Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C887
  Reference Plasmid   NZ_CP072253.1
  Reference Plasmid Size   98140
  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
M0188107 LMNAIJEC_00073 65120 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -3889T>C None
M0188108 LMNAIJEC_00042 39641 3 Gut 0.03 protein_coding synonymous_variant LOW 729A>C Ser243Ser
M0188109 LMNAIJEC_00065 62176 6 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -4737G>A None
M0188110 LMNAIJEC_00065 62180 6 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -4741C>A None
M0188111 LMNAIJEC_00024 27640 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4196T>G None
M0188112 LMNAIJEC_00065 62177 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4738G>A None
M0188113 LMNAIJEC_00065 62230 5 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4791G>A None
M0188114 LMNAIJEC_00065 62266 5 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4827C>T None
M0188115 LMNAIJEC_00065 62281 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4842G>A None
M0188116 LMNAIJEC_00065 62312 5 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4873T>A None
M0188117 LMNAIJEC_00065 62327 5 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4888A>G None
M0188118 LMNAIJEC_00065 62336 5 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4897C>A None
M0188119 LMNAIJEC_00065 62348 5 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4909G>A None
M0188120 LMNAIJEC_00065 62359 5 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4920G>A None
M0188121 LMNAIJEC_00040 37608 4 Gut 0.03 protein_coding missense_variant MODERATE 136A>G Ser46Gly
M0188122 LMNAIJEC_00092 73520 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -567A>G None
M0188123 LMNAIJEC_00092 73547 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -594A>G None
M0188124 LMNAIJEC_00092 73549 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -596G>A None
M0188125 LMNAIJEC_00003 2222 3 Gut 0.03 protein_coding synonymous_variant LOW 411T>C Asp137Asp
M0188126 LMNAIJEC_00003 2228 3 Gut 0.03 protein_coding synonymous_variant LOW 417T>G Arg139Arg
M0188127 LMNAIJEC_00003 2258 3 Gut 0.03 protein_coding synonymous_variant LOW 447A>G Glu149Glu
M0188128 LMNAIJEC_00003 2295 3 Gut 0.03 protein_coding missense_variant MODERATE 484G>C Val162Leu
M0188129 LMNAIJEC_00003 2387 3 Gut 0.03 protein_coding synonymous_variant LOW 576A>G Lys192Lys
M0188130 LMNAIJEC_00003 2491 3 Gut 0.03 protein_coding missense_variant MODERATE 680T>C Val227Ala
M0188131 LMNAIJEC_00003 2759 3 Gut 0.03 protein_coding synonymous_variant LOW 948G>A Gly316Gly
M0188132 LMNAIJEC_00005 2821 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -294A>T None
M0188133 LMNAIJEC_00039 37353 3 Gut 0.03 protein_coding missense_variant MODERATE 25T>A Ser9Thr
M0188134 LMNAIJEC_00039 37354 3 Gut 0.03 protein_coding synonymous_variant LOW 24C>T Ala8Ala
M0188135 LMNAIJEC_00040 37613 3 Gut 0.03 protein_coding synonymous_variant LOW 141A>G Ala47Ala
M0188136 LMNAIJEC_00024 27748 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4304A>G None
M0188137 LMNAIJEC_00024 27803 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4359A>G None
M0188138 LMNAIJEC_00027 25331 4 Gut 0.03 protein_coding synonymous_variant LOW 18A>C Ala6Ala
M0188139 LMNAIJEC_00073 65584 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4353T>A None
M0188140 LMNAIJEC_00073 65587 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4356G>A None
M0188141 LMNAIJEC_00042 39621 3 Gut 0.03 protein_coding synonymous_variant LOW 709T>C Leu237Leu
M0188142 LMNAIJEC_00042 39676 3 Gut 0.03 protein_coding missense_variant MODERATE 764G>A Gly255Asp






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
LMNAIJEC_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
LMNAIJEC_00009 QUT64421.1|GT4 100 1.11e-279 1 378 1 1
LMNAIJEC_00011 QUT55894.1|GT2 100 1.57e-228 1 304 1 1
LMNAIJEC_00013 QRP91616.1|GT4 100 5.41e-274 1 366 1 1
LMNAIJEC_00014 BBK89584.1|GT2 100 6.37e-226 1 300 1 1
LMNAIJEC_00015 QRP91614.1|GT4 100 4.79e-292 1 391 1 1
LMNAIJEC_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