Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C97
  Reference Plasmid   CP054203.1
  Reference Plasmid Size   57281
  Reference Plasmid GC Content   0.45
  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
M0143918 ALJHCNBK_00049 35485 6 Gut 0.13 protein_coding stop_lost&splice_region_variant HIGH 679T>C Ter227Argext*?
M0143919 ALJHCNBK_00051 35784 6 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -642A>G None
M0143920 ALJHCNBK_00050 35944 6 Gut 0.13 protein_coding missense_variant MODERATE 314A>G Asn105Ser
M0143921 ALJHCNBK_00050 35945 6 Gut 0.13 protein_coding missense_variant MODERATE 313A>G Asn105Asp
M0143922 ALJHCNBK_00050 36205 6 Gut 0.13 protein_coding missense_variant MODERATE 53C>T Ala18Val
M0143923 ALJHCNBK_00050 36401 8 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -144T>C None
M0143924 ALJHCNBK_00051 36456 5 Gut 0.11 protein_coding missense_variant MODERATE 31A>G Thr11Ala
M0143925 ALJHCNBK_00052 36872 5 Gut 0.11 protein_coding synonymous_variant LOW 33T>C Ala11Ala
M0143926 ALJHCNBK_00053 37224 8 Gut 0.18 protein_coding missense_variant MODERATE 13A>C Ile5Leu
M0143927 ALJHCNBK_00054 37435 8 Gut 0.18 protein_coding missense_variant MODERATE 164T>C Leu55Pro
M0143928 ALJHCNBK_00055 37727 8 Gut 0.18 protein_coding synonymous_variant LOW 102T>C Ala34Ala
M0143929 ALJHCNBK_00050 38012 9 Gut 0.20 protein_coding upstream_gene_variant MODIFIER -1755A>G None
M0143930 ALJHCNBK_00058 39080 14 Gut 0.31 protein_coding missense_variant MODERATE 437C>G Thr146Ser
M0143931 ALJHCNBK_00058 39142 15 Gut 0.33 protein_coding synonymous_variant LOW 375T>C Ala125Ala
M0143932 ALJHCNBK_00059 39631 15 Gut 0.33 protein_coding missense_variant MODERATE 221C>T Ala74Val
M0143933 ALJHCNBK_00060 39973 6 Gut 0.13 protein_coding synonymous_variant LOW 576A>G Leu192Leu
M0143934 ALJHCNBK_00053 42106 4 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -4870A>T None
M0143935 ALJHCNBK_00053 42107 4 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -4871C>G None
M0143936 ALJHCNBK_00063 42521 4 Gut 0.09 protein_coding missense_variant MODERATE 5T>C Leu2Pro
M0143937 ALJHCNBK_00049 35057 3 Gut 0.07 protein_coding missense_variant MODERATE 251A>G Gln84Arg
M0143938 ALJHCNBK_00049 35109 3 Gut 0.07 protein_coding synonymous_variant LOW 303A>G Lys101Lys
M0143939 ALJHCNBK_00049 35116 3 Gut 0.07 protein_coding missense_variant MODERATE 310A>G Thr104Ala
M0143940 ALJHCNBK_00049 35369 3 Gut 0.07 protein_coding missense_variant MODERATE 563A>G Asn188Ser
M0143941 ALJHCNBK_00049 35448 3 Gut 0.07 protein_coding synonymous_variant LOW 642A>G Thr214Thr
M0143942 ALJHCNBK_00051 35558 4 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -868A>G None
M0143943 ALJHCNBK_00050 35918 4 Gut 0.09 protein_coding missense_variant MODERATE 340A>G Ile114Val
M0143944 ALJHCNBK_00050 35939 4 Gut 0.09 protein_coding missense_variant MODERATE 319T>C Cys107Arg
M0143945 ALJHCNBK_00050 36340 4 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -83A>G None
M0143946 ALJHCNBK_00050 36362 3 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -105G>A None
M0143947 ALJHCNBK_00050 36370 4 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -113A>G None
M0143948 ALJHCNBK_00051 36488 4 Gut 0.09 protein_coding synonymous_variant LOW 63T>C Arg21Arg
M0143949 ALJHCNBK_00051 36605 3 Gut 0.07 protein_coding synonymous_variant LOW 180A>G Glu60Glu
M0143950 ALJHCNBK_00051 36644 3 Gut 0.07 protein_coding synonymous_variant LOW 219T>C Ala73Ala
M0143951 ALJHCNBK_00051 36647 3 Gut 0.07 protein_coding synonymous_variant LOW 222A>G Leu74Leu
M0143952 ALJHCNBK_00051 36674 3 Gut 0.07 protein_coding synonymous_variant LOW 249A>T Ala83Ala
M0143953 ALJHCNBK_00051 36680 3 Gut 0.07 protein_coding synonymous_variant LOW 255C>T Asn85Asn
M0143954 ALJHCNBK_00051 36686 3 Gut 0.07 protein_coding synonymous_variant LOW 261T>G Val87Val
M0143955 ALJHCNBK_00051 36738 3 Gut 0.07 protein_coding synonymous_variant LOW 313A>C Arg105Arg
M0143956 ALJHCNBK_00051 36749 3 Gut 0.07 protein_coding synonymous_variant LOW 324A>G Thr108Thr
M0143957 ALJHCNBK_00051 36755 3 Gut 0.07 protein_coding synonymous_variant LOW 330T>C Tyr110Tyr
M0143958 ALJHCNBK_00052 36818 4 Gut 0.09 protein_coding synonymous_variant LOW 87A>G Leu29Leu
M0143959 ALJHCNBK_00054 37347 4 Gut 0.09 protein_coding synonymous_variant LOW 252T>C Ala84Ala
M0143960 ALJHCNBK_00054 37443 4 Gut 0.09 protein_coding synonymous_variant LOW 156A>G Val52Val
M0143961 ALJHCNBK_00054 37446 4 Gut 0.09 protein_coding synonymous_variant LOW 153G>T Arg51Arg
M0143962 ALJHCNBK_00050 38082 4 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -1825T>C None
M0143963 ALJHCNBK_00050 38174 5 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -1917T>C None
M0143964 ALJHCNBK_00050 38189 5 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -1932G>A None
M0143965 ALJHCNBK_00050 38195 4 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -1938A>G None
M0143966 ALJHCNBK_00050 38207 4 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -1950G>A None
M0143967 ALJHCNBK_00050 38216 3 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -1959T>C None
M0143968 ALJHCNBK_00050 38222 4 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -1965A>G None
M0143969 ALJHCNBK_00050 38231 3 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -1974A>G None
M0143970 ALJHCNBK_00050 38239 3 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -1982G>C None
M0143971 ALJHCNBK_00050 38252 4 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -1995A>T None
M0143972 ALJHCNBK_00050 38335 6 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -2078T>C None
M0143973 ALJHCNBK_00050 38347 6 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -2090C>T None
M0143974 ALJHCNBK_00056 38352 3 Gut 0.07 protein_coding initiator_codon_variant LOW 1A>T Met1?
M0143975 ALJHCNBK_00056 38353 3 Gut 0.07 protein_coding start_lost HIGH 2T>A Met1?
M0143976 ALJHCNBK_00056 38359 3 Gut 0.07 protein_coding missense_variant MODERATE 8A>G His3Arg
M0143977 ALJHCNBK_00056 38368 6 Gut 0.13 protein_coding missense_variant MODERATE 17A>G Lys6Arg
M0143978 ALJHCNBK_00056 38377 6 Gut 0.13 protein_coding missense_variant MODERATE 26A>G Gln9Arg
M0143979 ALJHCNBK_00056 38392 6 Gut 0.13 protein_coding missense_variant MODERATE 41A>G Tyr14Cys
M0143980 ALJHCNBK_00056 38694 3 Gut 0.07 protein_coding missense_variant MODERATE 343G>A Gly115Ser
M0143981 ALJHCNBK_00056 38721 4 Gut 0.09 protein_coding synonymous_variant LOW 370T>C Leu124Leu
M0143982 ALJHCNBK_00056 38745 7 Gut 0.16 protein_coding missense_variant MODERATE 394C>T Leu132Phe
M0143983 ALJHCNBK_00056 38753 7 Gut 0.16 protein_coding synonymous_variant LOW 402A>G Gln134Gln
M0143984 ALJHCNBK_00056 38754 7 Gut 0.16 protein_coding missense_variant MODERATE 403G>A Val135Met
M0143985 ALJHCNBK_00056 38760 7 Gut 0.16 protein_coding missense_variant MODERATE 409G>A Val137Ile
M0143986 ALJHCNBK_00056 38769 7 Gut 0.16 protein_coding missense_variant MODERATE 418T>G Cys140Gly
M0143987 ALJHCNBK_00056 38789 7 Gut 0.16 protein_coding synonymous_variant LOW 438T>C Asp146Asp
M0143988 ALJHCNBK_00056 38790 6 Gut 0.13 protein_coding missense_variant MODERATE 439G>A Ala147Thr
M0143989 ALJHCNBK_00056 38796 7 Gut 0.16 protein_coding stop_gained HIGH 445C>T Gln149*
M0143990 ALJHCNBK_00056 38808 7 Gut 0.16 protein_coding missense_variant MODERATE 457A>G Ile153Val
M0143991 ALJHCNBK_00056 38820 6 Gut 0.13 protein_coding missense_variant MODERATE 469G>A Glu157Lys
M0143992 ALJHCNBK_00058 39345 9 Gut 0.20 protein_coding missense_variant MODERATE 172C>T Arg58Cys
M0143993 ALJHCNBK_00059 39606 8 Gut 0.18 protein_coding synonymous_variant LOW 246G>A Val82Val
M0143994 ALJHCNBK_00059 39640 7 Gut 0.16 protein_coding missense_variant MODERATE 212T>C Val71Ala
M0143995 ALJHCNBK_00059 39645 7 Gut 0.16 protein_coding synonymous_variant LOW 207A>G Glu69Glu
M0143996 ALJHCNBK_00059 39669 7 Gut 0.16 protein_coding synonymous_variant LOW 183A>G Leu61Leu
M0143997 ALJHCNBK_00059 39676 7 Gut 0.16 protein_coding missense_variant MODERATE 176T>C Val59Ala
M0143998 ALJHCNBK_00077 55961 8 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -4097T>A None
M0143999 ALJHCNBK_00077 55986 8 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -4122A>T None
M0144000 ALJHCNBK_00077 55993 8 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -4129T>G None
M0144001 ALJHCNBK_00077 55994 8 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -4130T>C None
M0144002 ALJHCNBK_00086 56124 8 Gut 0.18 protein_coding missense_variant MODERATE 94A>G Thr32Ala
M0144003 ALJHCNBK_00087 56294 8 Gut 0.18 protein_coding missense_variant MODERATE 122T>C Ile41Thr
M0144004 ALJHCNBK_00087 56296 8 Gut 0.18 protein_coding missense_variant MODERATE 124T>G Ser42Ala
M0144005 ALJHCNBK_00087 56301 8 Gut 0.18 protein_coding synonymous_variant LOW 129A>T Pro43Pro
M0144006 ALJHCNBK_00087 56306 8 Gut 0.18 protein_coding missense_variant MODERATE 134G>A Arg45Lys
M0144007 ALJHCNBK_00087 56307 8 Gut 0.18 protein_coding missense_variant MODERATE 135A>C Arg45Ser
M0144008 ALJHCNBK_00087 56356 8 Gut 0.18 protein_coding missense_variant MODERATE 184A>T Ile62Phe
M0144009 ALJHCNBK_00087 56367 7 Gut 0.16 protein_coding synonymous_variant LOW 195A>G Leu65Leu
M0144010 ALJHCNBK_00077 56599 4 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -4735G>A None
M0144011 ALJHCNBK_00073 48119 3 Gut 0.07 protein_coding synonymous_variant LOW 60T>C Phe20Phe
M0144012 ALJHCNBK_00057 43431 4 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -4367T>C None
M0144013 ALJHCNBK_00057 43509 5 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -4445C>T None
M0144014 ALJHCNBK_00057 43630 5 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -4566A>G None
M0144015 ALJHCNBK_00065 47994 4 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -3621A>G None
M0144016 ALJHCNBK_00077 51594 11 Gut 0.24 protein_coding missense_variant MODERATE 271C>T His91Tyr
M0144017 ALJHCNBK_00077 51595 11 Gut 0.24 protein_coding synonymous_variant LOW 270T>C Ile90Ile
M0144018 ALJHCNBK_00077 51708 11 Gut 0.24 protein_coding missense_variant MODERATE 157C>T Arg53Cys
M0144019 ALJHCNBK_00078 51957 11 Gut 0.24 protein_coding synonymous_variant LOW 456T>C His152His
M0144020 ALJHCNBK_00078 51959 11 Gut 0.24 protein_coding missense_variant MODERATE 454C>T His152Tyr
M0144021 ALJHCNBK_00079 52834 11 Gut 0.24 protein_coding missense_variant MODERATE 403A>G Thr135Ala
M0144022 ALJHCNBK_00065 44236 3 Gut 0.07 protein_coding synonymous_variant LOW 138A>G Pro46Pro
M0144023 ALJHCNBK_00065 44290 3 Gut 0.07 protein_coding synonymous_variant LOW 84G>A Ala28Ala
M0144024 ALJHCNBK_00065 44302 3 Gut 0.07 protein_coding synonymous_variant LOW 72A>G Arg24Arg
M0144025 ALJHCNBK_00077 50017 3 Gut 0.07 protein_coding synonymous_variant LOW 1848G>A Lys616Lys
M0144026 ALJHCNBK_00077 50512 3 Gut 0.07 protein_coding missense_variant MODERATE 1353C>A Asp451Glu
M0144027 ALJHCNBK_00077 50645 3 Gut 0.07 protein_coding missense_variant MODERATE 1220A>C Lys407Thr
M0144028 ALJHCNBK_00056 38413 5 Gut 0.11 protein_coding missense_variant MODERATE 62G>A Arg21His
M0144029 ALJHCNBK_00056 38463 5 Gut 0.11 protein_coding missense_variant MODERATE 112G>A Gly38Arg
M0144030 ALJHCNBK_00056 38481 5 Gut 0.11 protein_coding missense_variant MODERATE 130A>G Ser44Gly
M0144031 ALJHCNBK_00056 38535 5 Gut 0.11 protein_coding missense_variant MODERATE 184G>A Glu62Lys
M0144032 ALJHCNBK_00056 38538 5 Gut 0.11 protein_coding missense_variant MODERATE 187A>G Asn63Asp
M0144033 ALJHCNBK_00056 38572 3 Gut 0.07 protein_coding missense_variant MODERATE 221T>C Val74Ala
M0144034 ALJHCNBK_00056 38585 3 Gut 0.07 protein_coding synonymous_variant LOW 234G>A Gln78Gln
M0144035 ALJHCNBK_00056 38604 4 Gut 0.09 protein_coding missense_variant MODERATE 253C>T His85Tyr
M0144036 ALJHCNBK_00056 38613 4 Gut 0.09 protein_coding missense_variant MODERATE 262G>C Gly88Arg
M0144037 ALJHCNBK_00056 38634 4 Gut 0.09 protein_coding missense_variant MODERATE 283A>G Ile95Val
M0144038 ALJHCNBK_00056 38646 4 Gut 0.09 protein_coding missense_variant MODERATE 295T>A Ser99Thr
M0144039 ALJHCNBK_00056 38652 4 Gut 0.09 protein_coding missense_variant MODERATE 301G>A Ala101Thr
M0144040 ALJHCNBK_00056 38658 4 Gut 0.09 protein_coding missense_variant MODERATE 307T>A Tyr103Asn
M0144041 ALJHCNBK_00056 38685 5 Gut 0.11 protein_coding missense_variant MODERATE 334T>C Cys112Arg
M0144042 ALJHCNBK_00058 39178 4 Gut 0.09 protein_coding synonymous_variant LOW 339T>C Tyr113Tyr
M0144043 ALJHCNBK_00058 39184 4 Gut 0.09 protein_coding synonymous_variant LOW 333T>C Arg111Arg
M0144044 ALJHCNBK_00059 39624 5 Gut 0.11 protein_coding synonymous_variant LOW 228C>T Thr76Thr
M0144045 ALJHCNBK_00059 39625 5 Gut 0.11 protein_coding missense_variant MODERATE 227C>T Thr76Ile
M0144046 ALJHCNBK_00059 39660 5 Gut 0.11 protein_coding synonymous_variant LOW 192C>T Tyr64Tyr
M0144047 ALJHCNBK_00057 43471 3 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -4407G>A None
M0144048 ALJHCNBK_00057 43537 4 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -4473A>G None
M0144049 ALJHCNBK_00077 51341 9 Gut 0.20 protein_coding missense_variant MODERATE 524A>C Tyr175Ser
M0144050 ALJHCNBK_00079 53093 9 Gut 0.20 protein_coding synonymous_variant LOW 144T>C Ala48Ala
M0144051 ALJHCNBK_00059 39552 3 Gut 0.07 protein_coding synonymous_variant LOW 300T>C Cys100Cys
M0144052 ALJHCNBK_00051 35509 3 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -917T>C None
M0144053 ALJHCNBK_00051 35575 3 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -851C>T None
M0144054 ALJHCNBK_00050 35903 3 Gut 0.07 protein_coding missense_variant MODERATE 355G>A Val119Ile
M0144055 ALJHCNBK_00050 35982 3 Gut 0.07 protein_coding synonymous_variant LOW 276G>A Gln92Gln
M0144056 ALJHCNBK_00050 36074 3 Gut 0.07 protein_coding missense_variant MODERATE 184A>G Arg62Gly
M0144057 ALJHCNBK_00050 36173 3 Gut 0.07 protein_coding missense_variant MODERATE 85T>C Cys29Arg
M0144058 ALJHCNBK_00050 36182 3 Gut 0.07 protein_coding missense_variant MODERATE 76A>G Thr26Ala
M0144059 ALJHCNBK_00050 36209 3 Gut 0.07 protein_coding missense_variant MODERATE 49A>G Asn17Asp
M0144060 ALJHCNBK_00050 36273 3 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -16G>A None
M0144061 ALJHCNBK_00050 36349 3 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -92A>G None
M0144062 ALJHCNBK_00050 36412 3 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -155A>G None
M0144063 ALJHCNBK_00050 36424 3 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -167C>T None
M0144064 ALJHCNBK_00051 36459 3 Gut 0.07 protein_coding missense_variant MODERATE 34G>A Gly12Ser
M0144065 ALJHCNBK_00051 36587 3 Gut 0.07 protein_coding synonymous_variant LOW 162C>T Arg54Arg






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