant LOW 195G>T Pro65Pro
M0206546 IGKEHAEF_00060 55990 4 Gut 0.13 protein_coding missense_variant MODERATE 107G>A Cys36Tyr
M0206547 IGKEHAEF_00060 56005 4 Gut 0.13 protein_coding missense_variant MODERATE 92T>C Val31Ala
M0206548 IGKEHAEF_00055 56207 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3885T>C None
M0206549 IGKEHAEF_00055 56216 4 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -3894C>T None
M0206550 IGKEHAEF_00055 56434 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -4112C>T None






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
IGKEHAEF_00068 VFG041000 AAI/SCI-II T6SS 91.5 3.1e-98 1 188 1.0 1 Effector delivery system hypothetical protein 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
IGKEHAEF_00087 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Pyronin Y [class: Xanthene], Rhodamine 6G [class: Xanthene], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Acridine Orange [class: Acridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Sodium Deoxycholate (SDC) [class: Acid], Crystal Violet [class: Triarylmethane], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)] 100 1.1e-60 1 115 1.0000 1.0000 experiment






        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
IGKEHAEF_00002 ARO:3000165 99.7 7.17e-278 1 390 0.9774 0.9198 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
IGKEHAEF_00007 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
IGKEHAEF_00085 ARO:3003013 100 2.81e-114 1 157 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
IGKEHAEF_00086 ARO:3002601 95.8 5.56e-179 1 259 1.0000 0.9848 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
IGKEHAEF_00087 ARO:3005010 100 2.01e-78 1 115 1.0000 1.0000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
IGKEHAEF_00088 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement






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
IGKEHAEF_00067 PHI:3113 stbA 97.9 2.8e-182 1 326 1.0000 1.0000 rodents neonatal meningitis stability protein for the plasmid reduced virulence
IGKEHAEF_00084 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase 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
IGKEHAEF_00052 AXF94864.1|GH23 100 5.78e-107 1 150 1 1





        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
IGKEHAEF_00002 2.A.1.2.4 100 2.4e-223 1 399 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
IGKEHAEF_00003 2.A.7.3.67 100 2.7e-123 1 232 1.0000 0.7891 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
IGKEHAEF_00016 1.E.53.1.11 98.5 6.5e-33 1 68 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family