Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1402
  Reference Plasmid   NZ_OM574792.1
  Reference Plasmid Size   53274
  Reference Plasmid GC Content   0.35
  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
M0208909 EFCKFNBJ_00010 11006 3 Gut 0.23 protein_coding synonymous_variant LOW 729G>A Ala243Ala
M0208910 EFCKFNBJ_00010 11057 3 Gut 0.23 protein_coding synonymous_variant LOW 780T>C Asn260Asn
M0208911 EFCKFNBJ_00010 11195 3 Gut 0.23 protein_coding synonymous_variant LOW 918A>G Gly306Gly
M0208912 EFCKFNBJ_00010 11216 3 Gut 0.23 protein_coding synonymous_variant LOW 939G>A Thr313Thr
M0208913 EFCKFNBJ_00010 11240 3 Gut 0.23 protein_coding synonymous_variant LOW 963A>G Gly321Gly
M0208914 EFCKFNBJ_00010 11245 3 Gut 0.23 protein_coding missense_variant MODERATE 968C>T Ala323Val
M0208915 EFCKFNBJ_00010 11273 3 Gut 0.23 protein_coding synonymous_variant LOW 996C>A Val332Val
M0208916 EFCKFNBJ_00010 11281 3 Gut 0.23 protein_coding missense_variant MODERATE 1004T>C Val335Ala
M0208917 EFCKFNBJ_00010 11285 3 Gut 0.23 protein_coding synonymous_variant LOW 1008C>T Asn336Asn
M0208918 EFCKFNBJ_00010 11291 3 Gut 0.23 protein_coding synonymous_variant LOW 1014A>G Gly338Gly
M0208919 EFCKFNBJ_00010 11292 3 Gut 0.23 protein_coding missense_variant MODERATE 1015G>T Ala339Ser
M0208920 EFCKFNBJ_00010 11300 3 Gut 0.23 protein_coding synonymous_variant LOW 1023G>T Gly341Gly
M0208921 EFCKFNBJ_00010 11303 3 Gut 0.23 protein_coding synonymous_variant LOW 1026T>G Gly342Gly
M0208922 EFCKFNBJ_00010 11327 3 Gut 0.23 protein_coding synonymous_variant LOW 1050C>T Asn350Asn
M0208923 EFCKFNBJ_00010 11354 3 Gut 0.23 protein_coding synonymous_variant LOW 1077G>A Gly359Gly
M0208924 EFCKFNBJ_00010 11369 3 Gut 0.23 protein_coding synonymous_variant LOW 1092C>T Tyr364Tyr
M0208925 EFCKFNBJ_00010 11375 3 Gut 0.23 protein_coding synonymous_variant LOW 1098G>A Gly366Gly
M0208926 EFCKFNBJ_00010 11378 3 Gut 0.23 protein_coding synonymous_variant LOW 1101C>T Arg367Arg
M0208927 EFCKFNBJ_00010 11408 3 Gut 0.23 protein_coding synonymous_variant LOW 1131G>A Glu377Glu
M0208928 EFCKFNBJ_00010 11633 3 Gut 0.23 protein_coding synonymous_variant LOW 1356G>C Gly452Gly
M0208929 EFCKFNBJ_00010 11690 3 Gut 0.23 protein_coding synonymous_variant LOW 1413C>T Gly471Gly
M0208930 EFCKFNBJ_00010 11693 3 Gut 0.23 protein_coding synonymous_variant LOW 1416A>G Ser472Ser
M0208931 EFCKFNBJ_00010 11699 3 Gut 0.23 protein_coding synonymous_variant LOW 1422A>G Val474Val
M0208932 EFCKFNBJ_00010 11807 3 Gut 0.23 protein_coding synonymous_variant LOW 1530G>C Ala510Ala
M0208933 EFCKFNBJ_00010 11846 3 Gut 0.23 protein_coding synonymous_variant LOW 1569C>T Ile523Ile
M0208934 EFCKFNBJ_00010 11861 3 Gut 0.23 protein_coding synonymous_variant LOW 1584C>T Gly528Gly
M0208935 EFCKFNBJ_00010 12002 3 Gut 0.23 protein_coding synonymous_variant LOW 1725T>C Phe575Phe
M0208936 EFCKFNBJ_00010 12006 3 Gut 0.23 protein_coding missense_variant MODERATE 1729G>C Gly577Arg
M0208937 EFCKFNBJ_00010 12032 3 Gut 0.23 protein_coding synonymous_variant LOW 1755T>A Val585Val
M0208938 EFCKFNBJ_00010 12038 3 Gut 0.23 protein_coding synonymous_variant LOW 1761T>G Val587Val
M0208939 EFCKFNBJ_00010 12041 3 Gut 0.23 protein_coding synonymous_variant LOW 1764G>A Pro588Pro
M0208940 EFCKFNBJ_00010 12044 3 Gut 0.23 protein_coding synonymous_variant LOW 1767C>T Asn589Asn
M0208941 EFCKFNBJ_00010 12062 3 Gut 0.23 protein_coding synonymous_variant LOW 1785T>C Gly595Gly
M0208942 EFCKFNBJ_00010 12072 3 Gut 0.23 protein_coding missense_variant MODERATE 1795A>G Ile599Val
M0208943 EFCKFNBJ_00010 12092 3 Gut 0.23 protein_coding synonymous_variant LOW 1815A>G Lys605Lys
M0208944 EFCKFNBJ_00010 12101 3 Gut 0.23 protein_coding synonymous_variant LOW 1824C>T Asp608Asp
M0208945 EFCKFNBJ_00010 12125 4 Gut 0.31 protein_coding synonymous_variant LOW 1848A>G Gly616Gly
M0208946 EFCKFNBJ_00010 12167 4 Gut 0.31 protein_coding synonymous_variant LOW 1890A>C Thr630Thr
M0208947 EFCKFNBJ_00010 12260 4 Gut 0.31 protein_coding synonymous_variant LOW 1983A>G Glu661Glu
M0208948 EFCKFNBJ_00010 12268 4 Gut 0.31 protein_coding missense_variant MODERATE 1991T>C Leu664Ser
M0208949 EFCKFNBJ_00010 12301 4 Gut 0.31 protein_coding missense_variant MODERATE 2024A>G Lys675Arg
M0208950 EFCKFNBJ_00010 12317 4 Gut 0.31 protein_coding synonymous_variant LOW 2040C>T Thr680Thr
M0208951 EFCKFNBJ_00010 12329 4 Gut 0.31 protein_coding synonymous_variant LOW 2052C>T Asp684Asp
M0208952 EFCKFNBJ_00012 14983 5 Gut 0.38 protein_coding missense_variant MODERATE 349G>A Glu117Lys
M0208953 EFCKFNBJ_00015 17160 5 Gut 0.38 protein_coding synonymous_variant LOW 825T>G Gly275Gly
M0208954 EFCKFNBJ_00016 17281 5 Gut 0.38 protein_coding synonymous_variant LOW 60T>C Val20Val
M0208955 EFCKFNBJ_00016 17317 5 Gut 0.38 protein_coding synonymous_variant LOW 96A>G Thr32Thr
M0208956 EFCKFNBJ_00016 17473 5 Gut 0.38 protein_coding synonymous_variant LOW 252C>T Ala84Ala
M0208957 EFCKFNBJ_00016 17545 5 Gut 0.38 protein_coding synonymous_variant LOW 324G>A Ala108Ala
M0208958 EFCKFNBJ_00016 17854 5 Gut 0.38 protein_coding synonymous_variant LOW 633C>T Tyr211Tyr
M0208959 EFCKFNBJ_00016 17857 5 Gut 0.38 protein_coding synonymous_variant LOW 636C>T Asn212Asn
M0208960 EFCKFNBJ_00016 17869 5 Gut 0.38 protein_coding synonymous_variant LOW 648A>G Lys216Lys
M0208961 EFCKFNBJ_00016 17917 5 Gut 0.38 protein_coding synonymous_variant LOW 696A>G Ala232Ala
M0208962 EFCKFNBJ_00016 17943 5 Gut 0.38 protein_coding missense_variant MODERATE 722C>T Pro241Leu
M0208963 EFCKFNBJ_00016 17962 5 Gut 0.38 protein_coding synonymous_variant LOW 741G>C Ser247Ser
M0208964 EFCKFNBJ_00016 17982 5 Gut 0.38 protein_coding missense_variant MODERATE 761C>A Ser254Tyr
M0208965 EFCKFNBJ_00016 18073 5 Gut 0.38 protein_coding synonymous_variant LOW 852T>G Ala284Ala
M0208966 EFCKFNBJ_00016 18266 5 Gut 0.38 protein_coding missense_variant MODERATE 1045A>G Ile349Val
M0208967 EFCKFNBJ_00016 18415 5 Gut 0.38 protein_coding synonymous_variant LOW 1194A>C Gly398Gly
M0208968 EFCKFNBJ_00017 18750 5 Gut 0.38 protein_coding synonymous_variant LOW 255T>G Val85Val
M0208969 EFCKFNBJ_00017 18755 5 Gut 0.38 protein_coding missense_variant MODERATE 260G>C Gly87Ala
M0208970 EFCKFNBJ_00017 18769 5 Gut 0.38 protein_coding missense_variant MODERATE 274G>T Val92Leu
M0208971 EFCKFNBJ_00017 18954 5 Gut 0.38 protein_coding synonymous_variant LOW 459A>G Lys153Lys
M0208972 EFCKFNBJ_00017 18960 5 Gut 0.38 protein_coding synonymous_variant LOW 465G>A Thr155Thr
M0208973 EFCKFNBJ_00017 18962 5 Gut 0.38 protein_coding missense_variant MODERATE 467A>G Glu156Gly
M0208974 EFCKFNBJ_00017 18987 5 Gut 0.38 protein_coding synonymous_variant LOW 492A>G Arg164Arg
M0208975 EFCKFNBJ_00017 19021 5 Gut 0.38 protein_coding missense_variant MODERATE 526G>A Ala176Thr
M0208976 EFCKFNBJ_00017 19032 5 Gut 0.38 protein_coding synonymous_variant LOW 537C>A Gly179Gly
M0208977 EFCKFNBJ_00017 19044 5 Gut 0.38 protein_coding synonymous_variant LOW 549T>C Tyr183Tyr
M0208978 EFCKFNBJ_00017 19065 5 Gut 0.38 protein_coding synonymous_variant LOW 570G>A Glu190Glu
M0208979 EFCKFNBJ_00018 19132 5 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -13G>A None
M0208980 EFCKFNBJ_00018 19136 5 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -9G>A None
M0208981 EFCKFNBJ_00018 19144 5 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -1G>A None
M0208982 EFCKFNBJ_00018 19181 5 Gut 0.38 protein_coding missense_variant MODERATE 37C>A Leu13Met
M0208983 EFCKFNBJ_00018 19372 5 Gut 0.38 protein_coding synonymous_variant LOW 228G>T Pro76Pro
M0208984 EFCKFNBJ_00018 19396 5 Gut 0.38 protein_coding synonymous_variant LOW 252C>A Thr84Thr
M0208985 EFCKFNBJ_00018 19420 5 Gut 0.38 protein_coding synonymous_variant LOW 276G>A Thr92Thr
M0208986 EFCKFNBJ_00018 19462 5 Gut 0.38 protein_coding synonymous_variant LOW 318G>A Arg106Arg
M0208987 EFCKFNBJ_00025 24050 3 Gut 0.23 protein_coding synonymous_variant LOW 1443G>A Glu481Glu
M0208988 EFCKFNBJ_00025 24092 3 Gut 0.23 protein_coding synonymous_variant LOW 1485A>G Pro495Pro
M0208989 EFCKFNBJ_00025 24098 4 Gut 0.31 protein_coding synonymous_variant LOW 1491A>G Gly497Gly






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
EFCKFNBJ_00010 VFG002164 AS 96.8 0 1 1305 1.0 1 Adherence aggregation substance PrgB/Asc10 experiment
EFCKFNBJ_00010 VFG002164 AS 96.8 0 1 1305 1.0 1 Adherence aggregation substance PrgB/Asc10 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
EFCKFNBJ_00044 ARO:3002704 98.9 0 1 475 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
EFCKFNBJ_00046 ARO:3003746 100 0 1 639 1.0000 0.9756 oxazolidinone antibiotic Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins antibiotic target protection






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
EFCKFNBJ_00030 PHI:2999 EF0026 94.4 5.2e-89 1 162 1.0000 1.0000 moths nosocomial infection None increased virulence (hypervirulence)






        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
EFCKFNBJ_00016 BBD29393.1|GH73 100 4.65000000000497e-313 1 423 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
EFCKFNBJ_00034 3.A.7.19.1 82.2 1.9e-218 1 444 1.0000 0.7932 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
EFCKFNBJ_00046 3.A.1.211.25 99.7 0 1 639 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily