Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2478
  Reference Plasmid   1111525849768046_bin.37__k141_97280
  Reference Plasmid Size   7478
  Reference Plasmid GC Content   0.39
  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
M0129189 KGDDJEEM_00001 534 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -86A>T None
M0129190 KGDDJEEM_00001 539 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -81G>C None
M0129191 KGDDJEEM_00001 543 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -77A>T None
M0129192 KGDDJEEM_00001 561 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -59A>T None
M0129193 KGDDJEEM_00001 688 3 Oral 0.25 protein_coding synonymous_variant LOW 69A>G Glu23Glu
M0129194 KGDDJEEM_00001 712 4 Oral 0.33 protein_coding synonymous_variant LOW 93T>C Asn31Asn
M0129195 KGDDJEEM_00001 748 5 Oral 0.42 protein_coding synonymous_variant LOW 129T>C Gly43Gly
M0129196 KGDDJEEM_00001 943 6 Oral 0.50 protein_coding synonymous_variant LOW 324C>T Gly108Gly
M0129197 KGDDJEEM_00001 976 6 Oral 0.50 protein_coding synonymous_variant LOW 357G>A Glu119Glu
M0129198 KGDDJEEM_00001 1063 6 Oral 0.50 protein_coding synonymous_variant LOW 444T>C Asn148Asn
M0129199 KGDDJEEM_00001 1075 6 Oral 0.50 protein_coding synonymous_variant LOW 456T>C Asn152Asn
M0129200 KGDDJEEM_00001 1123 4 Oral 0.33 protein_coding synonymous_variant LOW 504A>T Ser168Ser
M0129201 KGDDJEEM_00001 1141 3 Oral 0.25 protein_coding synonymous_variant LOW 522A>G Val174Val
M0129202 KGDDJEEM_00001 1243 3 Oral 0.25 protein_coding synonymous_variant LOW 624C>T Phe208Phe
M0129203 KGDDJEEM_00001 1270 6 Oral 0.50 protein_coding synonymous_variant LOW 651T>C Gly217Gly
M0129204 KGDDJEEM_00001 1369 6 Oral 0.50 protein_coding synonymous_variant LOW 750T>A Ala250Ala
M0129205 KGDDJEEM_00001 1426 6 Oral 0.50 protein_coding synonymous_variant LOW 807C>T Arg269Arg
M0129206 KGDDJEEM_00001 1450 5 Oral 0.42 protein_coding synonymous_variant LOW 831C>T Gly277Gly
M0129207 KGDDJEEM_00001 1456 5 Oral 0.42 protein_coding synonymous_variant LOW 837G>A Leu279Leu
M0129208 KGDDJEEM_00001 1471 5 Oral 0.42 protein_coding synonymous_variant LOW 852A>T Val284Val
M0129209 KGDDJEEM_00001 1486 5 Oral 0.42 protein_coding synonymous_variant LOW 867C>T Ala289Ala
M0129210 KGDDJEEM_00001 1525 3 Oral 0.25 protein_coding synonymous_variant LOW 906G>A Glu302Glu
M0129211 KGDDJEEM_00001 1526 3 Oral 0.25 protein_coding missense_variant MODERATE 907T>G Ser303Ala
M0129212 KGDDJEEM_00001 1660 3 Oral 0.25 protein_coding synonymous_variant LOW 1041A>T Ile347Ile
M0129213 KGDDJEEM_00002 1752 5 Oral 0.42 protein_coding synonymous_variant LOW 84T>A Ile28Ile
M0129214 KGDDJEEM_00002 1971 5 Oral 0.42 protein_coding synonymous_variant LOW 303G>A Glu101Glu
M0129215 KGDDJEEM_00002 2073 6 Oral 0.50 protein_coding synonymous_variant LOW 405T>C Gly135Gly
M0129216 KGDDJEEM_00002 2138 6 Oral 0.50 protein_coding missense_variant MODERATE 470A>G Asn157Ser
M0129217 KGDDJEEM_00002 2202 5 Oral 0.42 protein_coding synonymous_variant LOW 534C>A Ala178Ala
M0129218 KGDDJEEM_00002 2268 5 Oral 0.42 protein_coding synonymous_variant LOW 600C>A Ala200Ala
M0129219 KGDDJEEM_00002 2292 6 Oral 0.50 protein_coding synonymous_variant LOW 624C>T Gly208Gly
M0129220 KGDDJEEM_00002 2364 6 Oral 0.50 protein_coding synonymous_variant LOW 696T>C Asn232Asn
M0129221 KGDDJEEM_00003 2609 6 Oral 0.50 protein_coding synonymous_variant LOW 210C>A Ala70Ala
M0129222 KGDDJEEM_00003 2696 5 Oral 0.42 protein_coding synonymous_variant LOW 297T>C Ser99Ser
M0129223 KGDDJEEM_00003 2699 3 Oral 0.25 protein_coding synonymous_variant LOW 300C>T Ser100Ser
M0129224 KGDDJEEM_00003 3062 6 Oral 0.50 protein_coding synonymous_variant LOW 663T>C Asp221Asp
M0129225 KGDDJEEM_00003 3071 5 Oral 0.42 protein_coding synonymous_variant LOW 672A>G Val224Val
M0129226 KGDDJEEM_00003 3129 3 Oral 0.25 protein_coding missense_variant MODERATE 730C>T Leu244Phe
M0129227 KGDDJEEM_00003 3131 3 Oral 0.25 protein_coding synonymous_variant LOW 732T>G Leu244Leu
M0129228 KGDDJEEM_00003 3137 3 Oral 0.25 protein_coding synonymous_variant LOW 738T>C Pro246Pro
M0129229 KGDDJEEM_00003 3167 4 Oral 0.33 protein_coding synonymous_variant LOW 768T>C His256His
M0129230 KGDDJEEM_00003 3179 4 Oral 0.33 protein_coding synonymous_variant LOW 780T>C Leu260Leu
M0129231 KGDDJEEM_00003 3206 5 Oral 0.42 protein_coding missense_variant MODERATE 807C>A His269Gln
M0129232 KGDDJEEM_00004 3244 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -448C>T None
M0129233 KGDDJEEM_00004 3267 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -425G>A None
M0129234 KGDDJEEM_00004 3280 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -412C>T None
M0129235 KGDDJEEM_00004 3366 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -326G>C None
M0129236 KGDDJEEM_00004 3435 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -257C>T None
M0129237 KGDDJEEM_00004 3627 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -65T>C None
M0129238 KGDDJEEM_00004 3745 5 Oral 0.42 protein_coding missense_variant MODERATE 54T>A Phe18Leu
M0129239 KGDDJEEM_00004 3805 6 Oral 0.50 protein_coding synonymous_variant LOW 114G>T Val38Val
M0129240 KGDDJEEM_00005 5133 4 Oral 0.33 protein_coding synonymous_variant LOW 297T>C Gly99Gly
M0129241 KGDDJEEM_00005 5184 3 Oral 0.25 protein_coding synonymous_variant LOW 348C>T Gly116Gly
M0129242 KGDDJEEM_00005 5220 6 Oral 0.50 protein_coding synonymous_variant LOW 384G>T Val128Val
M0129243 KGDDJEEM_00005 5265 6 Oral 0.50 protein_coding synonymous_variant LOW 429A>T Ala143Ala
M0129244 KGDDJEEM_00005 5330 7 Oral 0.58 protein_coding missense_variant MODERATE 494C>G Ala165Gly
M0129245 KGDDJEEM_00005 5400 4 Oral 0.33 protein_coding synonymous_variant LOW 564T>C Phe188Phe
M0129246 KGDDJEEM_00005 5549 7 Oral 0.58 protein_coding missense_variant MODERATE 713G>C Ser238Thr
M0129247 KGDDJEEM_00005 5560 7 Oral 0.58 protein_coding missense_variant MODERATE 724G>A Val242Ile
M0129248 KGDDJEEM_00006 5714 3 Oral 0.25 protein_coding missense_variant MODERATE 115T>G Ser39Ala
M0129249 KGDDJEEM_00006 5716 4 Oral 0.33 protein_coding synonymous_variant LOW 117G>A Ser39Ser
M0129250 KGDDJEEM_00006 5725 5 Oral 0.42 protein_coding synonymous_variant LOW 126A>T Thr42Thr
M0129251 KGDDJEEM_00006 5755 7 Oral 0.58 protein_coding synonymous_variant LOW 156A>G Ala52Ala
M0129252 KGDDJEEM_00006 6253 3 Oral 0.25 protein_coding synonymous_variant LOW 654G>A Val218Val
M0129253 KGDDJEEM_00006 6293 4 Oral 0.33 protein_coding missense_variant MODERATE 694G>A Asp232Asn
M0129254 KGDDJEEM_00006 6407 5 Oral 0.42 protein_coding missense_variant MODERATE 808G>A Val270Ile
M0129255 KGDDJEEM_00001 6502 6 Oral 0.50 protein_coding downstream_gene_variant MODIFIER *4830G>A None
M0129256 KGDDJEEM_00001 6506 5 Oral 0.42 protein_coding downstream_gene_variant MODIFIER *4834C>G None
M0129257 KGDDJEEM_00001 6614 5 Oral 0.42 protein_coding downstream_gene_variant MODIFIER *4942T>C None
M0129258 KGDDJEEM_00001 6633 6 Oral 0.50 protein_coding downstream_gene_variant MODIFIER *4961A>C None
M0129259 KGDDJEEM_00001 6641 6 Oral 0.50 protein_coding downstream_gene_variant MODIFIER *4969T>G None
M0129260 KGDDJEEM_00002 6678 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *4281G>A None
M0129261 KGDDJEEM_00007 7030 5 Oral 0.42 protein_coding synonymous_variant LOW 402C>T Asn134Asn
M0129262 KGDDJEEM_00007 7123 3 Oral 0.25 protein_coding synonymous_variant LOW 309T>C Thr103Thr
M0129263 KGDDJEEM_00007 7181 3 Oral 0.25 protein_coding missense_variant MODERATE 251C>A Thr84Asn
M0129264 KGDDJEEM_00007 7333 6 Oral 0.50 protein_coding synonymous_variant LOW 99T>C Asn33Asn
M0129265 KGDDJEEM_00007 7438 6 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -7T>C None
M0129266 KGDDJEEM_00007 7444 6 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -13T>A None
M0129267 KGDDJEEM_00001 1291 4 Oral 0.33 protein_coding synonymous_variant LOW 672A>G Gly224Gly
M0129268 KGDDJEEM_00001 1547 3 Oral 0.25 protein_coding missense_variant MODERATE 928C>G Gln310Glu
M0129269 KGDDJEEM_00002 2008 3 Oral 0.25 protein_coding missense_variant MODERATE 340C>A Leu114Ile
M0129270 KGDDJEEM_00002 2011 3 Oral 0.25 protein_coding synonymous_variant LOW 343T>C Leu115Leu
M0129271 KGDDJEEM_00002 2026 3 Oral 0.25 protein_coding missense_variant MODERATE 358A>G Met120Val
M0129272 KGDDJEEM_00002 2029 3 Oral 0.25 protein_coding missense_variant MODERATE 361G>T Ala121Ser
M0129273 KGDDJEEM_00002 2035 3 Oral 0.25 protein_coding missense_variant MODERATE 367G>A Glu123Lys
M0129274 KGDDJEEM_00002 2307 3 Oral 0.25 protein_coding synonymous_variant LOW 639A>T Val213Val
M0129275 KGDDJEEM_00003 2907 4 Oral 0.33 protein_coding synonymous_variant LOW 508T>C Leu170Leu
M0129276 KGDDJEEM_00004 3238 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -454T>C None
M0129277 KGDDJEEM_00004 3311 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -381C>T None
M0129278 KGDDJEEM_00004 3614 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -78G>A None
M0129279 KGDDJEEM_00004 3853 5 Oral 0.42 protein_coding synonymous_variant LOW 162C>T Asp54Asp
M0129280 KGDDJEEM_00004 3952 3 Oral 0.25 protein_coding synonymous_variant LOW 261T>A Thr87Thr
M0129281 KGDDJEEM_00004 4111 4 Oral 0.33 protein_coding synonymous_variant LOW 420A>T Ser140Ser
M0129282 KGDDJEEM_00004 4174 4 Oral 0.33 protein_coding synonymous_variant LOW 483T>C Asn161Asn
M0129283 KGDDJEEM_00004 4199 3 Oral 0.25 protein_coding synonymous_variant LOW 508T>C Leu170Leu
M0129284 KGDDJEEM_00004 4309 5 Oral 0.42 protein_coding synonymous_variant LOW 618T>C Gly206Gly
M0129285 KGDDJEEM_00004 4369 5 Oral 0.42 protein_coding synonymous_variant LOW 678T>C Asp226Asp
M0129286 KGDDJEEM_00005 4968 6 Oral 0.50 protein_coding synonymous_variant LOW 132T>C Val44Val
M0129287 KGDDJEEM_00005 4974 4 Oral 0.33 protein_coding synonymous_variant LOW 138A>C Ile46Ile
M0129288 KGDDJEEM_00006 5707 3 Oral 0.25 protein_coding synonymous_variant LOW 108C>T Phe36Phe
M0129289 KGDDJEEM_00006 5746 5 Oral 0.42 protein_coding synonymous_variant LOW 147A>T Ala49Ala
M0129290 KGDDJEEM_00006 5893 4 Oral 0.33 protein_coding synonymous_variant LOW 294T>C Tyr98Tyr
M0129291 KGDDJEEM_00006 5944 5 Oral 0.42 protein_coding synonymous_variant LOW 345A>G Ala115Ala
M0129292 KGDDJEEM_00006 6016 3 Oral 0.25 protein_coding synonymous_variant LOW 417T>C Phe139Phe
M0129293 KGDDJEEM_00006 6025 3 Oral 0.25 protein_coding synonymous_variant LOW 426A>G Glu142Glu
M0129294 KGDDJEEM_00006 6338 4 Oral 0.33 protein_coding missense_variant MODERATE 739G>A Val247Ile
M0129295 KGDDJEEM_00006 6418 4 Oral 0.33 protein_coding synonymous_variant LOW 819T>C Ser273Ser
M0129296 KGDDJEEM_00001 6491 4 Oral 0.33 protein_coding downstream_gene_variant MODIFIER *4819T>G None
M0129297 KGDDJEEM_00001 6494 4 Oral 0.33 protein_coding downstream_gene_variant MODIFIER *4822A>G None
M0129298 KGDDJEEM_00001 6533 6 Oral 0.50 protein_coding downstream_gene_variant MODIFIER *4861A>G None
M0129299 KGDDJEEM_00007 6919 5 Oral 0.42 protein_coding synonymous_variant LOW 513A>C Thr171Thr
M0129300 KGDDJEEM_00007 7039 3 Oral 0.25 protein_coding synonymous_variant LOW 393G>A Ser131Ser
M0129301 KGDDJEEM_00007 7393 5 Oral 0.42 protein_coding synonymous_variant LOW 39C>T Asn13Asn
M0129302 KGDDJEEM_00005 5415 4 Oral 0.33 protein_coding synonymous_variant LOW 579A>T Thr193Thr
M0129303 KGDDJEEM_00006 6100 5 Oral 0.42 protein_coding synonymous_variant LOW 501A>G Lys167Lys
M0129304 KGDDJEEM_00006 6157 4 Oral 0.33 protein_coding synonymous_variant LOW 558T>C Phe186Phe
M0129305 KGDDJEEM_00007 7441 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -10G>A None
M0129306 KGDDJEEM_00001 961 4 Oral 0.33 protein_coding synonymous_variant LOW 342G>A Pro114Pro
M0129307 KGDDJEEM_00004 4462 3 Oral 0.25 protein_coding synonymous_variant LOW 771A>G Ala257Ala
M0129308 KGDDJEEM_00004 4648 3 Oral 0.25 protein_coding synonymous_variant LOW 957C>T Phe319Phe
M0129309 KGDDJEEM_00005 4926 3 Oral 0.25 protein_coding missense_variant MODERATE 90G>C Lys30Asn
M0129310 KGDDJEEM_00006 5812 3 Oral 0.25 protein_coding synonymous_variant LOW 213T>A Ala71Ala
M0129311 KGDDJEEM_00001 6569 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *4897A>T 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






        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