Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2392
  Reference Plasmid   1111525849768046_bin.37__k141_162785
  Reference Plasmid Size   6004
  Reference Plasmid GC Content   0.36
  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
M0121327 GPNDNBAK_00004 3768 3 Oral 0.25 protein_coding synonymous_variant LOW 417G>A Ala139Ala
M0121328 GPNDNBAK_00004 3810 3 Oral 0.25 protein_coding synonymous_variant LOW 459G>A Ala153Ala
M0121329 GPNDNBAK_00004 3834 4 Oral 0.33 protein_coding synonymous_variant LOW 483T>A Ala161Ala
M0121330 GPNDNBAK_00004 3846 3 Oral 0.25 protein_coding synonymous_variant LOW 495T>C Thr165Thr
M0121331 GPNDNBAK_00004 4309 3 Oral 0.25 protein_coding missense_variant MODERATE 958T>A Ser320Thr
M0121332 GPNDNBAK_00004 4320 3 Oral 0.25 protein_coding synonymous_variant LOW 969C>T Thr323Thr
M0121333 GPNDNBAK_00004 4332 3 Oral 0.25 protein_coding synonymous_variant LOW 981G>T Val327Val
M0121334 GPNDNBAK_00005 4750 4 Oral 0.33 protein_coding missense_variant MODERATE 89T>A Phe30Tyr
M0121335 GPNDNBAK_00005 4760 5 Oral 0.42 protein_coding synonymous_variant LOW 99C>T Ala33Ala
M0121336 GPNDNBAK_00005 4979 3 Oral 0.25 protein_coding synonymous_variant LOW 318C>T Cys106Cys
M0121337 GPNDNBAK_00005 5030 3 Oral 0.25 protein_coding synonymous_variant LOW 369T>G Ala123Ala
M0121338 GPNDNBAK_00005 5066 3 Oral 0.25 protein_coding synonymous_variant LOW 405G>C Val135Val
M0121339 GPNDNBAK_00005 5123 3 Oral 0.25 protein_coding synonymous_variant LOW 462C>T Phe154Phe
M0121340 GPNDNBAK_00005 5540 6 Oral 0.50 protein_coding synonymous_variant LOW 879C>T Ile293Ile
M0121341 GPNDNBAK_00005 5600 6 Oral 0.50 protein_coding synonymous_variant LOW 939G>A Ala313Ala
M0121342 GPNDNBAK_00005 5603 3 Oral 0.25 protein_coding synonymous_variant LOW 942T>A Thr314Thr
M0121343 GPNDNBAK_00005 5606 4 Oral 0.33 protein_coding synonymous_variant LOW 945T>A Pro315Pro
M0121344 GPNDNBAK_00005 5612 4 Oral 0.33 protein_coding synonymous_variant LOW 951T>C Asn317Asn
M0121345 GPNDNBAK_00005 5627 4 Oral 0.33 protein_coding synonymous_variant LOW 966A>G Arg322Arg
M0121346 GPNDNBAK_00005 5642 3 Oral 0.25 protein_coding synonymous_variant LOW 981T>A Leu327Leu
M0121347 GPNDNBAK_00002 5758 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *3215G>A None
M0121348 GPNDNBAK_00002 5872 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *3329G>A None
M0121349 GPNDNBAK_00002 5904 4 Oral 0.33 protein_coding downstream_gene_variant MODIFIER *3361G>A None
M0121350 GPNDNBAK_00002 5910 4 Oral 0.33 protein_coding downstream_gene_variant MODIFIER *3367A>T None
M0121351 GPNDNBAK_00001 232 4 Oral 0.33 protein_coding missense_variant MODERATE 200T>C Ile67Thr
M0121352 GPNDNBAK_00001 299 3 Oral 0.25 protein_coding synonymous_variant LOW 267C>T Gly89Gly
M0121353 GPNDNBAK_00001 333 3 Oral 0.25 protein_coding missense_variant MODERATE 301G>A Val101Ile
M0121354 GPNDNBAK_00001 377 3 Oral 0.25 protein_coding synonymous_variant LOW 345T>C Asn115Asn
M0121355 GPNDNBAK_00001 380 3 Oral 0.25 protein_coding synonymous_variant LOW 348A>G Lys116Lys
M0121356 GPNDNBAK_00001 411 3 Oral 0.25 protein_coding missense_variant MODERATE 379A>G Thr127Ala
M0121357 GPNDNBAK_00001 413 3 Oral 0.25 protein_coding synonymous_variant LOW 381A>T Thr127Thr
M0121358 GPNDNBAK_00001 417 3 Oral 0.25 protein_coding missense_variant MODERATE 385G>A Asp129Asn
M0121359 GPNDNBAK_00001 437 3 Oral 0.25 protein_coding synonymous_variant LOW 405C>T Ile135Ile
M0121360 GPNDNBAK_00001 536 3 Oral 0.25 protein_coding synonymous_variant LOW 504A>G Glu168Glu
M0121361 GPNDNBAK_00001 587 3 Oral 0.25 protein_coding synonymous_variant LOW 555T>C Asp185Asp
M0121362 GPNDNBAK_00002 601 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -182C>T None
M0121363 GPNDNBAK_00002 602 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -181C>T None
M0121364 GPNDNBAK_00002 618 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -165G>A None
M0121365 GPNDNBAK_00002 668 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -115G>A None
M0121366 GPNDNBAK_00001 55 4 Oral 0.33 protein_coding missense_variant MODERATE 23T>C Ile8Thr
M0121367 GPNDNBAK_00002 660 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -123T>A None
M0121368 GPNDNBAK_00002 956 3 Oral 0.25 protein_coding synonymous_variant LOW 174G>T Ala58Ala
M0121369 GPNDNBAK_00002 1227 3 Oral 0.25 protein_coding missense_variant MODERATE 445G>A Glu149Lys
M0121370 GPNDNBAK_00002 1319 3 Oral 0.25 protein_coding synonymous_variant LOW 537A>G Leu179Leu
M0121371 GPNDNBAK_00002 1329 3 Oral 0.25 protein_coding missense_variant MODERATE 547G>A Ala183Thr
M0121372 GPNDNBAK_00002 1395 3 Oral 0.25 protein_coding missense_variant MODERATE 613A>G Lys205Glu
M0121373 GPNDNBAK_00002 1481 3 Oral 0.25 protein_coding synonymous_variant LOW 699A>G Ala233Ala
M0121374 GPNDNBAK_00002 1616 6 Oral 0.50 protein_coding synonymous_variant LOW 834A>G Lys278Lys
M0121375 GPNDNBAK_00002 1655 6 Oral 0.50 protein_coding synonymous_variant LOW 873G>A Ser291Ser
M0121376 GPNDNBAK_00002 1669 4 Oral 0.33 protein_coding missense_variant MODERATE 887G>A Ser296Asn
M0121377 GPNDNBAK_00002 1673 4 Oral 0.33 protein_coding synonymous_variant LOW 891C>G Thr297Thr
M0121378 GPNDNBAK_00002 1678 4 Oral 0.33 protein_coding missense_variant MODERATE 896G>A Arg299Gln
M0121379 GPNDNBAK_00002 1700 3 Oral 0.25 protein_coding synonymous_variant LOW 918G>A Lys306Lys
M0121380 GPNDNBAK_00002 1713 6 Oral 0.50 protein_coding missense_variant MODERATE 931G>A Glu311Lys
M0121381 GPNDNBAK_00002 1745 3 Oral 0.25 protein_coding synonymous_variant LOW 963C>T Asn321Asn
M0121382 GPNDNBAK_00002 1825 4 Oral 0.33 protein_coding missense_variant MODERATE 1043A>G His348Arg
M0121383 GPNDNBAK_00002 1919 3 Oral 0.25 protein_coding synonymous_variant LOW 1137A>G Ser379Ser
M0121384 GPNDNBAK_00002 1946 4 Oral 0.33 protein_coding synonymous_variant LOW 1164C>T Thr388Thr
M0121385 GPNDNBAK_00002 1964 4 Oral 0.33 protein_coding synonymous_variant LOW 1182T>C Asp394Asp
M0121386 GPNDNBAK_00002 1969 4 Oral 0.33 protein_coding missense_variant MODERATE 1187A>G His396Arg
M0121387 GPNDNBAK_00002 2016 6 Oral 0.50 protein_coding missense_variant MODERATE 1234G>A Val412Ile
M0121388 GPNDNBAK_00002 2018 4 Oral 0.33 protein_coding synonymous_variant LOW 1236T>C Val412Val
M0121389 GPNDNBAK_00002 2105 3 Oral 0.25 protein_coding synonymous_variant LOW 1323C>T His441His
M0121390 GPNDNBAK_00002 2171 3 Oral 0.25 protein_coding synonymous_variant LOW 1389T>C Phe463Phe
M0121391 GPNDNBAK_00002 2213 6 Oral 0.50 protein_coding synonymous_variant LOW 1431T>A Val477Val
M0121392 GPNDNBAK_00002 2219 3 Oral 0.25 protein_coding synonymous_variant LOW 1437A>G Gln479Gln
M0121393 GPNDNBAK_00002 2228 6 Oral 0.50 protein_coding synonymous_variant LOW 1446T>C Gly482Gly
M0121394 GPNDNBAK_00002 2288 4 Oral 0.33 protein_coding synonymous_variant LOW 1506C>T Tyr502Tyr
M0121395 GPNDNBAK_00002 2321 6 Oral 0.50 protein_coding synonymous_variant LOW 1539T>C Gly513Gly
M0121396 GPNDNBAK_00002 2327 6 Oral 0.50 protein_coding synonymous_variant LOW 1545G>A Gly515Gly
M0121397 GPNDNBAK_00002 2330 6 Oral 0.50 protein_coding synonymous_variant LOW 1548A>G Glu516Glu
M0121398 GPNDNBAK_00002 2348 6 Oral 0.50 protein_coding synonymous_variant LOW 1566C>A Ala522Ala
M0121399 GPNDNBAK_00002 2354 4 Oral 0.33 protein_coding synonymous_variant LOW 1572C>A Ile524Ile
M0121400 GPNDNBAK_00002 2382 4 Oral 0.33 protein_coding missense_variant MODERATE 1600G>A Val534Ile
M0121401 GPNDNBAK_00002 2397 3 Oral 0.25 protein_coding missense_variant MODERATE 1615G>A Asp539Asn
M0121402 GPNDNBAK_00002 2399 4 Oral 0.33 protein_coding synonymous_variant LOW 1617C>T Asp539Asp
M0121403 GPNDNBAK_00002 2417 4 Oral 0.33 protein_coding synonymous_variant LOW 1635C>G Leu545Leu
M0121404 GPNDNBAK_00002 2420 4 Oral 0.33 protein_coding synonymous_variant LOW 1638A>G Leu546Leu
M0121405 GPNDNBAK_00002 2423 4 Oral 0.33 protein_coding missense_variant MODERATE 1641A>C Lys547Asn
M0121406 GPNDNBAK_00002 2429 6 Oral 0.50 protein_coding synonymous_variant LOW 1647T>A Ile549Ile
M0121407 GPNDNBAK_00002 2444 4 Oral 0.33 protein_coding synonymous_variant LOW 1662T>G Val554Val
M0121408 GPNDNBAK_00002 2462 4 Oral 0.33 protein_coding synonymous_variant LOW 1680C>T Asn560Asn
M0121409 GPNDNBAK_00002 2495 3 Oral 0.25 protein_coding synonymous_variant LOW 1713A>T Thr571Thr
M0121410 GPNDNBAK_00002 2497 7 Oral 0.58 protein_coding missense_variant MODERATE 1715G>A Arg572Lys
M0121411 GPNDNBAK_00002 2501 3 Oral 0.25 protein_coding synonymous_variant LOW 1719A>G Lys573Lys
M0121412 GPNDNBAK_00002 2525 3 Oral 0.25 protein_coding synonymous_variant LOW 1743C>T Leu581Leu
M0121413 GPNDNBAK_00003 2602 3 Oral 0.25 protein_coding synonymous_variant LOW 36G>A Leu12Leu
M0121414 GPNDNBAK_00003 2603 7 Oral 0.58 protein_coding synonymous_variant LOW 37T>C Leu13Leu
M0121415 GPNDNBAK_00003 2629 7 Oral 0.58 protein_coding synonymous_variant LOW 63G>T Ser21Ser
M0121416 GPNDNBAK_00003 2695 4 Oral 0.33 protein_coding synonymous_variant LOW 129A>T Val43Val
M0121417 GPNDNBAK_00003 2719 4 Oral 0.33 protein_coding missense_variant MODERATE 153T>G Asp51Glu
M0121418 GPNDNBAK_00003 2731 6 Oral 0.50 protein_coding synonymous_variant LOW 165G>A Leu55Leu
M0121419 GPNDNBAK_00003 2746 4 Oral 0.33 protein_coding synonymous_variant LOW 180T>A Pro60Pro
M0121420 GPNDNBAK_00003 2749 7 Oral 0.58 protein_coding missense_variant MODERATE 183T>G Asp61Glu
M0121421 GPNDNBAK_00003 2757 5 Oral 0.42 protein_coding missense_variant MODERATE 191G>A Gly64Glu
M0121422 GPNDNBAK_00003 2759 7 Oral 0.58 protein_coding missense_variant MODERATE 193G>C Ala65Pro
M0121423 GPNDNBAK_00003 2799 4 Oral 0.33 protein_coding missense_variant MODERATE 233G>A Gly78Glu
M0121424 GPNDNBAK_00003 2808 4 Oral 0.33 protein_coding missense_variant MODERATE 242A>C Lys81Thr
M0121425 GPNDNBAK_00003 2819 4 Oral 0.33 protein_coding missense_variant MODERATE 253G>A Asp85Asn
M0121426 GPNDNBAK_00003 2837 8 Oral 0.67 protein_coding missense_variant MODERATE 271G>T Val91Phe
M0121427 GPNDNBAK_00003 2857 3 Oral 0.25 protein_coding synonymous_variant LOW 291T>C His97His
M0121428 GPNDNBAK_00003 2869 3 Oral 0.25 protein_coding synonymous_variant LOW 303C>T His101His
M0121429 GPNDNBAK_00003 2896 8 Oral 0.67 protein_coding synonymous_variant LOW 330A>G Leu110Leu
M0121430 GPNDNBAK_00003 2905 3 Oral 0.25 protein_coding synonymous_variant LOW 339T>C Asn113Asn
M0121431 GPNDNBAK_00003 2926 8 Oral 0.67 protein_coding synonymous_variant LOW 360T>C Cys120Cys
M0121432 GPNDNBAK_00003 2932 5 Oral 0.42 protein_coding synonymous_variant LOW 366C>T His122His
M0121433 GPNDNBAK_00003 2940 5 Oral 0.42 protein_coding missense_variant MODERATE 374A>G Asn125Ser
M0121434 GPNDNBAK_00003 2944 5 Oral 0.42 protein_coding synonymous_variant LOW 378A>G Glu126Glu
M0121435 GPNDNBAK_00003 3067 5 Oral 0.42 protein_coding synonymous_variant LOW 501C>T Thr167Thr
M0121436 GPNDNBAK_00003 3196 4 Oral 0.33 protein_coding synonymous_variant LOW 630C>T Ala210Ala
M0121437 GPNDNBAK_00003 3250 3 Oral 0.25 protein_coding synonymous_variant LOW 684G>A Ala228Ala
M0121438 GPNDNBAK_00003 3269 3 Oral 0.25 protein_coding synonymous_variant LOW 703C>T Leu235Leu
M0121439 GPNDNBAK_00003 3287 6 Oral 0.50 protein_coding missense_variant MODERATE 721G>A Glu241Lys
M0121440 GPNDNBAK_00004 3468 4 Oral 0.33 protein_coding synonymous_variant LOW 117A>G Pro39Pro
M0121441 GPNDNBAK_00004 3486 6 Oral 0.50 protein_coding synonymous_variant LOW 135T>A Ser45Ser
M0121442 GPNDNBAK_00004 3504 4 Oral 0.33 protein_coding synonymous_variant LOW 153A>G Ala51Ala
M0121443 GPNDNBAK_00005 5084 3 Oral 0.25 protein_coding synonymous_variant LOW 423T>A Ser141Ser
M0121444 GPNDNBAK_00005 5087 3 Oral 0.25 protein_coding synonymous_variant LOW 426A>C Gly142Gly
M0121445 GPNDNBAK_00002 5841 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *3298C>T None
M0121446 GPNDNBAK_00002 5847 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *3304T>C None
M0121447 GPNDNBAK_00002 5859 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *3316C>T None
M0121448 GPNDNBAK_00005 5219 3 Oral 0.25 protein_coding synonymous_variant LOW 558A>G Leu186Leu
M0121449 GPNDNBAK_00002 2480 3 Oral 0.25 protein_coding synonymous_variant LOW 1698T>C Val566Val
M0121450 GPNDNBAK_00002 2485 4 Oral 0.33 protein_coding missense_variant MODERATE 1703T>C Leu568Ser
M0121451 GPNDNBAK_00003 2907 3 Oral 0.25 protein_coding missense_variant MODERATE 341G>C Ser114Thr
M0121452 GPNDNBAK_00003 2929 3 Oral 0.25 protein_coding synonymous_variant LOW 363G>A Leu121Leu
M0121453 GPNDNBAK_00004 3714 4 Oral 0.33 protein_coding synonymous_variant LOW 363C>T Val121Val
M0121454 GPNDNBAK_00002 1538 3 Oral 0.25 protein_coding synonymous_variant LOW 756T>C Asp252Asp
M0121455 GPNDNBAK_00002 1547 3 Oral 0.25 protein_coding synonymous_variant LOW 765T>C Arg255Arg
M0121456 GPNDNBAK_00002 1595 3 Oral 0.25 protein_coding synonymous_variant LOW 813C>T Ile271Ile
M0121457 GPNDNBAK_00002 1934 3 Oral 0.25 protein_coding synonymous_variant LOW 1152A>T Leu384Leu
M0121458 GPNDNBAK_00003 2547 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -20G>T None
M0121459 GPNDNBAK_00004 3480 3 Oral 0.25 protein_coding synonymous_variant LOW 129C>T Ala43Ala
M0121460 GPNDNBAK_00004 3579 3 Oral 0.25 protein_coding synonymous_variant LOW 228G>A Ala76Ala
M0121461 GPNDNBAK_00004 3642 3 Oral 0.25 protein_coding synonymous_variant LOW 291C>T Tyr97Tyr
M0121462 GPNDNBAK_00004 3657 3 Oral 0.25 protein_coding synonymous_variant LOW 306A>G Ser102Ser
M0121463 GPNDNBAK_00004 3682 3 Oral 0.25 protein_coding missense_variant MODERATE 331A>T Ile111Phe
M0121464 GPNDNBAK_00004 3696 3 Oral 0.25 protein_coding synonymous_variant LOW 345G>T Ala115Ala






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