Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C475
  Reference Plasmid   NZ_CP020430.1
  Reference Plasmid Size   20536
  Reference Plasmid GC Content   0.37
  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
M0166957 NEGHDOEA_00017 11417 3 Gut 0.75 protein_coding missense_variant MODERATE 2518A>G Ile840Val
M0166958 NEGHDOEA_00017 11421 3 Gut 0.75 protein_coding synonymous_variant LOW 2514G>A Thr838Thr
M0166959 NEGHDOEA_00017 11454 3 Gut 0.75 protein_coding synonymous_variant LOW 2481A>T Gly827Gly
M0166960 NEGHDOEA_00017 11542 3 Gut 0.75 protein_coding missense_variant MODERATE 2393C>T Thr798Ile
M0166961 NEGHDOEA_00017 11550 4 Gut 1.00 protein_coding synonymous_variant LOW 2385A>T Ala795Ala
M0166962 NEGHDOEA_00017 11560 3 Gut 0.75 protein_coding missense_variant MODERATE 2375A>T Glu792Val
M0166963 NEGHDOEA_00017 11565 3 Gut 0.75 protein_coding missense_variant MODERATE 2370C>A Asp790Glu
M0166964 NEGHDOEA_00017 11571 3 Gut 0.75 protein_coding synonymous_variant LOW 2364C>T Phe788Phe
M0166965 NEGHDOEA_00017 11575 3 Gut 0.75 protein_coding missense_variant MODERATE 2360C>G Ala787Gly
M0166966 NEGHDOEA_00017 11579 3 Gut 0.75 protein_coding missense_variant MODERATE 2356G>A Ala786Thr
M0166967 NEGHDOEA_00017 11604 3 Gut 0.75 protein_coding synonymous_variant LOW 2331C>T Ile777Ile
M0166968 NEGHDOEA_00017 11916 4 Gut 1.00 protein_coding synonymous_variant LOW 2019T>C Leu673Leu
M0166969 NEGHDOEA_00017 11961 4 Gut 1.00 protein_coding synonymous_variant LOW 1974G>A Gln658Gln
M0166970 NEGHDOEA_00017 12018 4 Gut 1.00 protein_coding synonymous_variant LOW 1917C>T Ile639Ile
M0166971 NEGHDOEA_00017 12027 4 Gut 1.00 protein_coding synonymous_variant LOW 1908A>G Leu636Leu
M0166972 NEGHDOEA_00017 12030 4 Gut 1.00 protein_coding synonymous_variant LOW 1905T>C Asp635Asp
M0166973 NEGHDOEA_00017 12056 4 Gut 1.00 protein_coding missense_variant MODERATE 1879G>C Ala627Pro
M0166974 NEGHDOEA_00017 12240 3 Gut 0.75 protein_coding synonymous_variant LOW 1695C>T Val565Val
M0166975 NEGHDOEA_00017 12300 4 Gut 1.00 protein_coding synonymous_variant LOW 1635G>A Ala545Ala
M0166976 NEGHDOEA_00017 12483 4 Gut 1.00 protein_coding synonymous_variant LOW 1452A>G Ala484Ala
M0166977 NEGHDOEA_00017 12630 3 Gut 0.75 protein_coding synonymous_variant LOW 1305C>T Thr435Thr
M0166978 NEGHDOEA_00017 12657 4 Gut 1.00 protein_coding synonymous_variant LOW 1278A>C Arg426Arg
M0166979 NEGHDOEA_00017 12732 3 Gut 0.75 protein_coding synonymous_variant LOW 1203T>C His401His
M0166980 NEGHDOEA_00017 12897 3 Gut 0.75 protein_coding synonymous_variant LOW 1038A>G Gly346Gly
M0166981 NEGHDOEA_00017 12900 3 Gut 0.75 protein_coding synonymous_variant LOW 1035A>T Arg345Arg
M0166982 NEGHDOEA_00017 13028 4 Gut 1.00 protein_coding synonymous_variant LOW 907A>C Arg303Arg
M0166983 NEGHDOEA_00017 13176 4 Gut 1.00 protein_coding synonymous_variant LOW 759T>C Asp253Asp
M0166984 NEGHDOEA_00017 13221 3 Gut 0.75 protein_coding synonymous_variant LOW 714G>T Thr238Thr
M0166985 NEGHDOEA_00017 13290 3 Gut 0.75 protein_coding synonymous_variant LOW 645T>C Ile215Ile
M0166986 NEGHDOEA_00017 13452 4 Gut 1.00 protein_coding synonymous_variant LOW 483C>T His161His
M0166987 NEGHDOEA_00017 13743 4 Gut 1.00 protein_coding synonymous_variant LOW 192T>C Asn64Asn
M0166988 NEGHDOEA_00016 13938 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2864A>T None
M0166989 NEGHDOEA_00016 13953 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2879C>G None
M0166990 NEGHDOEA_00018 13983 4 Gut 1.00 protein_coding missense_variant MODERATE 488A>C Asp163Ala
M0166991 NEGHDOEA_00018 14078 3 Gut 0.75 protein_coding synonymous_variant LOW 393G>A Pro131Pro
M0166992 NEGHDOEA_00018 14177 4 Gut 1.00 protein_coding synonymous_variant LOW 294C>T Leu98Leu
M0166993 NEGHDOEA_00018 14180 4 Gut 1.00 protein_coding synonymous_variant LOW 291C>G Leu97Leu
M0166994 NEGHDOEA_00018 14213 3 Gut 0.75 protein_coding synonymous_variant LOW 258G>C Ala86Ala
M0166995 NEGHDOEA_00018 14219 4 Gut 1.00 protein_coding synonymous_variant LOW 252A>G Lys84Lys
M0166996 NEGHDOEA_00018 14255 4 Gut 1.00 protein_coding synonymous_variant LOW 216C>G Gly72Gly
M0166997 NEGHDOEA_00018 14393 3 Gut 0.75 protein_coding synonymous_variant LOW 78G>A Glu26Glu
M0166998 NEGHDOEA_00016 14504 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3430T>G None
M0166999 NEGHDOEA_00019 14592 3 Gut 0.75 protein_coding synonymous_variant LOW 1255T>C Leu419Leu
M0167000 NEGHDOEA_00019 14659 4 Gut 1.00 protein_coding synonymous_variant LOW 1188G>C Leu396Leu
M0167001 NEGHDOEA_00019 14668 4 Gut 1.00 protein_coding synonymous_variant LOW 1179A>G Lys393Lys
M0167002 NEGHDOEA_00019 14848 4 Gut 1.00 protein_coding synonymous_variant LOW 999T>C Cys333Cys
M0167003 NEGHDOEA_00019 14860 4 Gut 1.00 protein_coding synonymous_variant LOW 987C>T Ala329Ala
M0167004 NEGHDOEA_00019 14863 4 Gut 1.00 protein_coding synonymous_variant LOW 984A>T Leu328Leu
M0167005 NEGHDOEA_00019 14944 4 Gut 1.00 protein_coding synonymous_variant LOW 903A>G Val301Val
M0167006 NEGHDOEA_00019 15079 4 Gut 1.00 protein_coding synonymous_variant LOW 768T>C Leu256Leu
M0167007 NEGHDOEA_00019 15100 4 Gut 1.00 protein_coding synonymous_variant LOW 747C>T Thr249Thr
M0167008 NEGHDOEA_00019 15133 4 Gut 1.00 protein_coding synonymous_variant LOW 714C>T Val238Val
M0167009 NEGHDOEA_00019 15172 4 Gut 1.00 protein_coding synonymous_variant LOW 675G>A Glu225Glu
M0167010 NEGHDOEA_00019 15323 3 Gut 0.75 protein_coding missense_variant MODERATE 524C>T Thr175Ile
M0167011 NEGHDOEA_00019 15382 3 Gut 0.75 protein_coding synonymous_variant LOW 465C>T Ile155Ile
M0167012 NEGHDOEA_00019 15604 4 Gut 1.00 protein_coding synonymous_variant LOW 243G>A Glu81Glu
M0167013 NEGHDOEA_00019 15613 4 Gut 1.00 protein_coding synonymous_variant LOW 234A>T Arg78Arg
M0167014 NEGHDOEA_00019 15656 4 Gut 1.00 protein_coding missense_variant MODERATE 191A>G His64Arg
M0167015 NEGHDOEA_00019 15772 3 Gut 0.75 protein_coding synonymous_variant LOW 75G>A Val25Val
M0167016 NEGHDOEA_00019 15832 4 Gut 1.00 protein_coding synonymous_variant LOW 15C>T Ser5Ser
M0167017 NEGHDOEA_00020 15895 3 Gut 0.75 protein_coding missense_variant MODERATE 956T>C Phe319Ser
M0167018 NEGHDOEA_00020 15987 3 Gut 0.75 protein_coding synonymous_variant LOW 864C>T Phe288Phe
M0167019 NEGHDOEA_00020 16000 3 Gut 0.75 protein_coding missense_variant MODERATE 851C>A Thr284Asn
M0167020 NEGHDOEA_00020 16119 4 Gut 1.00 protein_coding synonymous_variant LOW 732T>C Ser244Ser
M0167021 NEGHDOEA_00020 16185 4 Gut 1.00 protein_coding synonymous_variant LOW 666A>T Ala222Ala
M0167022 NEGHDOEA_00020 16296 4 Gut 1.00 protein_coding synonymous_variant LOW 555G>A Pro185Pro
M0167023 NEGHDOEA_00020 16409 4 Gut 1.00 protein_coding missense_variant MODERATE 442G>A Val148Ile
M0167024 NEGHDOEA_00020 16584 4 Gut 1.00 protein_coding synonymous_variant LOW 267A>G Leu89Leu
M0167025 NEGHDOEA_00020 16760 4 Gut 1.00 protein_coding missense_variant MODERATE 91T>G Ser31Ala
M0167026 NEGHDOEA_00020 16764 4 Gut 1.00 protein_coding synonymous_variant LOW 87A>C Leu29Leu
M0167027 NEGHDOEA_00021 17012 3 Gut 0.75 protein_coding missense_variant MODERATE 475A>G Thr159Ala
M0167028 NEGHDOEA_00021 17322 3 Gut 0.75 protein_coding synonymous_variant LOW 165A>G Lys55Lys
M0167029 NEGHDOEA_00017 17699 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3765T>C None
M0167030 NEGHDOEA_00022 17757 3 Gut 0.75 protein_coding synonymous_variant LOW 297T>G Gly99Gly
M0167031 NEGHDOEA_00022 17962 4 Gut 1.00 protein_coding missense_variant MODERATE 92G>A Ser31Asn
M0167032 NEGHDOEA_00022 18045 4 Gut 1.00 protein_coding synonymous_variant LOW 9G>T Leu3Leu
M0167033 NEGHDOEA_00024 19054 3 Gut 0.75 protein_coding synonymous_variant LOW 81C>T Phe27Phe
M0167034 NEGHDOEA_00024 19060 3 Gut 0.75 protein_coding missense_variant MODERATE 75A>T Glu25Asp
M0167035 NEGHDOEA_00024 19072 3 Gut 0.75 protein_coding missense_variant MODERATE 63A>C Glu21Asp
M0167036 NEGHDOEA_00024 19074 3 Gut 0.75 protein_coding missense_variant MODERATE 61G>C Glu21Gln
M0167037 NEGHDOEA_00024 19075 3 Gut 0.75 protein_coding missense_variant MODERATE 60T>A Asp20Glu
M0167038 NEGHDOEA_00024 19076 3 Gut 0.75 protein_coding missense_variant MODERATE 59A>G Asp20Gly
M0167039 NEGHDOEA_00024 19087 3 Gut 0.75 protein_coding synonymous_variant LOW 48C>T Tyr16Tyr
M0167040 NEGHDOEA_00025 19216 4 Gut 1.00 protein_coding missense_variant MODERATE 395C>T Ala132Val
M0167041 NEGHDOEA_00025 19241 4 Gut 1.00 protein_coding missense_variant MODERATE 370T>C Phe124Leu
M0167042 NEGHDOEA_00025 19371 4 Gut 1.00 protein_coding synonymous_variant LOW 240G>A Lys80Lys
M0167043 NEGHDOEA_00025 19479 4 Gut 1.00 protein_coding synonymous_variant LOW 132T>C Ser44Ser
M0167044 NEGHDOEA_00026 19852 4 Gut 1.00 protein_coding synonymous_variant LOW 324A>T Gly108Gly
M0167045 NEGHDOEA_00026 19876 4 Gut 1.00 protein_coding synonymous_variant LOW 300A>G Lys100Lys
M0167046 NEGHDOEA_00026 19885 4 Gut 1.00 protein_coding synonymous_variant LOW 291T>C Thr97Thr
M0167047 NEGHDOEA_00026 19897 4 Gut 1.00 protein_coding synonymous_variant LOW 279G>A Lys93Lys
M0167048 NEGHDOEA_00026 19918 4 Gut 1.00 protein_coding synonymous_variant LOW 258T>C Ala86Ala
M0167049 NEGHDOEA_00026 19978 4 Gut 1.00 protein_coding synonymous_variant LOW 198T>C Cys66Cys
M0167050 NEGHDOEA_00026 19985 4 Gut 1.00 protein_coding missense_variant MODERATE 191G>C Gly64Ala
M0167051 NEGHDOEA_00026 20026 4 Gut 1.00 protein_coding synonymous_variant LOW 150A>G Gly50Gly
M0167052 NEGHDOEA_00026 20055 3 Gut 0.75 protein_coding missense_variant MODERATE 121C>A His41Asn
M0167053 NEGHDOEA_00026 20095 4 Gut 1.00 protein_coding synonymous_variant LOW 81C>T His27His
M0167054 NEGHDOEA_00026 20098 4 Gut 1.00 protein_coding synonymous_variant LOW 78T>A Ala26Ala
M0167055 NEGHDOEA_00026 20104 4 Gut 1.00 protein_coding synonymous_variant LOW 72A>T Ala24Ala
M0167056 NEGHDOEA_00026 20113 4 Gut 1.00 protein_coding missense_variant MODERATE 63T>A Asp21Glu
M0167057 NEGHDOEA_00026 20165 3 Gut 0.75 protein_coding missense_variant MODERATE 11A>C Lys4Thr
M0167058 NEGHDOEA_00026 20170 3 Gut 0.75 protein_coding synonymous_variant LOW 6A>T Thr2Thr
M0167059 NEGHDOEA_00027 20199 3 Gut 0.75 protein_coding missense_variant MODERATE 325G>A Val109Ile
M0167060 NEGHDOEA_00027 20226 3 Gut 0.75 protein_coding missense_variant MODERATE 298C>A Gln100Lys
M0167061 NEGHDOEA_00027 20278 3 Gut 0.75 protein_coding synonymous_variant LOW 246C>T Ala82Ala
M0167062 NEGHDOEA_00027 20290 3 Gut 0.75 protein_coding synonymous_variant LOW 234T>C Val78Val
M0167063 NEGHDOEA_00017 11739 3 Gut 0.75 protein_coding synonymous_variant LOW 2196T>C Ile732Ile
M0167064 NEGHDOEA_00017 11772 3 Gut 0.75 protein_coding synonymous_variant LOW 2163A>G Lys721Lys
M0167065 NEGHDOEA_00017 11781 3 Gut 0.75 protein_coding synonymous_variant LOW 2154T>C Asp718Asp
M0167066 NEGHDOEA_00017 11784 3 Gut 0.75 protein_coding synonymous_variant LOW 2151A>G Glu717Glu
M0167067 NEGHDOEA_00017 12522 3 Gut 0.75 protein_coding synonymous_variant LOW 1413T>C Asp471Asp
M0167068 NEGHDOEA_00017 13073 3 Gut 0.75 protein_coding missense_variant MODERATE 862T>C Phe288Leu
M0167069 NEGHDOEA_00017 13077 3 Gut 0.75 protein_coding synonymous_variant LOW 858G>A Ala286Ala
M0167070 NEGHDOEA_00017 13083 3 Gut 0.75 protein_coding synonymous_variant LOW 852G>T Leu284Leu
M0167071 NEGHDOEA_00017 13095 3 Gut 0.75 protein_coding synonymous_variant LOW 840C>T Asp280Asp
M0167072 NEGHDOEA_00017 13299 3 Gut 0.75 protein_coding synonymous_variant LOW 636C>T Thr212Thr
M0167073 NEGHDOEA_00018 14441 3 Gut 0.75 protein_coding synonymous_variant LOW 30G>T Pro10Pro
M0167074 NEGHDOEA_00019 15034 3 Gut 0.75 protein_coding synonymous_variant LOW 813G>A Ser271Ser
M0167075 NEGHDOEA_00020 16586 3 Gut 0.75 protein_coding synonymous_variant LOW 265T>C Leu89Leu
M0167076 NEGHDOEA_00020 16833 3 Gut 0.75 protein_coding missense_variant MODERATE 18A>T Gln6His
M0167077 NEGHDOEA_00020 16835 3 Gut 0.75 protein_coding missense_variant MODERATE 16C>A Gln6Lys






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





        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