Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1212
  Reference Plasmid   NZ_CP135163.1
  Reference Plasmid Size   242774
  Reference Plasmid GC Content   0.41
  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
M0199527 AMCFLNPI_00071 66163 25 Gut 0.52 protein_coding synonymous_variant LOW 351T>C Asn117Asn
M0199528 AMCFLNPI_00071 66191 26 Gut 0.54 protein_coding missense_variant MODERATE 323T>A Leu108Gln
M0199529 AMCFLNPI_00071 66262 24 Gut 0.50 protein_coding synonymous_variant LOW 252A>G Gln84Gln
M0199530 AMCFLNPI_00071 66265 24 Gut 0.50 protein_coding synonymous_variant LOW 249T>C Asn83Asn
M0199531 AMCFLNPI_00071 66268 24 Gut 0.50 protein_coding synonymous_variant LOW 246C>A Thr82Thr
M0199532 AMCFLNPI_00071 66272 24 Gut 0.50 protein_coding missense_variant MODERATE 242G>A Ser81Asn
M0199533 AMCFLNPI_00071 66358 7 Gut 0.15 protein_coding synonymous_variant LOW 156G>T Thr52Thr
M0199534 AMCFLNPI_00071 66472 24 Gut 0.50 protein_coding synonymous_variant LOW 42C>T Ile14Ile
M0199535 AMCFLNPI_00071 66493 12 Gut 0.25 protein_coding synonymous_variant LOW 21T>A Ile7Ile
M0199536 AMCFLNPI_00071 66503 11 Gut 0.23 protein_coding missense_variant MODERATE 11G>A Arg4Lys
M0199537 AMCFLNPI_00064 66520 25 Gut 0.52 protein_coding upstream_gene_variant MODIFIER -4927G>A None
M0199538 AMCFLNPI_00068 64823 12 Gut 0.25 protein_coding missense_variant MODERATE 448T>G Ser150Ala
M0199539 AMCFLNPI_00068 64937 11 Gut 0.23 protein_coding missense_variant MODERATE 334A>G Ser112Gly
M0199540 AMCFLNPI_00068 64971 8 Gut 0.17 protein_coding synonymous_variant LOW 300A>G Thr100Thr
M0199541 AMCFLNPI_00068 64974 8 Gut 0.17 protein_coding synonymous_variant LOW 297G>T Leu99Leu
M0199542 AMCFLNPI_00068 64977 8 Gut 0.17 protein_coding synonymous_variant LOW 294A>G Lys98Lys
M0199543 AMCFLNPI_00068 64992 5 Gut 0.10 protein_coding synonymous_variant LOW 279G>A Leu93Leu
M0199544 AMCFLNPI_00068 65096 10 Gut 0.21 protein_coding missense_variant MODERATE 175C>T Leu59Phe
M0199545 AMCFLNPI_00068 65116 4 Gut 0.08 protein_coding missense_variant MODERATE 155G>A Gly52Glu
M0199546 AMCFLNPI_00069 65449 9 Gut 0.19 protein_coding missense_variant MODERATE 419A>C Gln140Pro
M0199547 AMCFLNPI_00069 65477 9 Gut 0.19 protein_coding missense_variant MODERATE 391T>C Ser131Pro
M0199548 AMCFLNPI_00069 65672 14 Gut 0.29 protein_coding missense_variant MODERATE 196T>C Tyr66His
M0199549 AMCFLNPI_00069 65738 8 Gut 0.17 protein_coding missense_variant MODERATE 130T>C Cys44Arg
M0199550 AMCFLNPI_00069 65778 14 Gut 0.29 protein_coding synonymous_variant LOW 90T>C Ile30Ile
M0199551 AMCFLNPI_00069 65805 14 Gut 0.29 protein_coding synonymous_variant LOW 63T>C Asp21Asp
M0199552 AMCFLNPI_00063 65889 10 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -4421A>G None
M0199553 AMCFLNPI_00070 65910 10 Gut 0.21 protein_coding synonymous_variant LOW 138T>C Asp46Asp
M0199554 AMCFLNPI_00070 65949 10 Gut 0.21 protein_coding synonymous_variant LOW 99G>A Pro33Pro
M0199555 AMCFLNPI_00070 65997 10 Gut 0.21 protein_coding synonymous_variant LOW 51A>C Gly17Gly
M0199556 AMCFLNPI_00070 66000 10 Gut 0.21 protein_coding synonymous_variant LOW 48A>G Lys16Lys
M0199557 AMCFLNPI_00073 67928 11 Gut 0.23 protein_coding synonymous_variant LOW 753A>G Lys251Lys
M0199558 AMCFLNPI_00073 68034 7 Gut 0.15 protein_coding missense_variant MODERATE 647A>C Glu216Ala
M0199559 AMCFLNPI_00073 68120 5 Gut 0.10 protein_coding synonymous_variant LOW 561G>A Pro187Pro
M0199560 AMCFLNPI_00073 68333 6 Gut 0.13 protein_coding synonymous_variant LOW 348A>G Val116Val
M0199561 AMCFLNPI_00073 68398 7 Gut 0.15 protein_coding missense_variant MODERATE 283A>C Lys95Gln
M0199562 AMCFLNPI_00073 68399 7 Gut 0.15 protein_coding synonymous_variant LOW 282A>G Glu94Glu
M0199563 AMCFLNPI_00073 68414 7 Gut 0.15 protein_coding synonymous_variant LOW 267A>G Lys89Lys
M0199564 AMCFLNPI_00073 68426 7 Gut 0.15 protein_coding synonymous_variant LOW 255G>A Arg85Arg
M0199565 AMCFLNPI_00073 68456 4 Gut 0.08 protein_coding synonymous_variant LOW 225A>G Leu75Leu
M0199566 AMCFLNPI_00073 68465 4 Gut 0.08 protein_coding synonymous_variant LOW 216G>A Gln72Gln
M0199567 AMCFLNPI_00073 68492 3 Gut 0.06 protein_coding synonymous_variant LOW 189A>T Thr63Thr
M0199568 AMCFLNPI_00073 68495 3 Gut 0.06 protein_coding synonymous_variant LOW 186C>T Phe62Phe
M0199569 AMCFLNPI_00073 68510 3 Gut 0.06 protein_coding synonymous_variant LOW 171G>A Gln57Gln
M0199570 AMCFLNPI_00073 68528 3 Gut 0.06 protein_coding synonymous_variant LOW 153C>T Tyr51Tyr
M0199571 AMCFLNPI_00073 68537 3 Gut 0.06 protein_coding synonymous_variant LOW 144A>G Lys48Lys
M0199572 AMCFLNPI_00073 68543 3 Gut 0.06 protein_coding synonymous_variant LOW 138C>A Val46Val
M0199573 AMCFLNPI_00073 68546 3 Gut 0.06 protein_coding synonymous_variant LOW 135C>T Cys45Cys
M0199574 AMCFLNPI_00073 68570 3 Gut 0.06 protein_coding synonymous_variant LOW 111A>G Ser37Ser
M0199575 AMCFLNPI_00073 68582 3 Gut 0.06 protein_coding synonymous_variant LOW 99T>A Ile33Ile
M0199576 AMCFLNPI_00073 68624 3 Gut 0.06 protein_coding synonymous_variant LOW 57A>G Arg19Arg
M0199577 AMCFLNPI_00073 68627 3 Gut 0.06 protein_coding synonymous_variant LOW 54C>A Ala18Ala
M0199578 AMCFLNPI_00073 68636 3 Gut 0.06 protein_coding synonymous_variant LOW 45G>A Val15Val
M0199579 AMCFLNPI_00072 66636 27 Gut 0.56 protein_coding missense_variant MODERATE 814G>T Ala272Ser
M0199580 AMCFLNPI_00072 66759 27 Gut 0.56 protein_coding missense_variant MODERATE 691A>T Ser231Cys
M0199581 AMCFLNPI_00072 67011 27 Gut 0.56 protein_coding missense_variant MODERATE 439A>T Asn147Tyr
M0199582 AMCFLNPI_00072 67181 26 Gut 0.54 protein_coding missense_variant MODERATE 269T>C Val90Ala
M0199583 AMCFLNPI_00072 67246 25 Gut 0.52 protein_coding synonymous_variant LOW 204T>C Val68Val
M0199584 AMCFLNPI_00072 67265 25 Gut 0.52 protein_coding missense_variant MODERATE 185A>C Asp62Ala
M0199585 AMCFLNPI_00072 67324 25 Gut 0.52 protein_coding synonymous_variant LOW 126C>T Ser42Ser
M0199586 AMCFLNPI_00072 67427 25 Gut 0.52 protein_coding missense_variant MODERATE 23C>G Ala8Gly
M0199587 AMCFLNPI_00060 64524 7 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4925G>T None
M0199588 AMCFLNPI_00060 64532 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -4933G>A None
M0199589 AMCFLNPI_00060 64534 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -4935A>G None
M0199590 AMCFLNPI_00060 64535 7 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4936C>T None
M0199591 AMCFLNPI_00061 64624 8 Gut 0.17 protein_coding upstream_gene_variant MODIFIER -4857A>G None
M0199592 AMCFLNPI_00061 64625 9 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -4858A>T None
M0199593 AMCFLNPI_00061 64628 9 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -4861G>A None
M0199594 AMCFLNPI_00068 64643 9 Gut 0.19 protein_coding missense_variant MODERATE 628A>G Arg210Gly
M0199595 AMCFLNPI_00068 64685 4 Gut 0.08 protein_coding missense_variant MODERATE 586G>A Val196Ile
M0199596 AMCFLNPI_00068 64736 11 Gut 0.23 protein_coding missense_variant MODERATE 535A>T Thr179Ser
M0199597 AMCFLNPI_00068 64764 11 Gut 0.23 protein_coding synonymous_variant LOW 507T>C Thr169Thr
M0199598 AMCFLNPI_00073 67642 4 Gut 0.08 protein_coding missense_variant MODERATE 1039G>T Ala347Ser
M0199599 AMCFLNPI_00067 64281 3 Gut 0.06 protein_coding synonymous_variant LOW 243G>A Gln81Gln
M0199600 AMCFLNPI_00067 64301 3 Gut 0.06 protein_coding missense_variant MODERATE 223T>A Leu75Ile
M0199601 AMCFLNPI_00067 64332 3 Gut 0.06 protein_coding synonymous_variant LOW 192A>G Glu64Glu
M0199602 AMCFLNPI_00067 64341 3 Gut 0.06 protein_coding synonymous_variant LOW 183A>T Thr61Thr
M0199603 AMCFLNPI_00067 64342 3 Gut 0.06 protein_coding missense_variant MODERATE 182C>G Thr61Arg
M0199604 AMCFLNPI_00067 64347 3 Gut 0.06 protein_coding synonymous_variant LOW 177T>C His59His
M0199605 AMCFLNPI_00067 64364 3 Gut 0.06 protein_coding missense_variant MODERATE 160G>A Asp54Asn
M0199606 AMCFLNPI_00067 64365 3 Gut 0.06 protein_coding synonymous_variant LOW 159T>A Arg53Arg
M0199607 AMCFLNPI_00067 64368 3 Gut 0.06 protein_coding synonymous_variant LOW 156T>C Leu52Leu
M0199608 AMCFLNPI_00067 64377 3 Gut 0.06 protein_coding synonymous_variant LOW 147G>A Leu49Leu
M0199609 AMCFLNPI_00067 64386 3 Gut 0.06 protein_coding synonymous_variant LOW 138C>T Asp46Asp
M0199610 AMCFLNPI_00067 64392 3 Gut 0.06 protein_coding synonymous_variant LOW 132A>G Arg44Arg
M0199611 AMCFLNPI_00067 64407 3 Gut 0.06 protein_coding synonymous_variant LOW 117A>G Pro39Pro
M0199612 AMCFLNPI_00067 64414 3 Gut 0.06 protein_coding missense_variant MODERATE 110A>T Tyr37Phe
M0199613 AMCFLNPI_00067 64419 3 Gut 0.06 protein_coding synonymous_variant LOW 105C>T Asp35Asp
M0199614 AMCFLNPI_00067 64476 3 Gut 0.06 protein_coding synonymous_variant LOW 48T>C Asp16Asp
M0199615 AMCFLNPI_00067 64491 3 Gut 0.06 protein_coding synonymous_variant LOW 33A>T Gly11Gly
M0199616 AMCFLNPI_00060 64568 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -4969A>T None
M0199617 AMCFLNPI_00068 64677 3 Gut 0.06 protein_coding synonymous_variant LOW 594T>G Ser198Ser
M0199618 AMCFLNPI_00068 64710 3 Gut 0.06 protein_coding synonymous_variant LOW 561C>T Leu187Leu
M0199619 AMCFLNPI_00068 65242 3 Gut 0.06 protein_coding missense_variant MODERATE 29T>C Met10Thr
M0199620 AMCFLNPI_00068 65254 3 Gut 0.06 protein_coding missense_variant MODERATE 17A>G Asn6Ser
M0199621 AMCFLNPI_00068 65255 3 Gut 0.06 protein_coding missense_variant MODERATE 16A>G Asn6Asp
M0199622 AMCFLNPI_00063 65280 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -3812T>C None
M0199623 AMCFLNPI_00069 65371 9 Gut 0.19 protein_coding stop_lost&splice_region_variant HIGH 497A>G Ter166Trpext*?
M0199624 AMCFLNPI_00069 65392 8 Gut 0.17 protein_coding missense_variant MODERATE 476A>C Lys159Thr
M0199625 AMCFLNPI_00069 65394 8 Gut 0.17 protein_coding synonymous_variant LOW 474T>C Asn158Asn
M0199626 AMCFLNPI_00069 65436 8 Gut 0.17 protein_coding synonymous_variant LOW 432A>G Arg144Arg
M0199627 AMCFLNPI_00069 65679 3 Gut 0.06 protein_coding synonymous_variant LOW 189T>C Ala63Ala
M0199628 AMCFLNPI_00069 65736 5 Gut 0.10 protein_coding synonymous_variant LOW 132C>T Cys44Cys
M0199629 AMCFLNPI_00069 65817 3 Gut 0.06 protein_coding synonymous_variant LOW 51T>A Ser17Ser
M0199630 AMCFLNPI_00069 65830 3 Gut 0.06 protein_coding missense_variant MODERATE 38C>T Ala13Val
M0199631 AMCFLNPI_00069 65840 3 Gut 0.06 protein_coding missense_variant MODERATE 28A>G Ile10Val
M0199632 AMCFLNPI_00069 65841 6 Gut 0.13 protein_coding synonymous_variant LOW 27C>T Ile9Ile
M0199633 AMCFLNPI_00063 65870 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -4402C>T None
M0199634 AMCFLNPI_00063 66049 9 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -4581A>G None
M0199635 AMCFLNPI_00063 66127 9 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -4659A>C None
M0199636 AMCFLNPI_00071 66139 9 Gut 0.19 protein_coding splice_region_variant&stop_retained_variant LOW 375G>A Ter125Ter
M0199637 AMCFLNPI_00072 66607 4 Gut 0.08 protein_coding synonymous_variant LOW 843G>A Glu281Glu
M0199638 AMCFLNPI_00072 66926 3 Gut 0.06 protein_coding missense_variant MODERATE 524C>T Ala175Val
M0199639 AMCFLNPI_00072 66931 3 Gut 0.06 protein_coding synonymous_variant LOW 519T>A Val173Val
M0199640 AMCFLNPI_00072 67021 3 Gut 0.06 protein_coding synonymous_variant LOW 429C>A Ala143Ala
M0199641 AMCFLNPI_00071 66208 4 Gut 0.08 protein_coding synonymous_variant LOW 306T>C Cys102Cys
M0199642 AMCFLNPI_00072 67405 4 Gut 0.08 protein_coding synonymous_variant LOW 45G>A Leu15Leu
M0199643 AMCFLNPI_00072 67407 4 Gut 0.08 protein_coding synonymous_variant LOW 43C>T Leu15Leu
M0199644 AMCFLNPI_00072 67414 4 Gut 0.08 protein_coding synonymous_variant LOW 36A>C Val12Val
M0199645 AMCFLNPI_00072 67417 4 Gut 0.08 protein_coding synonymous_variant LOW 33G>A Ser11Ser
M0199646 AMCFLNPI_00072 67420 4 Gut 0.08 protein_coding synonymous_variant LOW 30A>G Ala10Ala
M0199647 AMCFLNPI_00072 67429 4 Gut 0.08 protein_coding synonymous_variant LOW 21T>C Val7Val
M0199648 AMCFLNPI_00072 67435 4 Gut 0.08 protein_coding synonymous_variant LOW 15C>T Gly5Gly
M0199649 AMCFLNPI_00066 67474 5 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3885A>C None
M0199650 AMCFLNPI_00066 67478 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -3889G>A None
M0199651 AMCFLNPI_00068 65268 3 Gut 0.06 protein_coding start_lost HIGH 3G>A Met1?
M0199652 AMCFLNPI_00069 65688 3 Gut 0.06 protein_coding synonymous_variant LOW 180C>T Ala60Ala
M0199653 AMCFLNPI_00069 65787 4 Gut 0.08 protein_coding missense_variant MODERATE 81G>T Leu27Phe
M0199654 AMCFLNPI_00070 65896 3 Gut 0.06 protein_coding missense_variant MODERATE 152C>A Ala51Glu
M0199655 AMCFLNPI_00068 64955 3 Gut 0.06 protein_coding missense_variant MODERATE 316A>G Lys106Glu
M0199656 AMCFLNPI_00068 65049 3 Gut 0.06 protein_coding missense_variant MODERATE 222T>G Ile74Met
M0199657 AMCFLNPI_00063 65338 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -3870G>A None
M0199658 AMCFLNPI_00063 65346 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -3878A>G None
M0199659 AMCFLNPI_00063 65352 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -3884C>T None
M0199660 AMCFLNPI_00063 65353 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -3885A>T None
M0199661 AMCFLNPI_00072 67042 3 Gut 0.06 protein_coding synonymous_variant LOW 408G>A Ser136Ser
M0199662 AMCFLNPI_00073 67766 4 Gut 0.08 protein_coding missense_variant MODERATE 915T>A Asp305Glu
M0199663 AMCFLNPI_00073 68096 3 Gut 0.06 protein_coding synonymous_variant LOW 585C>T Cys195Cys
M0199664 AMCFLNPI_00063 66118 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -4650A>G None
M0199665 AMCFLNPI_00073 67565 3 Gut 0.06 protein_coding synonymous_variant LOW 1116G>A Ala372Ala
M0199666 AMCFLNPI_00069 65595 3 Gut 0.06 protein_coding synonymous_variant LOW 273C>A Ser91Ser






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
AMCFLNPI_00083 ACR77021.1|CBM34|GH13_20 89.9 0 1 572 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