Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C903
  Reference Plasmid   NZ_CP075666.1
  Reference Plasmid Size   129935
  Reference Plasmid GC Content   0.51
  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
M0188273 MNDMKIOB_00085 66158 4 Gut 0.20 protein_coding upstream_gene_variant MODIFIER -2665T>C None
M0188274 MNDMKIOB_00079 57548 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -1983A>T None
M0188275 MNDMKIOB_00079 57616 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -2051G>A None
M0188276 MNDMKIOB_00079 57617 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -2052T>C None
M0188277 MNDMKIOB_00083 58729 3 Gut 0.15 protein_coding missense_variant MODERATE 741A>G Ile247Met
M0188278 MNDMKIOB_00084 61071 3 Gut 0.15 protein_coding missense_variant MODERATE 268T>A Ser90Thr
M0188279 MNDMKIOB_00154 123153 3 Gut 0.15 protein_coding synonymous_variant LOW 87G>A Thr29Thr
M0188280 MNDMKIOB_00154 123225 3 Gut 0.15 protein_coding synonymous_variant LOW 15A>T Ser5Ser
M0188281 MNDMKIOB_00154 123231 3 Gut 0.15 protein_coding synonymous_variant LOW 9G>A Lys3Lys
M0188282 MNDMKIOB_00154 123236 3 Gut 0.15 protein_coding missense_variant MODERATE 4A>C Lys2Gln
M0188283 MNDMKIOB_00149 123256 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4983C>T None
M0188284 MNDMKIOB_00149 123258 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4985T>A None
M0188285 MNDMKIOB_00149 123259 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4986A>T None
M0188286 MNDMKIOB_00150 123285 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4511A>C None
M0188287 MNDMKIOB_00150 123292 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4518T>A None
M0188288 MNDMKIOB_00150 123295 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4521A>G None
M0188289 MNDMKIOB_00150 123315 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4541G>A None
M0188290 MNDMKIOB_00155 123763 3 Gut 0.15 protein_coding synonymous_variant LOW 267C>A Ile89Ile
M0188291 MNDMKIOB_00156 123918 3 Gut 0.15 protein_coding synonymous_variant LOW 744T>C Ser248Ser
M0188292 MNDMKIOB_00156 124091 3 Gut 0.15 protein_coding missense_variant MODERATE 571C>T Leu191Phe
M0188293 MNDMKIOB_00156 124546 3 Gut 0.15 protein_coding missense_variant MODERATE 116A>G Asp39Gly
M0188294 MNDMKIOB_00151 124811 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4752C>T None
M0188295 MNDMKIOB_00151 124816 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4757G>A None






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
MNDMKIOB_00085 VFG012633 Iron-regulated element 98.8 0 1 682 1.0 1 Nutritional/Metabolic factor TonB-dependent siderophore receptor IreA 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






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
MNDMKIOB_00014 PHI:123867 NAL (LC602499) 78.1 2.5e-129 9 296 0.9697 0.9931 bony fishes gastroenteritis N-acetylneuraminate lyase increased virulence (hypervirulence)
MNDMKIOB_00015 PHI:124245 nanT 88.6 1.6e-250 1 481 0.9717 0.9698 rodents None sialic acid transporter reduced virulence
MNDMKIOB_00085 PHI:6654 ireA 98.7 0 1 682 1.0000 1.0000 birds avian colibacillosis iron-regulated outer membrane virulence protein unaffected pathogenicity
MNDMKIOB_00088 PHI:6654 ireA 72.1 5e-24 9 76 0.8500 1.0000 birds avian colibacillosis iron-regulated outer membrane virulence protein unaffected pathogenicity






        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
MNDMKIOB_00141 ASX09209.1|GH23 98.8 1.19e-113 1 160 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
MNDMKIOB_00015 2.A.1.12.1 88 8.1e-250 1 487 0.9838 0.9879 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
MNDMKIOB_00018 1.B.35.2.1 84.9 3.3e-124 1 237 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.35 The Oligogalacturonate-specific Porin (KdgM) Family
MNDMKIOB_00032 2.A.123.2.16 100 1.7e-41 1 89 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.123 The Sweet; PQ-loop; Saliva; MtN3 (Sweet) Family
MNDMKIOB_00090 3.A.7.10.1 79.4 0 1 724 0.9439 7.5417 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
MNDMKIOB_00092 3.A.7.10.1 76.2 7.1e-189 1 399 0.9110 4.1563 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
MNDMKIOB_00124 3.A.7.10.1 76.8 5.9e-140 1 324 1.0000 3.4063 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
MNDMKIOB_00125 3.A.7.10.1 70.7 2.3e-90 6 227 0.9610 2.2917 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
MNDMKIOB_00126 3.A.7.10.1 73.3 1.2e-39 1 116 1.0000 1.1979 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
MNDMKIOB_00128 3.A.7.10.1 71.3 1.3e-39 1 94 0.9792 0.9792 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
MNDMKIOB_00129 3.A.7.10.1 78.5 4.2e-177 4 379 0.9843 3.9167 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
MNDMKIOB_00130 3.A.7.10.1 79 1.3e-124 1 271 0.9748 2.8021 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