Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C874
  Reference Plasmid   NZ_CP072228.1
  Reference Plasmid Size   98236
  Reference Plasmid GC Content   0.43
  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
M0185680 AODLGNPH_00065 62171 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4737G>A None
M0185681 AODLGNPH_00065 62175 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4741C>A None
M0185682 AODLGNPH_00024 22807 7 Gut 0.05 protein_coding missense_variant MODERATE 638C>T Ala213Val
M0185683 AODLGNPH_00024 27640 8 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -4196T>G None
M0185684 AODLGNPH_00024 27705 7 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -4261G>A None
M0185685 AODLGNPH_00024 27721 7 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -4277G>T None
M0185686 AODLGNPH_00024 27748 8 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -4304A>G None
M0185687 AODLGNPH_00024 27803 11 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -4359A>G None
M0185688 AODLGNPH_00073 65100 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -3874G>A None
M0185689 AODLGNPH_00073 65115 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -3889T>C None
M0185690 AODLGNPH_00068 59164 4 Gut 0.03 protein_coding synonymous_variant LOW 57G>A Glu19Glu
M0185691 AODLGNPH_00069 59366 4 Gut 0.03 protein_coding missense_variant MODERATE 17G>A Gly6Glu
M0185692 AODLGNPH_00069 59468 3 Gut 0.02 protein_coding missense_variant MODERATE 119T>C Ile40Thr
M0185693 AODLGNPH_00067 63191 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4517T>C None
M0185694 AODLGNPH_00077 63273 3 Gut 0.02 protein_coding missense_variant MODERATE 62A>G His21Arg
M0185695 AODLGNPH_00078 63610 3 Gut 0.02 protein_coding synonymous_variant LOW 120G>A Ala40Ala
M0185696 AODLGNPH_00078 64111 3 Gut 0.02 protein_coding synonymous_variant LOW 621C>T Asp207Asp
M0185697 AODLGNPH_00073 65242 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4016G>A None
M0185698 AODLGNPH_00109 88388 3 Gut 0.02 protein_coding synonymous_variant LOW 75A>G Thr25Thr
M0185699 AODLGNPH_00112 90098 3 Gut 0.02 protein_coding synonymous_variant LOW 1794T>C Asn598Asn
M0185700 AODLGNPH_00112 91178 3 Gut 0.02 protein_coding synonymous_variant LOW 714T>C Ala238Ala
M0185701 AODLGNPH_00112 91487 3 Gut 0.02 protein_coding synonymous_variant LOW 405T>C Ser135Ser
M0185702 AODLGNPH_00112 91865 3 Gut 0.02 protein_coding synonymous_variant LOW 27C>A Ser9Ser
M0185703 AODLGNPH_00117 93501 3 Gut 0.02 protein_coding synonymous_variant LOW 225T>C Tyr75Tyr
M0185704 AODLGNPH_00034 36262 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4290C>T None
M0185705 AODLGNPH_00034 36269 5 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4297T>G None
M0185706 AODLGNPH_00034 36274 5 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4302A>C None
M0185707 AODLGNPH_00039 36334 6 Gut 0.04 protein_coding missense_variant MODERATE 1044G>C Glu348Asp
M0185708 AODLGNPH_00039 36337 6 Gut 0.04 protein_coding synonymous_variant LOW 1041A>G Glu347Glu
M0185709 AODLGNPH_00039 36650 4 Gut 0.03 protein_coding missense_variant MODERATE 728A>G Asn243Ser
M0185710 AODLGNPH_00039 36995 3 Gut 0.02 protein_coding missense_variant MODERATE 383C>G Thr128Ser
M0185711 AODLGNPH_00039 37247 4 Gut 0.03 protein_coding missense_variant MODERATE 131T>C Val44Ala
M0185712 AODLGNPH_00039 37276 4 Gut 0.03 protein_coding synonymous_variant LOW 102A>T Arg34Arg
M0185713 AODLGNPH_00039 37353 4 Gut 0.03 protein_coding missense_variant MODERATE 25T>A Ser9Thr
M0185714 AODLGNPH_00039 37354 4 Gut 0.03 protein_coding synonymous_variant LOW 24C>T Ala8Ala
M0185715 AODLGNPH_00041 38047 4 Gut 0.03 protein_coding synonymous_variant LOW 327C>T Ser109Ser
M0185716 AODLGNPH_00041 38134 3 Gut 0.02 protein_coding synonymous_variant LOW 414C>A Val138Val
M0185717 AODLGNPH_00041 38163 3 Gut 0.02 protein_coding missense_variant MODERATE 443T>G Leu148Trp
M0185718 AODLGNPH_00042 39255 3 Gut 0.02 protein_coding synonymous_variant LOW 348G>T Val116Val
M0185719 AODLGNPH_00042 39257 3 Gut 0.02 protein_coding missense_variant MODERATE 350A>G Gln117Arg
M0185720 AODLGNPH_00042 39294 3 Gut 0.02 protein_coding synonymous_variant LOW 387T>C Pro129Pro
M0185721 AODLGNPH_00042 39320 3 Gut 0.02 protein_coding missense_variant MODERATE 413A>G Glu138Gly
M0185722 AODLGNPH_00042 39616 3 Gut 0.02 protein_coding synonymous_variant LOW 709T>C Leu237Leu
M0185723 AODLGNPH_00042 39636 3 Gut 0.02 protein_coding synonymous_variant LOW 729A>C Ser243Ser
M0185724 AODLGNPH_00042 39671 3 Gut 0.02 protein_coding missense_variant MODERATE 764G>A Gly255Asp
M0185725 AODLGNPH_00042 39695 3 Gut 0.02 protein_coding missense_variant MODERATE 788T>C Val263Ala
M0185726 AODLGNPH_00042 39744 3 Gut 0.02 protein_coding synonymous_variant LOW 837T>A Val279Val
M0185727 AODLGNPH_00039 39831 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -2454A>G None
M0185728 AODLGNPH_00039 39859 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -2482C>T None
M0185729 AODLGNPH_00043 39915 3 Gut 0.02 protein_coding synonymous_variant LOW 24T>A Ala8Ala
M0185730 AODLGNPH_00044 42488 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -1032C>T None
M0185731 AODLGNPH_00057 54358 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -3805G>A None
M0185732 AODLGNPH_00087 69389 3 Gut 0.02 protein_coding synonymous_variant LOW 234A>G Ala78Ala
M0185733 AODLGNPH_00083 70331 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -2058G>A None
M0185734 AODLGNPH_00083 70358 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -2085G>A None
M0185735 AODLGNPH_00083 70360 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -2087A>G None
M0185736 AODLGNPH_00069 59436 4 Gut 0.03 protein_coding synonymous_variant LOW 87A>C Val29Val
M0185737 AODLGNPH_00071 60397 3 Gut 0.02 protein_coding synonymous_variant LOW 180T>C Ala60Ala
M0185738 AODLGNPH_00096 76032 3 Gut 0.02 protein_coding missense_variant MODERATE 584C>T Ala195Val
M0185739 AODLGNPH_00092 76741 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -3793C>A None
M0185740 AODLGNPH_00097 77098 3 Gut 0.02 protein_coding missense_variant MODERATE 184T>C Cys62Arg
M0185741 AODLGNPH_00098 77430 3 Gut 0.02 protein_coding missense_variant MODERATE 931A>G Lys311Glu
M0185742 AODLGNPH_00098 77512 3 Gut 0.02 protein_coding synonymous_variant LOW 849T>C Thr283Thr






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
AODLGNPH_00021 PHI:3281 AS87_04050 71.4 3e-136 1 325 1.0000 1.0000 birds fibrinous serositis; caseous salpingitis; vegetative disorder lipopolysaccharide biosynthesis and pathogenicity 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
AODLGNPH_00009 QUT64421.1|GT4 100 1.11e-279 1 378 1 1
AODLGNPH_00011 QUT55894.1|GT2 100 1.57e-228 1 304 1 1
AODLGNPH_00013 QRP91616.1|GT4 100 5.41e-274 1 366 1 1
AODLGNPH_00014 BBK89584.1|GT2 100 6.37e-226 1 300 1 1
AODLGNPH_00015 QRP91614.1|GT4 100 4.79e-292 1 391 1 1
AODLGNPH_00016 QUT83193.1|GT4 100 0 1 444 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