Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1656
  Reference Plasmid   1111525849484910_bin.15__k141_136913
  Reference Plasmid Size   42853
  Reference Plasmid GC Content   0.64
  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
M0010111 AMMFCDDB_00003 4594 3 Skin 0.03 protein_coding synonymous_variant LOW 1959T>G Ala653Ala
M0010112 AMMFCDDB_00003 4600 3 Skin 0.03 protein_coding synonymous_variant LOW 1965G>C Ala655Ala
M0010113 AMMFCDDB_00003 4603 3 Skin 0.03 protein_coding synonymous_variant LOW 1968T>C Ile656Ile
M0010114 AMMFCDDB_00003 4606 3 Skin 0.03 protein_coding synonymous_variant LOW 1971C>G Ala657Ala
M0010115 AMMFCDDB_00003 4609 27 Skin 0.24 protein_coding synonymous_variant LOW 1974C>A Ala658Ala
M0010116 AMMFCDDB_00003 4612 3 Skin 0.03 protein_coding synonymous_variant LOW 1977G>C Ala659Ala
M0010117 AMMFCDDB_00003 4613 3 Skin 0.03 protein_coding synonymous_variant LOW 1978C>T Leu660Leu
M0010118 AMMFCDDB_00003 4622 3 Skin 0.03 protein_coding missense_variant MODERATE 1987A>C Lys663Gln
M0010119 AMMFCDDB_00003 4633 3 Skin 0.03 protein_coding synonymous_variant LOW 1998C>T Asp666Asp
M0010120 AMMFCDDB_00003 4672 3 Skin 0.03 protein_coding synonymous_variant LOW 2037C>G Pro679Pro
M0010121 AMMFCDDB_00003 4675 3 Skin 0.03 protein_coding synonymous_variant LOW 2040G>A Val680Val
M0010122 AMMFCDDB_00003 4696 3 Skin 0.03 protein_coding synonymous_variant LOW 2061T>C Gly687Gly
M0010123 AMMFCDDB_00003 4732 3 Skin 0.03 protein_coding synonymous_variant LOW 2097C>G Leu699Leu
M0010124 AMMFCDDB_00003 4745 3 Skin 0.03 protein_coding synonymous_variant LOW 2110T>C Leu704Leu
M0010125 AMMFCDDB_00004 5951 50 Skin 0.45 protein_coding missense_variant MODERATE 140G>T Arg47Leu
M0010126 AMMFCDDB_00011 15796 60 Skin 0.54 protein_coding synonymous_variant LOW 384G>A Gln128Gln
M0010127 AMMFCDDB_00012 17169 42 Skin 0.38 protein_coding synonymous_variant LOW 666C>T Ile222Ile
M0010128 AMMFCDDB_00018 22854 23 Skin 0.21 protein_coding synonymous_variant LOW 654A>G Ala218Ala
M0010129 AMMFCDDB_00022 26253 3 Skin 0.03 protein_coding synonymous_variant LOW 132T>C Thr44Thr
M0010130 AMMFCDDB_00023 27178 5 Skin 0.04 protein_coding synonymous_variant LOW 2959C>T Leu987Leu
M0010131 AMMFCDDB_00023 27583 21 Skin 0.19 protein_coding missense_variant MODERATE 2554C>T Arg852Cys
M0010132 AMMFCDDB_00023 29174 19 Skin 0.17 protein_coding synonymous_variant LOW 963T>C Phe321Phe
M0010133 AMMFCDDB_00023 29180 19 Skin 0.17 protein_coding synonymous_variant LOW 957T>C Val319Val
M0010134 AMMFCDDB_00003 3040 5 Skin 0.04 protein_coding synonymous_variant LOW 405C>G Ser135Ser
M0010135 AMMFCDDB_00003 3070 5 Skin 0.04 protein_coding synonymous_variant LOW 435A>C Thr145Thr
M0010136 AMMFCDDB_00003 4618 24 Skin 0.21 protein_coding synonymous_variant LOW 1983C>T Asn661Asn
M0010137 AMMFCDDB_00006 8855 3 Skin 0.03 protein_coding missense_variant MODERATE 1760T>G Ile587Ser
M0010138 AMMFCDDB_00006 8870 3 Skin 0.03 protein_coding missense_variant MODERATE 1745T>C Val582Ala
M0010139 AMMFCDDB_00006 10654 12 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -40G>C None
M0010140 AMMFCDDB_00012 16811 5 Skin 0.04 protein_coding missense_variant MODERATE 1024G>A Asp342Asn
M0010141 AMMFCDDB_00012 16820 5 Skin 0.04 protein_coding synonymous_variant LOW 1015T>C Leu339Leu
M0010142 AMMFCDDB_00012 16830 5 Skin 0.04 protein_coding synonymous_variant LOW 1005A>G Ser335Ser
M0010143 AMMFCDDB_00012 16833 5 Skin 0.04 protein_coding synonymous_variant LOW 1002T>C Tyr334Tyr
M0010144 AMMFCDDB_00012 16860 5 Skin 0.04 protein_coding synonymous_variant LOW 975T>C Ile325Ile
M0010145 AMMFCDDB_00012 16866 5 Skin 0.04 protein_coding missense_variant MODERATE 969G>T Gln323His
M0010146 AMMFCDDB_00012 16887 5 Skin 0.04 protein_coding synonymous_variant LOW 948T>C Leu316Leu
M0010147 AMMFCDDB_00012 16889 5 Skin 0.04 protein_coding missense_variant MODERATE 946C>A Leu316Ile
M0010148 AMMFCDDB_00012 16893 5 Skin 0.04 protein_coding synonymous_variant LOW 942C>T Asp314Asp
M0010149 AMMFCDDB_00012 16899 5 Skin 0.04 protein_coding synonymous_variant LOW 936G>A Glu312Glu
M0010150 AMMFCDDB_00003 5209 3 Skin 0.03 protein_coding synonymous_variant LOW 2574G>A Gln858Gln
M0010151 AMMFCDDB_00003 5212 3 Skin 0.03 protein_coding synonymous_variant LOW 2577A>G Glu859Glu
M0010152 AMMFCDDB_00006 9445 8 Skin 0.07 protein_coding synonymous_variant LOW 1170C>G Ala390Ala
M0010153 AMMFCDDB_00007 10843 5 Skin 0.04 protein_coding synonymous_variant LOW 69C>A Gly23Gly
M0010154 AMMFCDDB_00010 13890 4 Skin 0.04 protein_coding synonymous_variant LOW 96A>G Val32Val
M0010155 AMMFCDDB_00010 14321 9 Skin 0.08 protein_coding missense_variant MODERATE 527T>C Ile176Thr
M0010156 AMMFCDDB_00011 15589 8 Skin 0.07 protein_coding synonymous_variant LOW 177T>C Gly59Gly
M0010157 AMMFCDDB_00011 15601 8 Skin 0.07 protein_coding synonymous_variant LOW 189C>T Ala63Ala
M0010158 AMMFCDDB_00012 16740 3 Skin 0.03 protein_coding synonymous_variant LOW 1095C>T Ser365Ser
M0010159 AMMFCDDB_00012 16746 3 Skin 0.03 protein_coding synonymous_variant LOW 1089T>C Ser363Ser
M0010160 AMMFCDDB_00012 16748 3 Skin 0.03 protein_coding missense_variant MODERATE 1087T>A Ser363Thr
M0010161 AMMFCDDB_00012 16752 3 Skin 0.03 protein_coding missense_variant MODERATE 1083C>G Phe361Leu
M0010162 AMMFCDDB_00012 16754 3 Skin 0.03 protein_coding missense_variant MODERATE 1081T>C Phe361Leu
M0010163 AMMFCDDB_00012 16755 3 Skin 0.03 protein_coding synonymous_variant LOW 1080A>G Glu360Glu
M0010164 AMMFCDDB_00012 16766 3 Skin 0.03 protein_coding synonymous_variant LOW 1069T>C Leu357Leu
M0010165 AMMFCDDB_00003 5461 3 Skin 0.03 protein_coding synonymous_variant LOW 2826G>A Val942Val
M0010166 AMMFCDDB_00003 5491 3 Skin 0.03 protein_coding synonymous_variant LOW 2856T>C Ile952Ile
M0010167 AMMFCDDB_00010 15090 10 Skin 0.09 protein_coding synonymous_variant LOW 1296C>T Asp432Asp
M0010168 AMMFCDDB_00012 20179 3 Skin 0.03 protein_coding upstream_gene_variant MODIFIER -2345G>A None
M0010169 AMMFCDDB_00004 6036 4 Skin 0.04 protein_coding synonymous_variant LOW 225T>C Arg75Arg
M0010170 AMMFCDDB_00006 10240 6 Skin 0.05 protein_coding synonymous_variant LOW 375A>G Lys125Lys
M0010171 AMMFCDDB_00006 8515 11 Skin 0.10 protein_coding synonymous_variant LOW 2100T>C Ser700Ser
M0010172 AMMFCDDB_00007 10788 4 Skin 0.04 protein_coding missense_variant MODERATE 14T>A Ile5Asn
M0010173 AMMFCDDB_00007 10810 4 Skin 0.04 protein_coding synonymous_variant LOW 36G>C Thr12Thr
M0010174 AMMFCDDB_00004 6465 7 Skin 0.06 protein_coding synonymous_variant LOW 654C>G Val218Val
M0010175 AMMFCDDB_00005 7343 3 Skin 0.03 protein_coding upstream_gene_variant MODIFIER -54T>C None
M0010176 AMMFCDDB_00005 7930 7 Skin 0.06 protein_coding synonymous_variant LOW 534G>A Gln178Gln
M0010177 AMMFCDDB_00005 7933 8 Skin 0.07 protein_coding synonymous_variant LOW 537A>G Val179Val
M0010178 AMMFCDDB_00005 7936 7 Skin 0.06 protein_coding synonymous_variant LOW 540T>C His180His
M0010179 AMMFCDDB_00006 9169 3 Skin 0.03 protein_coding synonymous_variant LOW 1446C>G Leu482Leu
M0010180 AMMFCDDB_00006 9184 3 Skin 0.03 protein_coding synonymous_variant LOW 1431A>G Thr477Thr
M0010181 AMMFCDDB_00012 16353 9 Skin 0.08 protein_coding synonymous_variant LOW 1482T>C Gly494Gly
M0010182 AMMFCDDB_00010 14587 7 Skin 0.06 protein_coding synonymous_variant LOW 793C>T Leu265Leu
M0010183 AMMFCDDB_00025 31772 3 Skin 0.03 protein_coding missense_variant MODERATE 407A>G Glu136Gly
M0010184 AMMFCDDB_00003 5557 5 Skin 0.04 protein_coding synonymous_variant LOW 2922G>A Glu974Glu
M0010185 AMMFCDDB_00003 4978 7 Skin 0.06 protein_coding synonymous_variant LOW 2343A>C Val781Val
M0010186 AMMFCDDB_00003 5011 3 Skin 0.03 protein_coding synonymous_variant LOW 2376G>A Glu792Glu
M0010187 AMMFCDDB_00003 5024 5 Skin 0.04 protein_coding synonymous_variant LOW 2389C>T Leu797Leu
M0010188 AMMFCDDB_00003 5044 5 Skin 0.04 protein_coding synonymous_variant LOW 2409C>G Leu803Leu
M0010189 AMMFCDDB_00003 5056 3 Skin 0.03 protein_coding synonymous_variant LOW 2421C>T Ile807Ile
M0010190 AMMFCDDB_00007 10976 6 Skin 0.05 protein_coding missense_variant MODERATE 202T>A Trp68Arg
M0010191 AMMFCDDB_00003 5614 3 Skin 0.03 protein_coding synonymous_variant LOW 2979C>T Gly993Gly
M0010192 AMMFCDDB_00003 5620 3 Skin 0.03 protein_coding synonymous_variant LOW 2985A>G Val995Val
M0010193 AMMFCDDB_00003 5659 3 Skin 0.03 protein_coding synonymous_variant LOW 3024C>T Arg1008Arg
M0010194 AMMFCDDB_00003 5662 3 Skin 0.03 protein_coding synonymous_variant LOW 3027T>C His1009His
M0010195 AMMFCDDB_00003 5698 3 Skin 0.03 protein_coding synonymous_variant LOW 3063C>G Gly1021Gly
M0010196 AMMFCDDB_00003 5704 3 Skin 0.03 protein_coding synonymous_variant LOW 3069T>C Thr1023Thr
M0010197 AMMFCDDB_00018 22470 3 Skin 0.03 protein_coding synonymous_variant LOW 1038T>C Ala346Ala
M0010198 AMMFCDDB_00018 22569 3 Skin 0.03 protein_coding synonymous_variant LOW 939T>C Ala313Ala
M0010199 AMMFCDDB_00018 22602 3 Skin 0.03 protein_coding synonymous_variant LOW 906A>C Arg302Arg
M0010200 AMMFCDDB_00016 20859 6 Skin 0.05 protein_coding synonymous_variant LOW 600T>C Ala200Ala
M0010201 AMMFCDDB_00019 23998 5 Skin 0.04 protein_coding synonymous_variant LOW 357C>T Pro119Pro
M0010202 AMMFCDDB_00023 28925 3 Skin 0.03 protein_coding synonymous_variant LOW 1212T>C Asn404Asn
M0010203 AMMFCDDB_00024 30574 3 Skin 0.03 protein_coding synonymous_variant LOW 978G>A Leu326Leu
M0010204 AMMFCDDB_00031 36123 7 Skin 0.06 protein_coding synonymous_variant LOW 495A>G Lys165Lys
M0010205 AMMFCDDB_00003 3136 3 Skin 0.03 protein_coding missense_variant MODERATE 501C>G Asp167Glu
M0010206 AMMFCDDB_00003 3749 5 Skin 0.04 protein_coding synonymous_variant LOW 1114T>C Leu372Leu
M0010207 AMMFCDDB_00006 9553 6 Skin 0.05 protein_coding synonymous_variant LOW 1062G>C Leu354Leu
M0010208 AMMFCDDB_00012 16581 9 Skin 0.08 protein_coding synonymous_variant LOW 1254T>C Ile418Ile
M0010209 AMMFCDDB_00010 14175 3 Skin 0.03 protein_coding synonymous_variant LOW 381T>C Gly127Gly
M0010210 AMMFCDDB_00003 4960 3 Skin 0.03 protein_coding synonymous_variant LOW 2325C>T Arg775Arg
M0010211 AMMFCDDB_00018 23365 3 Skin 0.03 protein_coding missense_variant MODERATE 143G>C Gly48Ala
M0010212 AMMFCDDB_00002 1603 3 Skin 0.03 protein_coding synonymous_variant LOW 222T>C Ile74Ile
M0010213 AMMFCDDB_00006 9382 4 Skin 0.04 protein_coding synonymous_variant LOW 1233G>A Val411Val






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
AMMFCDDB_00002 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 97.3 2e-221 1 413 1.0000 1.0000 experiment
AMMFCDDB_00003 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 90.3 0 1 1056 0.9972 0.9972 experiment
AMMFCDDB_00004 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 75.9 2.9e-189 14 465 0.9576 0.9576 experiment
AMMFCDDB_00002 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 100 3.5e-224 1 413 1.0000 1.0000 prediction
AMMFCDDB_00003 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 99.7 0 1 1059 1.0000 1.0000 prediction
AMMFCDDB_00004 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 99.4 1.3e-254 1 472 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
AMMFCDDB_00002 ARO:3000803 72 3.3e-189 9 413 0.9855 0.9831 fluoroquinolone antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
AMMFCDDB_00003 ARO:3000804 89.2 0 1 1049 0.9924 0.9896 fluoroquinolone antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
AMMFCDDB_00004 ARO:3000805 79.2 5.28e-246 14 465 0.9576 0.9576 fluoroquinolone antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux






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
AMMFCDDB_00002 PHI:11919 mexE 71.5 1e-152 9 413 0.9806 0.9783 rodents infection efflux pump membrane transporter increased virulence (hypervirulence)
AMMFCDDB_00003 PHI:10532 mexF 88.4 0 1 1057 0.9981 0.9944 eudicots infection multidrug efflux RND transporter 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





        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
AMMFCDDB_00003 2.A.6.2.16 89.2 0 1 1049 0.9906 0.9896 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily