Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C162
  Reference Plasmid   CP093089.1
  Reference Plasmid Size   93379
  Reference Plasmid GC Content   0.54
  Reference Plasmid Mobility Type   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
M0145880 JMPCBMOH_00009 10117 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -2243A>T None
M0145881 JMPCBMOH_00010 12972 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -3463C>T None
M0145882 JMPCBMOH_00010 12988 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -3479C>T None
M0145883 JMPCBMOH_00010 13126 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -3617G>A None
M0145884 JMPCBMOH_00019 15313 3 Gut 0.75 protein_coding synonymous_variant LOW 552G>A Glu184Glu
M0145885 JMPCBMOH_00019 15322 3 Gut 0.75 protein_coding synonymous_variant LOW 543A>T Pro181Pro
M0145886 JMPCBMOH_00019 15333 3 Gut 0.75 protein_coding missense_variant MODERATE 532G>A Gly178Arg
M0145887 JMPCBMOH_00019 15339 3 Gut 0.75 protein_coding synonymous_variant LOW 526C>T Leu176Leu
M0145888 JMPCBMOH_00019 15343 3 Gut 0.75 protein_coding missense_variant MODERATE 522G>C Leu174Phe
M0145889 JMPCBMOH_00019 15344 3 Gut 0.75 protein_coding missense_variant MODERATE 521T>G Leu174Trp
M0145890 JMPCBMOH_00019 15427 3 Gut 0.75 protein_coding synonymous_variant LOW 438T>C Ala146Ala
M0145891 JMPCBMOH_00019 15451 3 Gut 0.75 protein_coding synonymous_variant LOW 414C>T Gly138Gly
M0145892 JMPCBMOH_00019 15481 3 Gut 0.75 protein_coding synonymous_variant LOW 384A>G Lys128Lys
M0145893 JMPCBMOH_00019 15493 3 Gut 0.75 protein_coding synonymous_variant LOW 372G>A Arg124Arg
M0145894 JMPCBMOH_00019 15513 3 Gut 0.75 protein_coding missense_variant MODERATE 352T>G Phe118Val
M0145895 JMPCBMOH_00019 15530 3 Gut 0.75 protein_coding missense_variant MODERATE 335A>G His112Arg
M0145896 JMPCBMOH_00019 15532 3 Gut 0.75 protein_coding synonymous_variant LOW 333T>C Asn111Asn
M0145897 JMPCBMOH_00019 15535 3 Gut 0.75 protein_coding missense_variant MODERATE 330A>G Ile110Met
M0145898 JMPCBMOH_00019 15537 3 Gut 0.75 protein_coding missense_variant MODERATE 328A>G Ile110Val
M0145899 JMPCBMOH_00019 15609 3 Gut 0.75 protein_coding missense_variant MODERATE 256G>A Ala86Thr
M0145900 JMPCBMOH_00019 15685 3 Gut 0.75 protein_coding synonymous_variant LOW 180G>A Gln60Gln
M0145901 JMPCBMOH_00021 16385 3 Gut 0.75 protein_coding synonymous_variant LOW 162A>T Thr54Thr
M0145902 JMPCBMOH_00019 16605 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -741T>C None
M0145903 JMPCBMOH_00019 16712 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -848G>A None
M0145904 JMPCBMOH_00019 16726 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -862T>C None
M0145905 JMPCBMOH_00019 16728 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -864A>G None
M0145906 JMPCBMOH_00022 17051 3 Gut 0.75 protein_coding missense_variant MODERATE 112G>A Asp38Asn
M0145907 JMPCBMOH_00022 17215 3 Gut 0.75 protein_coding synonymous_variant LOW 276G>A Val92Val
M0145908 JMPCBMOH_00022 17218 3 Gut 0.75 protein_coding synonymous_variant LOW 279A>G Leu93Leu
M0145909 JMPCBMOH_00022 17227 3 Gut 0.75 protein_coding synonymous_variant LOW 288A>G Glu96Glu
M0145910 JMPCBMOH_00022 17266 3 Gut 0.75 protein_coding synonymous_variant LOW 327T>C Ser109Ser
M0145911 JMPCBMOH_00022 17275 3 Gut 0.75 protein_coding synonymous_variant LOW 336C>A Gly112Gly
M0145912 JMPCBMOH_00022 17305 3 Gut 0.75 protein_coding missense_variant MODERATE 366G>T Glu122Asp
M0145913 JMPCBMOH_00022 17323 3 Gut 0.75 protein_coding synonymous_variant LOW 384C>T Thr128Thr
M0145914 JMPCBMOH_00022 17338 3 Gut 0.75 protein_coding synonymous_variant LOW 399C>A Ala133Ala
M0145915 JMPCBMOH_00022 17358 3 Gut 0.75 protein_coding missense_variant MODERATE 419G>A Gly140Asp
M0145916 JMPCBMOH_00022 17360 3 Gut 0.75 protein_coding missense_variant MODERATE 421T>A Phe141Ile
M0145917 JMPCBMOH_00022 17366 3 Gut 0.75 protein_coding missense_variant MODERATE 427A>G Ser143Gly
M0145918 JMPCBMOH_00022 17410 3 Gut 0.75 protein_coding synonymous_variant LOW 471T>C Asn157Asn
M0145919 JMPCBMOH_00022 17413 3 Gut 0.75 protein_coding synonymous_variant LOW 474A>C Val158Val
M0145920 JMPCBMOH_00022 17458 3 Gut 0.75 protein_coding synonymous_variant LOW 519C>G Pro173Pro
M0145921 JMPCBMOH_00022 17521 3 Gut 0.75 protein_coding synonymous_variant LOW 582G>A Ala194Ala
M0145922 JMPCBMOH_00022 17536 3 Gut 0.75 protein_coding synonymous_variant LOW 597G>C Thr199Thr
M0145923 JMPCBMOH_00022 17541 3 Gut 0.75 protein_coding missense_variant MODERATE 602A>G Gln201Arg
M0145924 JMPCBMOH_00022 17561 3 Gut 0.75 protein_coding missense_variant MODERATE 622G>T Val208Leu
M0145925 JMPCBMOH_00022 17562 3 Gut 0.75 protein_coding missense_variant MODERATE 623T>G Val208Gly
M0145926 JMPCBMOH_00022 17563 3 Gut 0.75 protein_coding synonymous_variant LOW 624G>T Val208Val
M0145927 JMPCBMOH_00022 17572 3 Gut 0.75 protein_coding missense_variant MODERATE 633G>C Glu211Asp
M0145928 JMPCBMOH_00022 17573 3 Gut 0.75 protein_coding missense_variant MODERATE 634G>C Val212Leu
M0145929 JMPCBMOH_00022 17713 3 Gut 0.75 protein_coding synonymous_variant LOW 774T>C Cys258Cys
M0145930 JMPCBMOH_00022 17714 3 Gut 0.75 protein_coding missense_variant MODERATE 775G>A Asp259Asn
M0145931 JMPCBMOH_00022 17845 3 Gut 0.75 protein_coding missense_variant MODERATE 906T>G Asn302Lys
M0145932 JMPCBMOH_00022 17857 3 Gut 0.75 protein_coding synonymous_variant LOW 918T>C Tyr306Tyr
M0145933 JMPCBMOH_00022 17860 3 Gut 0.75 protein_coding synonymous_variant LOW 921C>T Gly307Gly
M0145934 JMPCBMOH_00019 18036 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -2172T>C None
M0145935 JMPCBMOH_00019 18037 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -2173G>A None
M0145936 JMPCBMOH_00019 18106 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -2242T>C None
M0145937 JMPCBMOH_00019 18118 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -2254C>T None
M0145938 JMPCBMOH_00023 18786 3 Gut 0.75 protein_coding synonymous_variant LOW 537T>C Val179Val
M0145939 JMPCBMOH_00023 18795 3 Gut 0.75 protein_coding synonymous_variant LOW 546C>T Leu182Leu
M0145940 JMPCBMOH_00023 18900 3 Gut 0.75 protein_coding synonymous_variant LOW 651G>T Ala217Ala
M0145941 JMPCBMOH_00025 19222 3 Gut 0.75 protein_coding missense_variant MODERATE 55A>T Asn19Tyr
M0145942 JMPCBMOH_00025 19240 3 Gut 0.75 protein_coding missense_variant MODERATE 73C>G Leu25Val
M0145943 JMPCBMOH_00025 19243 3 Gut 0.75 protein_coding missense_variant MODERATE 76A>G Ile26Val
M0145944 JMPCBMOH_00025 19260 3 Gut 0.75 protein_coding missense_variant MODERATE 93G>T Glu31Asp
M0145945 JMPCBMOH_00025 19275 3 Gut 0.75 protein_coding synonymous_variant LOW 108C>T Ala36Ala
M0145946 JMPCBMOH_00025 19328 3 Gut 0.75 protein_coding missense_variant MODERATE 161A>G His54Arg
M0145947 JMPCBMOH_00025 19379 3 Gut 0.75 protein_coding missense_variant MODERATE 212C>G Ala71Gly
M0145948 JMPCBMOH_00025 19380 3 Gut 0.75 protein_coding synonymous_variant LOW 213C>T Ala71Ala
M0145949 JMPCBMOH_00025 19383 3 Gut 0.75 protein_coding synonymous_variant LOW 216T>G Ala72Ala
M0145950 JMPCBMOH_00025 19421 3 Gut 0.75 protein_coding missense_variant MODERATE 254T>A Leu85Gln
M0145951 JMPCBMOH_00025 19477 3 Gut 0.75 protein_coding synonymous_variant LOW 310C>T Leu104Leu
M0145952 JMPCBMOH_00025 19485 3 Gut 0.75 protein_coding synonymous_variant LOW 318A>G Lys106Lys
M0145953 JMPCBMOH_00025 19515 3 Gut 0.75 protein_coding synonymous_variant LOW 348T>C Leu116Leu
M0145954 JMPCBMOH_00025 19516 3 Gut 0.75 protein_coding missense_variant MODERATE 349G>A Ala117Thr
M0145955 JMPCBMOH_00025 19530 3 Gut 0.75 protein_coding synonymous_variant LOW 363T>C Cys121Cys
M0145956 JMPCBMOH_00025 19533 3 Gut 0.75 protein_coding synonymous_variant LOW 366T>C Val122Val
M0145957 JMPCBMOH_00025 19539 3 Gut 0.75 protein_coding synonymous_variant LOW 372C>T Arg124Arg
M0145958 JMPCBMOH_00025 19548 3 Gut 0.75 protein_coding synonymous_variant LOW 381A>G Ala127Ala
M0145959 JMPCBMOH_00025 19552 3 Gut 0.75 protein_coding missense_variant MODERATE 385A>G Ile129Val
M0145960 JMPCBMOH_00025 19568 3 Gut 0.75 protein_coding missense_variant MODERATE 401C>G Thr134Ser
M0145961 JMPCBMOH_00026 19659 3 Gut 0.75 protein_coding missense_variant MODERATE 58A>G Lys20Glu
M0145962 JMPCBMOH_00026 19670 3 Gut 0.75 protein_coding synonymous_variant LOW 69T>C Asn23Asn
M0145963 JMPCBMOH_00026 19677 3 Gut 0.75 protein_coding missense_variant MODERATE 76G>A Val26Ile
M0145964 JMPCBMOH_00026 19694 3 Gut 0.75 protein_coding synonymous_variant LOW 93T>C Arg31Arg
M0145965 JMPCBMOH_00026 19745 3 Gut 0.75 protein_coding synonymous_variant LOW 144A>T Arg48Arg
M0145966 JMPCBMOH_00026 19748 3 Gut 0.75 protein_coding synonymous_variant LOW 147T>C Asn49Asn
M0145967 JMPCBMOH_00026 19754 3 Gut 0.75 protein_coding missense_variant MODERATE 153C>G Asn51Lys
M0145968 JMPCBMOH_00026 19778 3 Gut 0.75 protein_coding synonymous_variant LOW 177C>T Tyr59Tyr
M0145969 JMPCBMOH_00026 19781 3 Gut 0.75 protein_coding synonymous_variant LOW 180G>T Val60Val
M0145970 JMPCBMOH_00026 19783 3 Gut 0.75 protein_coding missense_variant MODERATE 182G>T Arg61Leu
M0145971 JMPCBMOH_00026 19808 3 Gut 0.75 protein_coding synonymous_variant LOW 207G>C Thr69Thr
M0145972 JMPCBMOH_00026 19835 3 Gut 0.75 protein_coding synonymous_variant LOW 234A>G Val78Val
M0145973 JMPCBMOH_00026 20054 3 Gut 0.75 protein_coding missense_variant MODERATE 453C>A Asp151Glu
M0145974 JMPCBMOH_00026 20312 3 Gut 0.75 protein_coding synonymous_variant LOW 711T>C Pro237Pro
M0145975 JMPCBMOH_00026 20319 3 Gut 0.75 protein_coding missense_variant MODERATE 718T>C Ser240Pro
M0145976 JMPCBMOH_00019 20443 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -4579G>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







        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
JMPCBMOH_00009 Hydrogen Peroxide (H2O2) [class: Peroxides], Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) [class: Hydrazone], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Sodium Nitrite (NaNo2) [class: Nitrites] 73.4 2.4e-154 8 369 0.9864 0.9973 experiment
JMPCBMOH_00009 Hydrogen Peroxide (H2O2) [class: Peroxides], Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) [class: Hydrazone], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Sodium Nitrite (NaNo2) [class: Nitrites] 81.2 6.7e-174 8 369 0.9810 0.9864 prediction






        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
JMPCBMOH_00009 ARO:3004114 80.7 3.31e-220 8 369 0.9810 0.9864 monobactam General Bacterial Porin with reduced permeability to beta-lactams reduced permeability to antibiotic






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
JMPCBMOH_00009 PHI:9892 OmpC 79.1 6.2e-170 8 369 0.9810 0.9866 primates shigellosis outer membrane protein C reduced virulence






        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
JMPCBMOH_00083 AWF74994.1|GH23 100 1.74e-118 1 166 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
JMPCBMOH_00009 1.B.1.1.3 78.7 2.2e-167 8 369 0.9810 0.9864 1 Channels/Pores 1.B β-Barrel Porins 1.B.1 The General Bacterial Porin (GBP) Family
JMPCBMOH_00053 1.E.53.1.10 90.7 8.4e-17 9 51 0.8431 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family