Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C96
  Reference Plasmid   CP054201.1
  Reference Plasmid Size   139496
  Reference Plasmid GC Content   0.42
  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
M0143886 GMAAHAIA_00045 36281 3 Gut 0.16 protein_coding synonymous_variant LOW 1041A>G Glu347Glu
M0143887 GMAAHAIA_00045 37010 3 Gut 0.16 protein_coding synonymous_variant LOW 312A>G Glu104Glu
M0143888 GMAAHAIA_00045 37220 3 Gut 0.16 protein_coding synonymous_variant LOW 102A>T Arg34Arg
M0143889 GMAAHAIA_00045 37297 3 Gut 0.16 protein_coding missense_variant MODERATE 25T>A Ser9Thr
M0143890 GMAAHAIA_00038 29630 3 Gut 0.16 protein_coding missense_variant MODERATE 163T>G Ser55Ala
M0143891 GMAAHAIA_00125 99363 5 Gut 0.26 protein_coding upstream_gene_variant MODIFIER -4912T>C None
M0143892 GMAAHAIA_00154 123496 5 Gut 0.26 protein_coding missense_variant MODERATE 640T>C Ser214Pro
M0143893 GMAAHAIA_00157 127197 3 Gut 0.16 protein_coding synonymous_variant LOW 42T>G Gly14Gly
M0143894 GMAAHAIA_00153 127261 3 Gut 0.16 protein_coding upstream_gene_variant MODIFIER -4260G>A None
M0143895 GMAAHAIA_00153 127277 3 Gut 0.16 protein_coding upstream_gene_variant MODIFIER -4276G>T None
M0143896 GMAAHAIA_00153 127304 3 Gut 0.16 protein_coding upstream_gene_variant MODIFIER -4303A>G None
M0143897 GMAAHAIA_00153 127358 3 Gut 0.16 protein_coding upstream_gene_variant MODIFIER -4357A>G None
M0143898 GMAAHAIA_00162 129237 5 Gut 0.26 protein_coding missense_variant MODERATE 163T>G Ser55Ala
M0143899 GMAAHAIA_00162 129477 5 Gut 0.26 protein_coding missense_variant MODERATE 403A>G Ile135Val
M0143900 GMAAHAIA_00164 130741 5 Gut 0.26 protein_coding missense_variant MODERATE 754T>C Tyr252His
M0143901 GMAAHAIA_00170 136394 3 Gut 0.16 protein_coding missense_variant MODERATE 124A>G Ile42Val
M0143902 GMAAHAIA_00165 136657 4 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -4824A>C None
M0143903 GMAAHAIA_00171 136798 4 Gut 0.21 protein_coding synonymous_variant LOW 162C>T Pro54Pro
M0143904 GMAAHAIA_00166 137073 3 Gut 0.16 protein_coding upstream_gene_variant MODIFIER -3632T>C None
M0143905 GMAAHAIA_00166 137512 4 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -4071A>G None
M0143906 GMAAHAIA_00166 137649 4 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -4208C>T None
M0143907 GMAAHAIA_00166 137817 4 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -4376C>T None
M0143908 GMAAHAIA_00173 137993 4 Gut 0.21 protein_coding missense_variant MODERATE 94A>G Lys32Glu
M0143909 GMAAHAIA_00173 137997 4 Gut 0.21 protein_coding missense_variant MODERATE 98G>T Gly33Val
M0143910 GMAAHAIA_00173 138017 4 Gut 0.21 protein_coding missense_variant MODERATE 118G>A Glu40Lys
M0143911 GMAAHAIA_00173 138095 4 Gut 0.21 protein_coding missense_variant MODERATE 196T>G Leu66Val
M0143912 GMAAHAIA_00173 138138 4 Gut 0.21 protein_coding missense_variant MODERATE 239G>A Arg80Gln
M0143913 GMAAHAIA_00173 138139 4 Gut 0.21 protein_coding synonymous_variant LOW 240A>G Arg80Arg
M0143914 GMAAHAIA_00173 138160 4 Gut 0.21 protein_coding synonymous_variant LOW 261G>A Glu87Glu
M0143915 GMAAHAIA_00164 135881 3 Gut 0.16 protein_coding upstream_gene_variant MODIFIER -4387A>G None
M0143916 GMAAHAIA_00171 136815 3 Gut 0.16 protein_coding missense_variant MODERATE 145A>T Ser49Cys
M0143917 GMAAHAIA_00171 136890 3 Gut 0.16 protein_coding missense_variant MODERATE 70T>A Ser24Thr






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
GMAAHAIA_00027 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
GMAAHAIA_00150 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
GMAAHAIA_00012 QUT64421.1|GT4 94.8 4.38e-211 30 336 0.9137 0.8122
GMAAHAIA_00017 QRP91616.1|GT4 100 5.41e-274 1 366 1 1
GMAAHAIA_00018 BBK89584.1|GT2 100 6.37e-226 1 300 1 1
GMAAHAIA_00021 QUT83193.1|GT4 100 0 1 444 1 1
GMAAHAIA_00137 QUT64421.1|GT4 100 1.11e-279 1 378 1 1
GMAAHAIA_00139 QUT55894.1|GT2 100 1.57e-228 1 304 1 1
GMAAHAIA_00142 QRP91616.1|GT4 100 5.41e-274 1 366 1 1
GMAAHAIA_00143 BBK89584.1|GT2 100 6.37e-226 1 300 1 1
GMAAHAIA_00144 QRP91614.1|GT4 100 4.79e-292 1 391 1 1
GMAAHAIA_00145 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