Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C101
  Reference Plasmid   CP056607.1
  Reference Plasmid Size   87886
  Reference Plasmid GC Content   0.53
  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
M0144090 LNOCIGBP_00041 29226 3 Gut 0.12 protein_coding stop_gained HIGH 331C>T Gln111*
M0144091 LNOCIGBP_00041 29279 3 Gut 0.12 protein_coding synonymous_variant LOW 384A>C Thr128Thr
M0144092 LNOCIGBP_00041 29307 3 Gut 0.12 protein_coding missense_variant MODERATE 412T>C Tyr138His
M0144093 LNOCIGBP_00041 29321 3 Gut 0.12 protein_coding synonymous_variant LOW 426T>C Ser142Ser
M0144094 LNOCIGBP_00041 29402 3 Gut 0.12 protein_coding synonymous_variant LOW 507C>T Arg169Arg
M0144095 LNOCIGBP_00041 29411 3 Gut 0.12 protein_coding synonymous_variant LOW 516A>G Lys172Lys
M0144096 LNOCIGBP_00041 29450 3 Gut 0.12 protein_coding synonymous_variant LOW 555T>C Asn185Asn
M0144097 LNOCIGBP_00041 29507 3 Gut 0.12 protein_coding synonymous_variant LOW 612G>T Pro204Pro
M0144098 LNOCIGBP_00040 29813 3 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -1496C>T None
M0144099 LNOCIGBP_00042 29953 3 Gut 0.12 protein_coding synonymous_variant LOW 213G>A Lys71Lys
M0144100 LNOCIGBP_00042 30019 3 Gut 0.12 protein_coding synonymous_variant LOW 147A>T Thr49Thr
M0144101 LNOCIGBP_00042 30033 3 Gut 0.12 protein_coding missense_variant MODERATE 133A>G Ile45Val
M0144102 LNOCIGBP_00042 30112 3 Gut 0.12 protein_coding synonymous_variant LOW 54T>C Ala18Ala
M0144103 LNOCIGBP_00040 30215 6 Gut 0.24 protein_coding upstream_gene_variant MODIFIER -1898T>G None
M0144104 LNOCIGBP_00044 32143 6 Gut 0.24 protein_coding missense_variant MODERATE 1402A>G Met468Val
M0144105 LNOCIGBP_00047 34615 6 Gut 0.24 protein_coding missense_variant MODERATE 19G>A Glu7Lys
M0144106 LNOCIGBP_00072 57553 6 Gut 0.24 protein_coding synonymous_variant LOW 159A>G Gly53Gly
M0144107 LNOCIGBP_00072 57563 6 Gut 0.24 protein_coding missense_variant MODERATE 149G>A Arg50His
M0144108 LNOCIGBP_00073 57942 6 Gut 0.24 protein_coding synonymous_variant LOW 480A>G Leu160Leu
M0144109 LNOCIGBP_00074 58940 6 Gut 0.24 protein_coding synonymous_variant LOW 810C>G Val270Val
M0144110 LNOCIGBP_00074 58960 6 Gut 0.24 protein_coding synonymous_variant LOW 790C>A Arg264Arg
M0144111 LNOCIGBP_00074 59027 6 Gut 0.24 protein_coding synonymous_variant LOW 723T>C Val241Val
M0144112 LNOCIGBP_00074 59033 6 Gut 0.24 protein_coding synonymous_variant LOW 717A>G Gly239Gly
M0144113 LNOCIGBP_00074 59045 6 Gut 0.24 protein_coding synonymous_variant LOW 705G>C Gly235Gly
M0144114 LNOCIGBP_00074 59069 6 Gut 0.24 protein_coding synonymous_variant LOW 681C>T Arg227Arg
M0144115 LNOCIGBP_00074 59097 6 Gut 0.24 protein_coding missense_variant MODERATE 653C>A Ala218Glu
M0144116 LNOCIGBP_00074 59102 6 Gut 0.24 protein_coding synonymous_variant LOW 648C>T Asp216Asp
M0144117 LNOCIGBP_00074 59105 6 Gut 0.24 protein_coding synonymous_variant LOW 645C>T Ile215Ile
M0144118 LNOCIGBP_00074 59111 6 Gut 0.24 protein_coding synonymous_variant LOW 639T>C Ala213Ala
M0144119 LNOCIGBP_00074 59151 6 Gut 0.24 protein_coding missense_variant MODERATE 599A>C Gln200Pro
M0144120 LNOCIGBP_00074 59158 6 Gut 0.24 protein_coding missense_variant MODERATE 592A>G Thr198Ala
M0144121 LNOCIGBP_00074 59159 6 Gut 0.24 protein_coding synonymous_variant LOW 591T>A Ala197Ala
M0144122 LNOCIGBP_00074 59165 6 Gut 0.24 protein_coding synonymous_variant LOW 585A>C Thr195Thr
M0144123 LNOCIGBP_00074 59198 6 Gut 0.24 protein_coding synonymous_variant LOW 552G>A Gln184Gln
M0144124 LNOCIGBP_00074 59218 6 Gut 0.24 protein_coding missense_variant MODERATE 532T>C Ser178Pro
M0144125 LNOCIGBP_00074 59231 6 Gut 0.24 protein_coding synonymous_variant LOW 519T>A Pro173Pro
M0144126 LNOCIGBP_00074 59246 6 Gut 0.24 protein_coding synonymous_variant LOW 504G>T Ala168Ala
M0144127 LNOCIGBP_00074 59248 6 Gut 0.24 protein_coding missense_variant MODERATE 502G>A Ala168Thr
M0144128 LNOCIGBP_00074 59281 6 Gut 0.24 protein_coding missense_variant MODERATE 469A>G Ile157Val
M0144129 LNOCIGBP_00074 59309 6 Gut 0.24 protein_coding synonymous_variant LOW 441C>T Asn147Asn
M0144130 LNOCIGBP_00074 59360 6 Gut 0.24 protein_coding synonymous_variant LOW 390G>T Thr130Thr
M0144131 LNOCIGBP_00074 59378 6 Gut 0.24 protein_coding synonymous_variant LOW 372T>C Pro124Pro
M0144132 LNOCIGBP_00074 59576 6 Gut 0.24 protein_coding synonymous_variant LOW 174A>G Gly58Gly
M0144133 LNOCIGBP_00074 59672 6 Gut 0.24 protein_coding synonymous_variant LOW 78T>C Ile26Ile
M0144134 LNOCIGBP_00075 60131 6 Gut 0.24 protein_coding synonymous_variant LOW 597A>G Thr199Thr
M0144135 LNOCIGBP_00075 60320 6 Gut 0.24 protein_coding synonymous_variant LOW 408T>G Thr136Thr
M0144136 LNOCIGBP_00075 60490 6 Gut 0.24 protein_coding missense_variant MODERATE 238G>A Gly80Ser
M0144137 LNOCIGBP_00076 61182 6 Gut 0.24 protein_coding synonymous_variant LOW 252G>T Leu84Leu
M0144138 LNOCIGBP_00078 62304 6 Gut 0.24 protein_coding synonymous_variant LOW 3570T>A Pro1190Pro
M0144139 LNOCIGBP_00078 62970 6 Gut 0.24 protein_coding synonymous_variant LOW 2904C>T Ala968Ala
M0144140 LNOCIGBP_00078 63597 6 Gut 0.24 protein_coding missense_variant MODERATE 2277A>T Glu759Asp
M0144141 LNOCIGBP_00078 63948 6 Gut 0.24 protein_coding synonymous_variant LOW 1926T>C Asn642Asn
M0144142 LNOCIGBP_00078 65061 6 Gut 0.24 protein_coding synonymous_variant LOW 813A>C Ala271Ala
M0144143 LNOCIGBP_00078 65382 6 Gut 0.24 protein_coding synonymous_variant LOW 492A>T Ala164Ala
M0144144 LNOCIGBP_00078 65808 6 Gut 0.24 protein_coding synonymous_variant LOW 66G>A Ala22Ala
M0144145 LNOCIGBP_00079 66092 6 Gut 0.24 protein_coding synonymous_variant LOW 136C>T Leu46Leu






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
LNOCIGBP_00087 SPE00673.1|GH23 100 1.33e-115 1 161 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
LNOCIGBP_00048 3.A.7.10.1 79.7 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
LNOCIGBP_00050 3.A.7.10.1 75.6 2.4e-189 1 401 0.9155 4.1771 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
LNOCIGBP_00058 1.E.53.1.10 97.7 9.7e-18 8 50 0.8600 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
LNOCIGBP_00075 3.A.7.10.1 74.9 1.5e-138 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
LNOCIGBP_00077 3.A.7.10.1 73.3 1.9e-40 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
LNOCIGBP_00080 3.A.7.10.1 77.8 1.7e-175 1 379 0.9921 3.9479 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
LNOCIGBP_00081 3.A.7.10.1 77.9 6.6e-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