Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C254
  Reference Plasmid   LR962249.1
  Reference Plasmid Size   119429
  Reference Plasmid GC Content   0.35
  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
M0149889 AGBPHAHL_00061 45589 3 Gut 1.00 protein_coding synonymous_variant LOW 2052C>T Gly684Gly
M0149890 AGBPHAHL_00061 45631 3 Gut 1.00 protein_coding synonymous_variant LOW 2010C>T Tyr670Tyr
M0149891 AGBPHAHL_00061 45703 3 Gut 1.00 protein_coding synonymous_variant LOW 1938T>G Val646Val
M0149892 AGBPHAHL_00061 45877 3 Gut 1.00 protein_coding synonymous_variant LOW 1764G>T Val588Val
M0149893 AGBPHAHL_00061 46072 3 Gut 1.00 protein_coding synonymous_variant LOW 1569G>A Leu523Leu
M0149894 AGBPHAHL_00061 46882 3 Gut 1.00 protein_coding synonymous_variant LOW 759T>C Leu253Leu
M0149895 AGBPHAHL_00062 47873 3 Gut 1.00 protein_coding synonymous_variant LOW 2100T>C Arg700Arg
M0149896 AGBPHAHL_00062 47924 3 Gut 1.00 protein_coding synonymous_variant LOW 2049A>G Arg683Arg
M0149897 AGBPHAHL_00062 47934 3 Gut 1.00 protein_coding missense_variant MODERATE 2039T>C Met680Thr
M0149898 AGBPHAHL_00062 48200 3 Gut 1.00 protein_coding synonymous_variant LOW 1773G>A Lys591Lys
M0149899 AGBPHAHL_00062 48272 3 Gut 1.00 protein_coding synonymous_variant LOW 1701G>A Lys567Lys
M0149900 AGBPHAHL_00062 48371 3 Gut 1.00 protein_coding synonymous_variant LOW 1602G>A Glu534Glu
M0149901 AGBPHAHL_00062 48377 3 Gut 1.00 protein_coding synonymous_variant LOW 1596T>C Arg532Arg
M0149902 AGBPHAHL_00062 48647 3 Gut 1.00 protein_coding synonymous_variant LOW 1326T>C Phe442Phe
M0149903 AGBPHAHL_00062 48908 3 Gut 1.00 protein_coding synonymous_variant LOW 1065T>G Ala355Ala
M0149904 AGBPHAHL_00062 49136 3 Gut 1.00 protein_coding synonymous_variant LOW 837C>T Asp279Asp
M0149905 AGBPHAHL_00062 49294 3 Gut 1.00 protein_coding missense_variant MODERATE 679A>G Ile227Val
M0149906 AGBPHAHL_00062 49568 3 Gut 1.00 protein_coding synonymous_variant LOW 405A>G Ala135Ala
M0149907 AGBPHAHL_00062 49616 3 Gut 1.00 protein_coding synonymous_variant LOW 357T>G Pro119Pro
M0149908 AGBPHAHL_00064 50937 3 Gut 1.00 protein_coding synonymous_variant LOW 1896T>C Ser632Ser
M0149909 AGBPHAHL_00064 51216 3 Gut 1.00 protein_coding synonymous_variant LOW 1617G>A Arg539Arg
M0149910 AGBPHAHL_00064 51223 3 Gut 1.00 protein_coding missense_variant MODERATE 1610A>G Lys537Arg
M0149911 AGBPHAHL_00064 51239 3 Gut 1.00 protein_coding synonymous_variant LOW 1594T>C Leu532Leu
M0149912 AGBPHAHL_00064 51294 3 Gut 1.00 protein_coding synonymous_variant LOW 1539A>G Lys513Lys
M0149913 AGBPHAHL_00064 51672 3 Gut 1.00 protein_coding synonymous_variant LOW 1161C>T Ala387Ala
M0149914 AGBPHAHL_00064 51735 3 Gut 1.00 protein_coding synonymous_variant LOW 1098T>C Asp366Asp
M0149915 AGBPHAHL_00064 51747 3 Gut 1.00 protein_coding synonymous_variant LOW 1086A>G Leu362Leu
M0149916 AGBPHAHL_00064 52053 3 Gut 1.00 protein_coding synonymous_variant LOW 780A>G Leu260Leu
M0149917 AGBPHAHL_00069 55423 3 Gut 1.00 protein_coding missense_variant MODERATE 268A>C Ile90Leu
M0149918 AGBPHAHL_00071 56108 3 Gut 1.00 protein_coding synonymous_variant LOW 306T>G Thr102Thr
M0149919 AGBPHAHL_00071 56343 3 Gut 1.00 protein_coding missense_variant MODERATE 71T>G Ile24Ser
M0149920 AGBPHAHL_00071 56348 3 Gut 1.00 protein_coding synonymous_variant LOW 66A>G Gly22Gly
M0149921 AGBPHAHL_00072 56445 3 Gut 1.00 protein_coding synonymous_variant LOW 570G>A Glu190Glu
M0149922 AGBPHAHL_00072 56721 3 Gut 1.00 protein_coding synonymous_variant LOW 294T>C Ser98Ser
M0149923 AGBPHAHL_00073 57056 3 Gut 1.00 protein_coding synonymous_variant LOW 1233A>G Thr411Thr
M0149924 AGBPHAHL_00073 57095 3 Gut 1.00 protein_coding synonymous_variant LOW 1194A>C Gly398Gly
M0149925 AGBPHAHL_00073 57244 3 Gut 1.00 protein_coding missense_variant MODERATE 1045A>G Ile349Val
M0149926 AGBPHAHL_00073 57596 3 Gut 1.00 protein_coding synonymous_variant LOW 693T>C Asn231Asn
M0149927 AGBPHAHL_00073 57641 3 Gut 1.00 protein_coding synonymous_variant LOW 648A>G Lys216Lys
M0149928 AGBPHAHL_00073 57685 3 Gut 1.00 protein_coding missense_variant MODERATE 604G>A Ala202Thr
M0149929 AGBPHAHL_00073 57755 3 Gut 1.00 protein_coding synonymous_variant LOW 534C>T Gly178Gly






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
AGBPHAHL_00079 VFG002173 AS 99.6 0 1 1296 1.0 1 Adherence aggregation substance Asa1 experiment
AGBPHAHL_00079 VFG002173 AS 99.6 0 1 1296 1.0 1 Adherence aggregation substance Asa1 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
AGBPHAHL_00010 ARO:3002647 100 1.07e-198 1 264 1.0000 1.0000 aminoglycoside antibiotic APH(3') antibiotic inactivation
AGBPHAHL_00011 ARO:3002897 99.4 1.34e-130 1 180 1.0000 1.0000 nucleoside antibiotic streptothricin acetyltransferase (SAT) antibiotic inactivation
AGBPHAHL_00012 ARO:3002628 100 1.04e-211 27 302 0.9139 1.0000 aminoglycoside antibiotic ANT(6) antibiotic inactivation
AGBPHAHL_00018 ARO:3000375 98.4 1.13e-173 1 245 1.0000 0.9879 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase antibiotic target alteration
AGBPHAHL_00091 ARO:3000375 98 3.24e-173 1 245 1.0000 0.9879 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase 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
AGBPHAHL_00059 PHI:2999 EF0026 98.1 3.3e-91 1 162 1.0000 1.0000 moths nosocomial infection None increased virulence (hypervirulence)
AGBPHAHL_00115 PHI:2999 EF0026 92.6 1.7e-87 1 162 1.0000 1.0000 moths nosocomial infection None 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
AGBPHAHL_00037 AQL55394.1|GT2 100 2.44e-264 1 381 1 1
AGBPHAHL_00073 QTO65677.1|GH73 100 9.37999999998728e-313 1 423 1 1
AGBPHAHL_00103 AAL59475.1|GT0 97.5 3.13e-206 116 430 0.7326 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
AGBPHAHL_00111 3.A.7.19.1 82.2 1.9e-218 1 444 1.0000 0.7932 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