Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1324
  Reference Plasmid   NZ_KM406416.1
  Reference Plasmid Size   190178
  Reference Plasmid GC Content   0.57
  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
M0206377 PHCGOMMF_00027 23462 3 Gut 0.27 protein_coding synonymous_variant LOW 1044T>C Pro348Pro
M0206378 PHCGOMMF_00027 23477 3 Gut 0.27 protein_coding synonymous_variant LOW 1029G>A Gly343Gly
M0206379 PHCGOMMF_00027 23629 3 Gut 0.27 protein_coding missense_variant MODERATE 877C>A Leu293Ile
M0206380 PHCGOMMF_00027 23661 3 Gut 0.27 protein_coding missense_variant MODERATE 845C>T Ala282Val
M0206381 PHCGOMMF_00027 23665 3 Gut 0.27 protein_coding missense_variant MODERATE 841G>A Asp281Asn
M0206382 PHCGOMMF_00027 23669 3 Gut 0.27 protein_coding synonymous_variant LOW 837T>C Asp279Asp
M0206383 PHCGOMMF_00027 23691 3 Gut 0.27 protein_coding missense_variant MODERATE 815A>G His272Arg
M0206384 PHCGOMMF_00027 23756 3 Gut 0.27 protein_coding synonymous_variant LOW 750A>G Val250Val
M0206385 PHCGOMMF_00027 23780 3 Gut 0.27 protein_coding synonymous_variant LOW 726A>C Pro242Pro
M0206386 PHCGOMMF_00027 23813 3 Gut 0.27 protein_coding synonymous_variant LOW 693G>A Lys231Lys
M0206387 PHCGOMMF_00027 23814 3 Gut 0.27 protein_coding missense_variant MODERATE 692A>G Lys231Arg
M0206388 PHCGOMMF_00027 23820 3 Gut 0.27 protein_coding missense_variant MODERATE 686C>G Ser229Cys
M0206389 PHCGOMMF_00027 23821 3 Gut 0.27 protein_coding missense_variant MODERATE 685T>A Ser229Thr
M0206390 PHCGOMMF_00027 23917 3 Gut 0.27 protein_coding missense_variant MODERATE 589A>G Ile197Val
M0206391 PHCGOMMF_00027 23925 3 Gut 0.27 protein_coding missense_variant MODERATE 581T>C Val194Ala
M0206392 PHCGOMMF_00027 23939 3 Gut 0.27 protein_coding synonymous_variant LOW 567T>C Asn189Asn
M0206393 PHCGOMMF_00027 23945 3 Gut 0.27 protein_coding missense_variant MODERATE 561C>A Asn187Lys
M0206394 PHCGOMMF_00027 23968 3 Gut 0.27 protein_coding missense_variant MODERATE 538A>G Lys180Glu
M0206395 PHCGOMMF_00027 23991 3 Gut 0.27 protein_coding missense_variant MODERATE 515T>C Val172Ala
M0206396 PHCGOMMF_00027 24026 3 Gut 0.27 protein_coding synonymous_variant LOW 480C>T Ile160Ile
M0206397 PHCGOMMF_00027 24049 3 Gut 0.27 protein_coding missense_variant MODERATE 457A>G Arg153Gly
M0206398 PHCGOMMF_00027 24144 3 Gut 0.27 protein_coding missense_variant MODERATE 362C>T Ser121Phe
M0206399 PHCGOMMF_00027 24182 3 Gut 0.27 protein_coding synonymous_variant LOW 324G>A Pro108Pro
M0206400 PHCGOMMF_00027 24386 3 Gut 0.27 protein_coding synonymous_variant LOW 120T>C Gly40Gly
M0206401 PHCGOMMF_00027 24410 3 Gut 0.27 protein_coding synonymous_variant LOW 96T>C Ser32Ser
M0206402 PHCGOMMF_00028 24529 3 Gut 0.27 protein_coding synonymous_variant LOW 285G>A Arg95Arg
M0206403 PHCGOMMF_00028 24532 3 Gut 0.27 protein_coding synonymous_variant LOW 282A>G Glu94Glu
M0206404 PHCGOMMF_00028 24610 3 Gut 0.27 protein_coding synonymous_variant LOW 204G>A Glu68Glu
M0206405 PHCGOMMF_00028 24651 3 Gut 0.27 protein_coding synonymous_variant LOW 163C>A Arg55Arg
M0206406 PHCGOMMF_00028 24652 3 Gut 0.27 protein_coding synonymous_variant LOW 162T>C Asp54Asp
M0206407 PHCGOMMF_00028 24664 3 Gut 0.27 protein_coding synonymous_variant LOW 150G>A Arg50Arg
M0206408 PHCGOMMF_00028 24670 3 Gut 0.27 protein_coding synonymous_variant LOW 144G>A Ser48Ser
M0206409 PHCGOMMF_00028 24780 3 Gut 0.27 protein_coding missense_variant MODERATE 34A>G Thr12Ala
M0206410 PHCGOMMF_00028 24786 3 Gut 0.27 protein_coding missense_variant MODERATE 28T>C Ser10Pro
M0206411 PHCGOMMF_00028 24805 3 Gut 0.27 protein_coding synonymous_variant LOW 9A>G Lys3Lys
M0206412 PHCGOMMF_00024 24814 3 Gut 0.27 protein_coding upstream_gene_variant MODIFIER -2479G>T None
M0206413 PHCGOMMF_00024 24816 3 Gut 0.27 protein_coding upstream_gene_variant MODIFIER -2481T>C None
M0206414 PHCGOMMF_00024 24817 3 Gut 0.27 protein_coding upstream_gene_variant MODIFIER -2482C>T None
M0206415 PHCGOMMF_00024 24899 3 Gut 0.27 protein_coding upstream_gene_variant MODIFIER -2564C>T None
M0206416 PHCGOMMF_00024 24901 3 Gut 0.27 protein_coding upstream_gene_variant MODIFIER -2566G>A None
M0206417 PHCGOMMF_00024 24902 3 Gut 0.27 protein_coding upstream_gene_variant MODIFIER -2567T>A None
M0206418 PHCGOMMF_00024 24903 3 Gut 0.27 protein_coding upstream_gene_variant MODIFIER -2568A>G None
M0206419 PHCGOMMF_00024 24929 3 Gut 0.27 protein_coding upstream_gene_variant MODIFIER -2594A>G None
M0206420 PHCGOMMF_00029 24955 3 Gut 0.27 protein_coding synonymous_variant LOW 24C>T Cys8Cys
M0206421 PHCGOMMF_00029 25030 3 Gut 0.27 protein_coding synonymous_variant LOW 99A>G Gly33Gly
M0206422 PHCGOMMF_00029 25057 3 Gut 0.27 protein_coding synonymous_variant LOW 126C>T Tyr42Tyr
M0206423 PHCGOMMF_00029 25093 3 Gut 0.27 protein_coding synonymous_variant LOW 162A>G Arg54Arg
M0206424 PHCGOMMF_00029 25096 3 Gut 0.27 protein_coding synonymous_variant LOW 165C>A Ile55Ile
M0206425 PHCGOMMF_00029 25127 3 Gut 0.27 protein_coding missense_variant MODERATE 196A>G Asn66Asp
M0206426 PHCGOMMF_00029 25171 3 Gut 0.27 protein_coding synonymous_variant LOW 240T>C Asp80Asp
M0206427 PHCGOMMF_00029 25213 3 Gut 0.27 protein_coding synonymous_variant LOW 282T>C Pro94Pro
M0206428 PHCGOMMF_00029 25219 3 Gut 0.27 protein_coding synonymous_variant LOW 288C>T Ser96Ser
M0206429 PHCGOMMF_00029 25234 3 Gut 0.27 protein_coding synonymous_variant LOW 303A>G Gln101Gln
M0206430 PHCGOMMF_00029 25240 3 Gut 0.27 protein_coding synonymous_variant LOW 309C>T Val103Val
M0206431 PHCGOMMF_00029 25246 3 Gut 0.27 protein_coding synonymous_variant LOW 315A>C Ile105Ile
M0206432 PHCGOMMF_00029 25252 3 Gut 0.27 protein_coding synonymous_variant LOW 321T>C Asp107Asp
M0206433 PHCGOMMF_00029 25255 3 Gut 0.27 protein_coding synonymous_variant LOW 324T>C Gly108Gly
M0206434 PHCGOMMF_00029 25257 3 Gut 0.27 protein_coding missense_variant MODERATE 326G>A Gly109Asp
M0206435 PHCGOMMF_00029 25261 3 Gut 0.27 protein_coding synonymous_variant LOW 330A>G Lys110Lys
M0206436 PHCGOMMF_00029 25267 3 Gut 0.27 protein_coding synonymous_variant LOW 336A>G Val112Val
M0206437 PHCGOMMF_00029 25274 3 Gut 0.27 protein_coding synonymous_variant LOW 343C>T Leu115Leu
M0206438 PHCGOMMF_00029 25276 3 Gut 0.27 protein_coding synonymous_variant LOW 345G>A Leu115Leu
M0206439 PHCGOMMF_00029 25342 3 Gut 0.27 protein_coding synonymous_variant LOW 411G>A Gly137Gly
M0206440 PHCGOMMF_00029 25344 3 Gut 0.27 protein_coding missense_variant MODERATE 413A>G Gln138Arg
M0206441 PHCGOMMF_00029 25357 3 Gut 0.27 protein_coding synonymous_variant LOW 426A>G Lys142Lys
M0206442 PHCGOMMF_00029 25363 3 Gut 0.27 protein_coding synonymous_variant LOW 432A>G Lys144Lys
M0206443 PHCGOMMF_00029 25366 3 Gut 0.27 protein_coding synonymous_variant LOW 435C>A Pro145Pro
M0206444 PHCGOMMF_00029 25432 3 Gut 0.27 protein_coding synonymous_variant LOW 501G>A Ala167Ala
M0206445 PHCGOMMF_00029 25435 3 Gut 0.27 protein_coding synonymous_variant LOW 504G>A Ala168Ala
M0206446 PHCGOMMF_00029 25471 3 Gut 0.27 protein_coding synonymous_variant LOW 540C>T Gly180Gly
M0206447 PHCGOMMF_00029 25477 3 Gut 0.27 protein_coding synonymous_variant LOW 546C>T Asp182Asp
M0206448 PHCGOMMF_00030 25582 3 Gut 0.27 protein_coding synonymous_variant LOW 4C>T Leu2Leu
M0206449 PHCGOMMF_00030 25649 3 Gut 0.27 protein_coding missense_variant MODERATE 71A>G Asp24Gly
M0206450 PHCGOMMF_00030 25651 3 Gut 0.27 protein_coding missense_variant MODERATE 73A>T Thr25Ser
M0206451 PHCGOMMF_00030 25741 3 Gut 0.27 protein_coding missense_variant MODERATE 163A>T Ile55Leu
M0206452 PHCGOMMF_00030 25794 3 Gut 0.27 protein_coding synonymous_variant LOW 216G>C Leu72Leu
M0206453 PHCGOMMF_00030 25812 3 Gut 0.27 protein_coding synonymous_variant LOW 234T>C Ala78Ala
M0206454 PHCGOMMF_00022 16457 5 Gut 0.45 protein_coding missense_variant MODERATE 914G>T Arg305Met
M0206455 PHCGOMMF_00022 16583 4 Gut 0.36 protein_coding missense_variant MODERATE 788G>A Arg263Lys
M0206456 PHCGOMMF_00022 16589 4 Gut 0.36 protein_coding missense_variant MODERATE 782C>T Thr261Met
M0206457 PHCGOMMF_00022 16825 6 Gut 0.55 protein_coding synonymous_variant LOW 546T>C Arg182Arg
M0206458 PHCGOMMF_00022 16837 6 Gut 0.55 protein_coding synonymous_variant LOW 534G>A Val178Val
M0206459 PHCGOMMF_00022 16846 6 Gut 0.55 protein_coding synonymous_variant LOW 525G>T Thr175Thr
M0206460 PHCGOMMF_00022 16856 4 Gut 0.36 protein_coding missense_variant MODERATE 515G>A Arg172Gln
M0206461 PHCGOMMF_00022 16912 6 Gut 0.55 protein_coding synonymous_variant LOW 459C>T Tyr153Tyr
M0206462 PHCGOMMF_00022 16922 6 Gut 0.55 protein_coding missense_variant MODERATE 449G>A Gly150Asp
M0206463 PHCGOMMF_00022 16928 4 Gut 0.36 protein_coding missense_variant MODERATE 443G>A Gly148Asp
M0206464 PHCGOMMF_00022 16930 6 Gut 0.55 protein_coding synonymous_variant LOW 441C>T Asn147Asn
M0206465 PHCGOMMF_00022 16960 6 Gut 0.55 protein_coding synonymous_variant LOW 411T>C His137His
M0206466 PHCGOMMF_00022 17019 6 Gut 0.55 protein_coding missense_variant MODERATE 352G>A Glu118Lys
M0206467 PHCGOMMF_00022 17026 4 Gut 0.36 protein_coding synonymous_variant LOW 345C>T Asp115Asp
M0206468 PHCGOMMF_00022 17029 4 Gut 0.36 protein_coding synonymous_variant LOW 342C>T Phe114Phe
M0206469 PHCGOMMF_00022 17037 4 Gut 0.36 protein_coding missense_variant MODERATE 334A>G Asn112Asp
M0206470 PHCGOMMF_00022 17054 4 Gut 0.36 protein_coding missense_variant MODERATE 317C>T Ala106Val
M0206471 PHCGOMMF_00022 17059 6 Gut 0.55 protein_coding synonymous_variant LOW 312G>A Gly104Gly
M0206472 PHCGOMMF_00022 17062 6 Gut 0.55 protein_coding synonymous_variant LOW 309C>T Asp103Asp
M0206473 PHCGOMMF_00022 17065 6 Gut 0.55 protein_coding synonymous_variant LOW 306G>A Thr102Thr
M0206474 PHCGOMMF_00022 17073 4 Gut 0.36 protein_coding missense_variant MODERATE 298T>C Tyr100His
M0206475 PHCGOMMF_00022 17077 4 Gut 0.36 protein_coding synonymous_variant LOW 294C>T Asn98Asn
M0206476 PHCGOMMF_00022 17120 6 Gut 0.55 protein_coding missense_variant MODERATE 251G>A Arg84Lys
M0206477 PHCGOMMF_00022 17127 6 Gut 0.55 protein_coding missense_variant MODERATE 244G>A Gly82Arg
M0206478 PHCGOMMF_00022 17146 4 Gut 0.36 protein_coding synonymous_variant LOW 225C>T Ser75Ser
M0206479 PHCGOMMF_00022 17153 4 Gut 0.36 protein_coding missense_variant MODERATE 218C>T Ala73Val
M0206480 PHCGOMMF_00022 17223 6 Gut 0.55 protein_coding missense_variant MODERATE 148A>G Thr50Ala
M0206481 PHCGOMMF_00022 17232 6 Gut 0.55 protein_coding missense_variant MODERATE 139G>A Ala47Thr
M0206482 PHCGOMMF_00022 17234 6 Gut 0.55 protein_coding missense_variant MODERATE 137C>T Pro46Leu
M0206483 PHCGOMMF_00022 17236 6 Gut 0.55 protein_coding missense_variant MODERATE 135A>C Arg45Ser
M0206484 PHCGOMMF_00023 18688 3 Gut 0.27 protein_coding missense_variant MODERATE 632C>G Ala211Gly
M0206485 PHCGOMMF_00022 15829 3 Gut 0.27 protein_coding synonymous_variant LOW 1542T>A Thr514Thr
M0206486 PHCGOMMF_00022 15869 3 Gut 0.27 protein_coding missense_variant MODERATE 1502T>A Met501Lys
M0206487 PHCGOMMF_00022 15870 3 Gut 0.27 protein_coding missense_variant MODERATE 1501A>G Met501Val
M0206488 PHCGOMMF_00022 15985 5 Gut 0.45 protein_coding synonymous_variant LOW 1386G>A Arg462Arg
M0206489 PHCGOMMF_00022 16073 3 Gut 0.27 protein_coding missense_variant MODERATE 1298C>T Ala433Val
M0206490 PHCGOMMF_00022 16075 3 Gut 0.27 protein_coding synonymous_variant LOW 1296T>C Gly432Gly
M0206491 PHCGOMMF_00022 16085 3 Gut 0.27 protein_coding missense_variant MODERATE 1286A>C Asp429Ala
M0206492 PHCGOMMF_00022 16097 3 Gut 0.27 protein_coding missense_variant MODERATE 1274G>A Arg425Lys
M0206493 PHCGOMMF_00022 16158 3 Gut 0.27 protein_coding missense_variant MODERATE 1213A>G Ile405Val
M0206494 PHCGOMMF_00142 118391 3 Gut 0.27 protein_coding upstream_gene_variant MODIFIER -806C>T None
M0206495 PHCGOMMF_00051 40009 3 Gut 0.27 protein_coding synonymous_variant LOW 660C>T Leu220Leu






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
PHCGOMMF_00209 AIW55245.1|GT2 100 9.11e-260 1 345 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