Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1474
  Reference Plasmid   OY726015.1
  Reference Plasmid Size   38234
  Reference Plasmid GC Content   0.32
  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
M0212778 ALCFPIHH_00018 13337 12 Gut 0.24 protein_coding synonymous_variant LOW 177T>C Gly59Gly
M0212779 ALCFPIHH_00021 15161 23 Gut 0.45 protein_coding synonymous_variant LOW 132G>A Arg44Arg
M0212780 ALCFPIHH_00022 16346 3 Gut 0.06 protein_coding missense_variant MODERATE 596G>A Gly199Asp
M0212781 ALCFPIHH_00022 17121 26 Gut 0.51 protein_coding synonymous_variant LOW 1371A>T Ser457Ser
M0212782 ALCFPIHH_00029 21124 19 Gut 0.37 protein_coding synonymous_variant LOW 45A>G Val15Val
M0212783 ALCFPIHH_00034 24914 14 Gut 0.27 protein_coding missense_variant MODERATE 355C>T Leu119Phe
M0212784 ALCFPIHH_00036 26620 14 Gut 0.27 protein_coding synonymous_variant LOW 966C>T Ile322Ile
M0212785 ALCFPIHH_00034 29051 6 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -3783A>G None
M0212786 ALCFPIHH_00034 29303 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -4035A>G None
M0212787 ALCFPIHH_00034 29304 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -4036C>T None
M0212788 ALCFPIHH_00034 29409 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -4141A>C None
M0212789 ALCFPIHH_00034 29411 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -4143G>A None
M0212790 ALCFPIHH_00038 29480 3 Gut 0.06 protein_coding synonymous_variant LOW 1110A>G Glu370Glu
M0212791 ALCFPIHH_00038 30137 3 Gut 0.06 protein_coding missense_variant MODERATE 453T>A Asp151Glu
M0212792 ALCFPIHH_00038 30169 3 Gut 0.06 protein_coding missense_variant MODERATE 421C>T Leu141Phe
M0212793 ALCFPIHH_00038 30293 3 Gut 0.06 protein_coding synonymous_variant LOW 297T>C Ser99Ser
M0212794 ALCFPIHH_00038 30361 3 Gut 0.06 protein_coding missense_variant MODERATE 229G>A Asp77Asn
M0212795 ALCFPIHH_00035 30592 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -4642A>G None
M0212796 ALCFPIHH_00040 31073 6 Gut 0.12 protein_coding missense_variant MODERATE 364C>T Pro122Ser
M0212797 ALCFPIHH_00040 31219 3 Gut 0.06 protein_coding missense_variant MODERATE 218T>A Phe73Tyr
M0212798 ALCFPIHH_00040 31348 3 Gut 0.06 protein_coding missense_variant MODERATE 89T>A Val30Asp
M0212799 ALCFPIHH_00040 31368 5 Gut 0.10 protein_coding synonymous_variant LOW 69A>G Leu23Leu
M0212800 ALCFPIHH_00041 31612 3 Gut 0.06 protein_coding missense_variant MODERATE 176A>G Asp59Gly
M0212801 ALCFPIHH_00037 32667 5 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -4375A>C None
M0212802 ALCFPIHH_00036 27064 4 Gut 0.08 protein_coding synonymous_variant LOW 522C>T Asp174Asp
M0212803 ALCFPIHH_00031 21850 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -131A>T None
M0212804 ALCFPIHH_00026 24690 3 Gut 0.06 protein_coding downstream_gene_variant MODIFIER *4241A>G None
M0212805 ALCFPIHH_00026 24697 3 Gut 0.06 protein_coding downstream_gene_variant MODIFIER *4248A>G None
M0212806 ALCFPIHH_00034 27735 7 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -2467T>A None
M0212807 ALCFPIHH_00014 10505 3 Gut 0.06 protein_coding missense_variant MODERATE 67C>A His23Asn
M0212808 ALCFPIHH_00022 16904 7 Gut 0.14 protein_coding missense_variant MODERATE 1154G>A Arg385Lys
M0212809 ALCFPIHH_00022 16951 5 Gut 0.10 protein_coding missense_variant MODERATE 1201A>C Thr401Pro
M0212810 ALCFPIHH_00034 27865 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -2597T>C None
M0212811 ALCFPIHH_00034 28581 5 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3313T>C None
M0212812 ALCFPIHH_00034 28700 7 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -3432A>G None
M0212813 ALCFPIHH_00034 28724 7 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -3456T>C None
M0212814 ALCFPIHH_00034 27759 5 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -2491T>A None
M0212815 ALCFPIHH_00034 27761 5 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -2493C>T None
M0212816 ALCFPIHH_00034 27762 5 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -2494G>A None
M0212817 ALCFPIHH_00034 27781 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -2513T>C None
M0212818 ALCFPIHH_00034 27783 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -2515C>T None
M0212819 ALCFPIHH_00034 27806 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -2538A>G None
M0212820 ALCFPIHH_00034 28702 6 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -3434T>C None
M0212821 ALCFPIHH_00034 28903 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -3635A>G None
M0212822 ALCFPIHH_00034 29209 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -3941A>C None
M0212823 ALCFPIHH_00022 16274 4 Gut 0.08 protein_coding missense_variant MODERATE 524C>T Pro175Leu
M0212824 ALCFPIHH_00021 15267 4 Gut 0.08 protein_coding missense_variant MODERATE 238A>G Ile80Val
M0212825 ALCFPIHH_00021 15538 4 Gut 0.08 protein_coding missense_variant MODERATE 509C>T Ala170Val
M0212826 ALCFPIHH_00022 16036 5 Gut 0.10 protein_coding missense_variant MODERATE 286G>A Glu96Lys
M0212827 ALCFPIHH_00020 14698 3 Gut 0.06 protein_coding missense_variant MODERATE 292A>G Ile98Val
M0212828 ALCFPIHH_00020 14798 3 Gut 0.06 protein_coding synonymous_variant LOW 192G>A Arg64Arg
M0212829 ALCFPIHH_00020 14962 4 Gut 0.08 protein_coding missense_variant MODERATE 28G>A Ala10Thr
M0212830 ALCFPIHH_00026 19681 3 Gut 0.06 protein_coding synonymous_variant LOW 69C>T Gly23Gly
M0212831 ALCFPIHH_00032 23837 3 Gut 0.06 protein_coding synonymous_variant LOW 1629C>T Gly543Gly






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
ALCFPIHH_00024 9.B.154.1.1 95.2 3.1e-84 1 167 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.154 The Putative Holin-2 (PH-2) Family