Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C257
  Reference Plasmid   LR962329.1
  Reference Plasmid Size   107711
  Reference Plasmid GC Content   0.36
  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
M0149942 LPIIBCNN_00053 49188 8 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -2740G>A None
M0149943 LPIIBCNN_00062 59362 7 Gut 0.10 protein_coding synonymous_variant LOW 121T>C Leu41Leu
M0149944 LPIIBCNN_00065 62678 6 Gut 0.09 protein_coding missense_variant MODERATE 1117T>C Ser373Pro
M0149945 LPIIBCNN_00070 70563 6 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -3099C>T None
M0149946 LPIIBCNN_00070 70712 6 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -3248T>C None
M0149947 LPIIBCNN_00070 70719 6 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -3255A>G None
M0149948 LPIIBCNN_00070 70745 6 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -3281T>A None
M0149949 LPIIBCNN_00070 70766 6 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -3302C>T None
M0149950 LPIIBCNN_00074 70985 6 Gut 0.09 protein_coding missense_variant MODERATE 64G>A Val22Ile
M0149951 LPIIBCNN_00074 71170 6 Gut 0.09 protein_coding synonymous_variant LOW 249G>A Leu83Leu
M0149952 LPIIBCNN_00074 71228 6 Gut 0.09 protein_coding missense_variant MODERATE 307G>A Val103Met
M0149953 LPIIBCNN_00074 71239 6 Gut 0.09 protein_coding synonymous_variant LOW 318G>C Arg106Arg
M0149954 LPIIBCNN_00074 71284 6 Gut 0.09 protein_coding synonymous_variant LOW 363T>C Arg121Arg
M0149955 LPIIBCNN_00075 71601 6 Gut 0.09 protein_coding synonymous_variant LOW 210A>G Val70Val
M0149956 LPIIBCNN_00075 71706 6 Gut 0.09 protein_coding synonymous_variant LOW 315T>C Thr105Thr
M0149957 LPIIBCNN_00075 71760 6 Gut 0.09 protein_coding synonymous_variant LOW 369C>T Gly123Gly
M0149958 LPIIBCNN_00075 71958 6 Gut 0.09 protein_coding synonymous_variant LOW 567A>G Gly189Gly
M0149959 LPIIBCNN_00075 72285 6 Gut 0.09 protein_coding synonymous_variant LOW 894G>A Leu298Leu
M0149960 LPIIBCNN_00075 72339 6 Gut 0.09 protein_coding synonymous_variant LOW 948T>C Phe316Phe
M0149961 LPIIBCNN_00075 72435 6 Gut 0.09 protein_coding synonymous_variant LOW 1044T>G Gly348Gly
M0149962 LPIIBCNN_00075 72453 6 Gut 0.09 protein_coding synonymous_variant LOW 1062A>C Gly354Gly
M0149963 LPIIBCNN_00075 72675 6 Gut 0.09 protein_coding synonymous_variant LOW 1284T>C Val428Val
M0149964 LPIIBCNN_00075 72678 6 Gut 0.09 protein_coding synonymous_variant LOW 1287G>T Thr429Thr
M0149965 LPIIBCNN_00075 72798 6 Gut 0.09 protein_coding synonymous_variant LOW 1407G>A Leu469Leu
M0149966 LPIIBCNN_00075 72804 6 Gut 0.09 protein_coding synonymous_variant LOW 1413G>A Gly471Gly
M0149967 LPIIBCNN_00075 72861 6 Gut 0.09 protein_coding synonymous_variant LOW 1470A>G Glu490Glu
M0149968 LPIIBCNN_00075 72882 6 Gut 0.09 protein_coding synonymous_variant LOW 1491A>G Pro497Pro
M0149969 LPIIBCNN_00075 72945 6 Gut 0.09 protein_coding synonymous_variant LOW 1554A>C Gly518Gly
M0149970 LPIIBCNN_00075 72987 6 Gut 0.09 protein_coding synonymous_variant LOW 1596A>C Ser532Ser
M0149971 LPIIBCNN_00075 73408 6 Gut 0.09 protein_coding missense_variant MODERATE 2017T>G Phe673Val
M0149972 LPIIBCNN_00071 73755 6 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -3931A>G None
M0149973 LPIIBCNN_00077 74995 6 Gut 0.09 protein_coding missense_variant MODERATE 138T>A Asp46Glu
M0149974 LPIIBCNN_00085 79950 4 Gut 0.06 protein_coding missense_variant MODERATE 68A>C Asp23Ala
M0149975 LPIIBCNN_00087 81126 4 Gut 0.06 protein_coding missense_variant MODERATE 71T>G Val24Gly
M0149976 LPIIBCNN_00084 82332 4 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -2641A>C None
M0149977 LPIIBCNN_00090 82825 7 Gut 0.10 protein_coding synonymous_variant LOW 93A>G Thr31Thr
M0149978 LPIIBCNN_00101 92193 11 Gut 0.16 protein_coding upstream_gene_variant MODIFIER -123G>A None
M0149979 LPIIBCNN_00106 95479 4 Gut 0.06 protein_coding missense_variant MODERATE 187G>T Val63Phe
M0149980 LPIIBCNN_00025 22560 6 Gut 0.09 protein_coding synonymous_variant LOW 87G>A Leu29Leu
M0149981 LPIIBCNN_00052 51540 3 Gut 0.04 protein_coding synonymous_variant LOW 168G>A Arg56Arg
M0149982 LPIIBCNN_00071 69360 3 Gut 0.04 protein_coding synonymous_variant LOW 465A>G Thr155Thr
M0149983 LPIIBCNN_00094 85328 7 Gut 0.10 protein_coding missense_variant MODERATE 184G>A Glu62Lys
M0149984 LPIIBCNN_00084 83904 4 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -4213C>T None
M0149985 LPIIBCNN_00094 85501 4 Gut 0.06 protein_coding synonymous_variant LOW 357C>T Asp119Asp
M0149986 LPIIBCNN_00100 91300 4 Gut 0.06 protein_coding synonymous_variant LOW 321C>T Asp107Asp
M0149987 LPIIBCNN_00101 92631 3 Gut 0.04 protein_coding missense_variant MODERATE 316T>C Ser106Pro
M0149988 LPIIBCNN_00101 92531 4 Gut 0.06 protein_coding synonymous_variant LOW 216G>A Leu72Leu
M0149989 LPIIBCNN_00101 92536 4 Gut 0.06 protein_coding missense_variant MODERATE 221T>C Ile74Thr
M0149990 LPIIBCNN_00101 92568 4 Gut 0.06 protein_coding missense_variant MODERATE 253T>C Phe85Leu
M0149991 LPIIBCNN_00101 92793 5 Gut 0.07 protein_coding missense_variant MODERATE 478C>T Pro160Ser
M0149992 LPIIBCNN_00105 94770 3 Gut 0.04 protein_coding missense_variant MODERATE 614C>T Ala205Val






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
LPIIBCNN_00107 VFG002162 BSH 73.8 1.9e-147 1 324 1.0 0.9969 Stress survival bile salt hydrolase experiment
LPIIBCNN_00107 VFG019385 BSH 74.4 3.3e-148 1 324 1.0 0.9969 Stress survival bile salt hydrolase 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
LPIIBCNN_00007 ARO:3002628 100 1.04e-211 27 302 0.9139 1.0000 aminoglycoside antibiotic ANT(6) antibiotic inactivation
LPIIBCNN_00008 ARO:3002897 99.4 1.34e-130 1 180 1.0000 1.0000 nucleoside antibiotic streptothricin acetyltransferase (SAT) antibiotic inactivation
LPIIBCNN_00009 ARO:3002647 100 1.07e-198 1 264 1.0000 1.0000 aminoglycoside antibiotic APH(3') antibiotic inactivation






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
LPIIBCNN_00030 QQR11341.1|GH105 100 1.97e-277 1 368 1 1
LPIIBCNN_00043 QFY91597.1|CBM50 100 1.22e-116 1 199 1 1
LPIIBCNN_00098 QZK92746.1|GH1 100 0 1 468 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
LPIIBCNN_00097 4.A.3.1.1 71.9 1.1e-239 1 568 1.0000 0.9965 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.3 The PTS Lactose-N,N'-Diacetylchitobiose-β-glucoside (Lac) Family