Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C535
  Reference Plasmid   NZ_CP026642.1
  Reference Plasmid Size   250778
  Reference Plasmid GC Content   0.47
  Reference Plasmid Mobility Type   conjugative





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
M0168008 HDHDKFFL_00129 106822 3 Gut 1.00 protein_coding synonymous_variant LOW 180T>C Asp60Asp
M0168009 HDHDKFFL_00129 106838 3 Gut 1.00 protein_coding missense_variant MODERATE 196G>A Gly66Arg
M0168010 HDHDKFFL_00129 106845 3 Gut 1.00 protein_coding missense_variant MODERATE 203G>A Gly68Glu
M0168011 HDHDKFFL_00129 106846 3 Gut 1.00 protein_coding synonymous_variant LOW 204G>A Gly68Gly
M0168012 HDHDKFFL_00129 106858 3 Gut 1.00 protein_coding synonymous_variant LOW 216T>A Ala72Ala
M0168013 HDHDKFFL_00129 106889 3 Gut 1.00 protein_coding missense_variant MODERATE 247G>C Glu83Gln
M0168014 HDHDKFFL_00129 106892 3 Gut 1.00 protein_coding missense_variant MODERATE 250G>A Glu84Lys
M0168015 HDHDKFFL_00129 106903 3 Gut 1.00 protein_coding missense_variant MODERATE 261T>A Asp87Glu
M0168016 HDHDKFFL_00129 106918 3 Gut 1.00 protein_coding synonymous_variant LOW 276G>A Val92Val
M0168017 HDHDKFFL_00129 106957 3 Gut 1.00 protein_coding synonymous_variant LOW 315T>A Pro105Pro
M0168018 HDHDKFFL_00129 107059 3 Gut 1.00 protein_coding synonymous_variant LOW 417T>C Tyr139Tyr
M0168019 HDHDKFFL_00129 107105 3 Gut 1.00 protein_coding synonymous_variant LOW 463C>T Leu155Leu
M0168020 HDHDKFFL_00130 108141 3 Gut 1.00 protein_coding synonymous_variant LOW 273T>C Thr91Thr
M0168021 HDHDKFFL_00130 108192 3 Gut 1.00 protein_coding synonymous_variant LOW 324A>G Val108Val
M0168022 HDHDKFFL_00131 108488 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -312T>C None
M0168023 HDHDKFFL_00131 109033 3 Gut 1.00 protein_coding synonymous_variant LOW 234T>C Thr78Thr
M0168024 HDHDKFFL_00131 109205 3 Gut 1.00 protein_coding missense_variant MODERATE 406A>G Ser136Gly
M0168025 HDHDKFFL_00132 109907 3 Gut 1.00 protein_coding synonymous_variant LOW 447T>C Ala149Ala
M0168026 HDHDKFFL_00132 109966 3 Gut 1.00 protein_coding missense_variant MODERATE 506T>G Val169Gly
M0168027 HDHDKFFL_00132 109968 3 Gut 1.00 protein_coding missense_variant MODERATE 508A>C Thr170Pro
M0168028 HDHDKFFL_00133 110155 3 Gut 1.00 protein_coding synonymous_variant LOW 57A>G Glu19Glu
M0168029 HDHDKFFL_00133 110413 3 Gut 1.00 protein_coding synonymous_variant LOW 315A>C Thr105Thr
M0168030 HDHDKFFL_00133 110680 3 Gut 1.00 protein_coding synonymous_variant LOW 582C>T Ile194Ile
M0168031 HDHDKFFL_00134 110766 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -57G>A None
M0168032 HDHDKFFL_00134 110883 3 Gut 1.00 protein_coding synonymous_variant LOW 61C>T Leu21Leu
M0168033 HDHDKFFL_00134 110916 3 Gut 1.00 protein_coding missense_variant MODERATE 94A>G Ile32Val
M0168034 HDHDKFFL_00134 111092 3 Gut 1.00 protein_coding synonymous_variant LOW 270A>G Val90Val
M0168035 HDHDKFFL_00134 111104 3 Gut 1.00 protein_coding synonymous_variant LOW 282C>T Thr94Thr
M0168036 HDHDKFFL_00134 111158 3 Gut 1.00 protein_coding synonymous_variant LOW 336T>C Tyr112Tyr
M0168037 HDHDKFFL_00134 111164 3 Gut 1.00 protein_coding synonymous_variant LOW 342T>C Leu114Leu
M0168038 HDHDKFFL_00134 111280 3 Gut 1.00 protein_coding missense_variant MODERATE 458C>T Thr153Ile
M0168039 HDHDKFFL_00134 111362 3 Gut 1.00 protein_coding synonymous_variant LOW 540A>G Thr180Thr
M0168040 HDHDKFFL_00134 111365 3 Gut 1.00 protein_coding synonymous_variant LOW 543C>T Ala181Ala
M0168041 HDHDKFFL_00134 111395 3 Gut 1.00 protein_coding synonymous_variant LOW 573A>G Gly191Gly
M0168042 HDHDKFFL_00134 111555 3 Gut 1.00 protein_coding missense_variant MODERATE 733A>G Ile245Val
M0168043 HDHDKFFL_00134 111623 3 Gut 1.00 protein_coding synonymous_variant LOW 801A>G Glu267Glu
M0168044 HDHDKFFL_00135 111876 3 Gut 1.00 protein_coding missense_variant MODERATE 14T>C Val5Ala
M0168045 HDHDKFFL_00135 111963 3 Gut 1.00 protein_coding missense_variant MODERATE 101A>C Asp34Ala
M0168046 HDHDKFFL_00135 112049 3 Gut 1.00 protein_coding missense_variant MODERATE 187T>G Tyr63Asp
M0168047 HDHDKFFL_00135 112070 3 Gut 1.00 protein_coding missense_variant MODERATE 208C>G Pro70Ala
M0168048 HDHDKFFL_00135 112310 3 Gut 1.00 protein_coding missense_variant MODERATE 448G>A Gly150Arg
M0168049 HDHDKFFL_00135 112352 3 Gut 1.00 protein_coding missense_variant MODERATE 490G>A Val164Ile
M0168050 HDHDKFFL_00135 112402 3 Gut 1.00 protein_coding synonymous_variant LOW 540A>C Ile180Ile
M0168051 HDHDKFFL_00135 112451 3 Gut 1.00 protein_coding synonymous_variant LOW 589A>C Arg197Arg
M0168052 HDHDKFFL_00135 112512 3 Gut 1.00 protein_coding missense_variant MODERATE 650G>A Ser217Asn
M0168053 HDHDKFFL_00135 112552 3 Gut 1.00 protein_coding synonymous_variant LOW 690G>A Ser230Ser
M0168054 HDHDKFFL_00135 112913 3 Gut 1.00 protein_coding synonymous_variant LOW 1051C>T Leu351Leu
M0168055 HDHDKFFL_00135 112927 3 Gut 1.00 protein_coding synonymous_variant LOW 1065C>T Ile355Ile
M0168056 HDHDKFFL_00135 112966 3 Gut 1.00 protein_coding missense_variant MODERATE 1104C>A Asn368Lys
M0168057 HDHDKFFL_00135 113101 3 Gut 1.00 protein_coding missense_variant MODERATE 1239C>A Asn413Lys
M0168058 HDHDKFFL_00135 113173 3 Gut 1.00 protein_coding synonymous_variant LOW 1311G>A Arg437Arg
M0168059 HDHDKFFL_00135 113230 3 Gut 1.00 protein_coding synonymous_variant LOW 1368G>A Gln456Gln
M0168060 HDHDKFFL_00135 113341 3 Gut 1.00 protein_coding synonymous_variant LOW 1479A>G Thr493Thr
M0168061 HDHDKFFL_00136 113502 3 Gut 1.00 protein_coding missense_variant MODERATE 31G>A Gly11Arg
M0168062 HDHDKFFL_00136 113512 3 Gut 1.00 protein_coding missense_variant MODERATE 41C>T Ser14Phe
M0168063 HDHDKFFL_00136 113518 3 Gut 1.00 protein_coding missense_variant MODERATE 47T>G Val16Gly
M0168064 HDHDKFFL_00136 113729 3 Gut 1.00 protein_coding synonymous_variant LOW 258C>T Gly86Gly
M0168065 HDHDKFFL_00136 114225 3 Gut 1.00 protein_coding missense_variant MODERATE 754T>A Ser252Thr
M0168066 HDHDKFFL_00136 114356 3 Gut 1.00 protein_coding synonymous_variant LOW 885A>G Ala295Ala
M0168067 HDHDKFFL_00136 114474 3 Gut 1.00 protein_coding synonymous_variant LOW 1003T>C Leu335Leu
M0168068 HDHDKFFL_00136 114523 3 Gut 1.00 protein_coding missense_variant MODERATE 1052A>C Asn351Thr
M0168069 HDHDKFFL_00136 114572 3 Gut 1.00 protein_coding synonymous_variant LOW 1101C>T Val367Val
M0168070 HDHDKFFL_00136 114660 3 Gut 1.00 protein_coding missense_variant MODERATE 1189G>A Gly397Ser
M0168071 HDHDKFFL_00136 114737 3 Gut 1.00 protein_coding synonymous_variant LOW 1266C>T Asp422Asp
M0168072 HDHDKFFL_00136 114935 3 Gut 1.00 protein_coding synonymous_variant LOW 1464G>T Gly488Gly
M0168073 HDHDKFFL_00136 114998 3 Gut 1.00 protein_coding synonymous_variant LOW 1527G>A Leu509Leu






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
HDHDKFFL_00118 Tellurium (Te) 88 2.4e-97 1 191 1.0000 1.0000 experiment
HDHDKFFL_00119 Tellurium (Te) 95.3 5.5e-102 1 192 1.0000 1.0000 experiment
HDHDKFFL_00120 Tellurium (Te) 90.5 1.4e-175 1 346 1.0000 1.0000 experiment
HDHDKFFL_00121 Tellurium (Te) 92.4 5e-58 1 118 0.7815 0.9672 experiment
HDHDKFFL_00122 Tellurium (Te) 77.3 8.6e-158 59 399 0.8596 1.0118 experiment
HDHDKFFL_00123 Tellurium (Te) 99 1.9e-110 1 193 1.0000 1.0000 experiment
HDHDKFFL_00130 Tellurium (Te) 99.4 3.1e-79 1 155 1.0000 1.0000 experiment
HDHDKFFL_00118 Tellurium (Te) 89 8.4e-96 1 191 1.0000 1.0000 prediction
HDHDKFFL_00119 Tellurium (Te) 99.5 8.5e-104 1 192 1.0000 1.0000 prediction
HDHDKFFL_00120 Tellurium (Te) 100 7.4e-191 1 346 1.0000 1.0000 prediction
HDHDKFFL_00121 Tellurium (Te) 99.3 7.4e-79 1 151 1.0000 1.0000 prediction
HDHDKFFL_00122 Tellurium (Te) 78.8 1.4e-177 20 399 0.9574 0.9974 prediction
HDHDKFFL_00123 Tellurium (Te) 100 3.9e-109 1 193 1.0000 1.0000 prediction
HDHDKFFL_00130 Tellurium (Te) 100 1.9e-77 1 155 1.0000 1.0000 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
HDHDKFFL_00022 ARO:3002705 99.3 2.67e-274 1 404 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
HDHDKFFL_00028 ARO:3000316 100 1e-217 1 301 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
HDHDKFFL_00035 ARO:3001926 100 6.93e-204 1 291 1.0000 1.0000 cephalosporin CTX-M beta-lactamase antibiotic inactivation
HDHDKFFL_00045 ARO:3000186 99.4 0 1 639 1.0000 1.0000 tetracycline antibiotic tetracycline-resistant ribosomal protection protein antibiotic target protection
HDHDKFFL_00069 ARO:3000165 99.5 1.02e-277 1 390 0.9774 0.9198 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
HDHDKFFL_00076 ARO:3002790 100 1.11e-111 1 218 1.0000 1.0000 fluoroquinolone antibiotic quinolone resistance protein (qnr) antibiotic target protection
HDHDKFFL_00080 ARO:3002847 100 3.97e-114 31 180 0.8333 1.0000 rifamycin antibiotic rifampin ADP-ribosyltransferase (Arr) antibiotic inactivation
HDHDKFFL_00081 ARO:3002695 100 1.06e-299 1 419 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
HDHDKFFL_00082 ARO:3001405 100 2.23e-192 1 266 1.0000 1.0000 cephalosporin OXA beta-lactamase antibiotic inactivation
HDHDKFFL_00083 ARO:3002601 99.6 1.12e-188 9 271 0.9705 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
HDHDKFFL_00084 ARO:3002859 100 7.18e-117 1 157 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
HDHDKFFL_00086 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
HDHDKFFL_00087 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
HDHDKFFL_00088 ARO:3002660 99.3 4.37e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) 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
HDHDKFFL_00079 PHI:9804 int 100 4.4e-14 1 37 0.1000 1.0000 rodents gastroenteritis integrase 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
HDHDKFFL_00005 AVR60602.1|GH23 100 6.42e-134 1 179 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
HDHDKFFL_00022 2.A.1.2.110 98.3 1.7e-213 1 404 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
HDHDKFFL_00068 2.A.7.3.67 100 1.8e-159 1 294 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
HDHDKFFL_00069 2.A.1.2.4 99.7 5.2e-223 1 399 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
HDHDKFFL_00081 2.A.1.2.3 99.3 1.1e-231 1 419 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
HDHDKFFL_00120 2.A.109.1.1 100 1.2e-191 1 346 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.109 The Tellurium Ion Resistance (TerC) Family
HDHDKFFL_00259 1.E.53.1.7 100 5.5e-24 1 52 1.0000 0.7324 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family