Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1332
  Reference Plasmid   NZ_KT780704.1
  Reference Plasmid Size   64127
  Reference Plasmid GC Content   0.30
  Reference Plasmid Mobility Type   conjugative





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
M0116418 IICPEKDE_00032 29399 5 Skin 0.17 protein_coding missense_variant MODERATE 30T>A Asp10Glu
M0116419 IICPEKDE_00032 29436 5 Skin 0.17 protein_coding missense_variant MODERATE 67G>A Asp23Asn
M0116420 IICPEKDE_00032 29443 5 Skin 0.17 protein_coding missense_variant MODERATE 74T>C Ile25Thr
M0116421 IICPEKDE_00032 29489 5 Skin 0.17 protein_coding synonymous_variant LOW 120A>G Gln40Gln
M0116422 IICPEKDE_00032 29504 5 Skin 0.17 protein_coding missense_variant MODERATE 135T>A Asp45Glu
M0116423 IICPEKDE_00032 29587 5 Skin 0.17 protein_coding missense_variant MODERATE 218G>A Ser73Asn
M0116424 IICPEKDE_00032 29726 5 Skin 0.17 protein_coding missense_variant MODERATE 357A>G Ile119Met
M0116425 IICPEKDE_00032 29772 5 Skin 0.17 protein_coding missense_variant MODERATE 403T>A Leu135Ile
M0116426 IICPEKDE_00032 30065 5 Skin 0.17 protein_coding synonymous_variant LOW 696A>G Leu232Leu
M0116427 IICPEKDE_00032 30122 4 Skin 0.13 protein_coding synonymous_variant LOW 753T>G Val251Val
M0116428 IICPEKDE_00034 31415 4 Skin 0.13 protein_coding missense_variant MODERATE 511A>G Lys171Glu
M0116429 IICPEKDE_00034 31504 4 Skin 0.13 protein_coding missense_variant MODERATE 600A>T Glu200Asp
M0116430 IICPEKDE_00034 31505 4 Skin 0.13 protein_coding missense_variant MODERATE 601A>G Thr201Ala
M0116431 IICPEKDE_00034 31506 4 Skin 0.13 protein_coding missense_variant MODERATE 602C>T Thr201Ile
M0116432 IICPEKDE_00034 31507 4 Skin 0.13 protein_coding synonymous_variant LOW 603C>T Thr201Thr
M0116433 IICPEKDE_00034 31516 4 Skin 0.13 protein_coding synonymous_variant LOW 612C>A Ala204Ala
M0116434 IICPEKDE_00034 31522 4 Skin 0.13 protein_coding synonymous_variant LOW 618C>T Ile206Ile
M0116435 IICPEKDE_00034 31525 4 Skin 0.13 protein_coding synonymous_variant LOW 621T>C Ile207Ile
M0116436 IICPEKDE_00034 31571 4 Skin 0.13 protein_coding missense_variant MODERATE 667T>G Ser223Ala
M0116437 IICPEKDE_00034 31597 4 Skin 0.13 protein_coding synonymous_variant LOW 693C>T Asn231Asn
M0116438 IICPEKDE_00034 31629 4 Skin 0.13 protein_coding missense_variant MODERATE 725A>G Asn242Ser
M0116439 IICPEKDE_00034 31722 4 Skin 0.13 protein_coding missense_variant MODERATE 818G>A Arg273Lys
M0116440 IICPEKDE_00034 31801 4 Skin 0.13 protein_coding synonymous_variant LOW 897G>A Thr299Thr
M0116441 IICPEKDE_00034 31841 4 Skin 0.13 protein_coding missense_variant MODERATE 937C>T His313Tyr
M0116442 IICPEKDE_00034 32131 4 Skin 0.13 protein_coding synonymous_variant LOW 1227A>G Ala409Ala
M0116443 IICPEKDE_00034 32539 3 Skin 0.10 protein_coding synonymous_variant LOW 1635T>C His545His
M0116444 IICPEKDE_00034 32553 3 Skin 0.10 protein_coding missense_variant MODERATE 1649T>A Val550Glu
M0116445 IICPEKDE_00034 32555 3 Skin 0.10 protein_coding missense_variant MODERATE 1651G>A Glu551Lys
M0116446 IICPEKDE_00034 32557 3 Skin 0.10 protein_coding synonymous_variant LOW 1653G>A Glu551Glu
M0116447 IICPEKDE_00034 32572 3 Skin 0.10 protein_coding synonymous_variant LOW 1668G>C Leu556Leu
M0116448 IICPEKDE_00034 32597 3 Skin 0.10 protein_coding missense_variant MODERATE 1693A>C Ile565Leu
M0116449 IICPEKDE_00034 32615 3 Skin 0.10 protein_coding missense_variant MODERATE 1711G>T Ala571Ser
M0116450 IICPEKDE_00034 32662 3 Skin 0.10 protein_coding missense_variant MODERATE 1758G>T Glu586Asp
M0116451 IICPEKDE_00034 32686 3 Skin 0.10 protein_coding synonymous_variant LOW 1782C>T His594His
M0116452 IICPEKDE_00030 32717 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4464G>A None
M0116453 IICPEKDE_00030 32834 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4581A>G None
M0116454 IICPEKDE_00030 32849 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4596T>C None
M0116455 IICPEKDE_00030 32863 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4610A>G None
M0116456 IICPEKDE_00030 32910 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4657A>G None
M0116457 IICPEKDE_00035 33000 3 Skin 0.10 protein_coding synonymous_variant LOW 69G>A Gln23Gln
M0116458 IICPEKDE_00046 45617 7 Skin 0.23 protein_coding upstream_gene_variant MODIFIER -2703G>A None
M0116459 IICPEKDE_00049 46324 6 Skin 0.20 protein_coding missense_variant MODERATE 675T>A Ser225Arg
M0116460 IICPEKDE_00048 49364 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -3814A>C None
M0116461 IICPEKDE_00048 49380 6 Skin 0.20 protein_coding upstream_gene_variant MODIFIER -3830C>A None
M0116462 IICPEKDE_00048 49385 4 Skin 0.13 protein_coding upstream_gene_variant MODIFIER -3835A>G None
M0116463 IICPEKDE_00048 49392 4 Skin 0.13 protein_coding upstream_gene_variant MODIFIER -3842A>T None
M0116464 IICPEKDE_00048 49394 6 Skin 0.20 protein_coding upstream_gene_variant MODIFIER -3844A>G None
M0116465 IICPEKDE_00048 49401 4 Skin 0.13 protein_coding upstream_gene_variant MODIFIER -3851T>C None
M0116466 IICPEKDE_00048 49403 4 Skin 0.13 protein_coding upstream_gene_variant MODIFIER -3853A>T None
M0116467 IICPEKDE_00048 49404 6 Skin 0.20 protein_coding upstream_gene_variant MODIFIER -3854C>A None
M0116468 IICPEKDE_00048 49405 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -3855T>C None
M0116469 IICPEKDE_00048 49409 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -3859G>A None
M0116470 IICPEKDE_00048 49420 5 Skin 0.17 protein_coding upstream_gene_variant MODIFIER -3870T>C None
M0116471 IICPEKDE_00048 49421 5 Skin 0.17 protein_coding upstream_gene_variant MODIFIER -3871T>A 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
IICPEKDE_00019 ARO:3000521 99.5 0 1 1024 1.0000 1.0000 mupirocin-like antibiotic antibiotic-resistant isoleucyl-tRNA synthetase (ileS) antibiotic target alteration
IICPEKDE_00022 ARO:3002623 99.2 2.96e-189 4 256 0.9883 1.0000 aminoglycoside antibiotic ANT(4') antibiotic inactivation
IICPEKDE_00047 ARO:3000124 100 8.56e-86 1 123 1.0000 1.0000 penicillin beta-lactam methicillin resistant PBP2 antibiotic target replacement
IICPEKDE_00048 ARO:3000215 100 0 1 585 1.0000 1.0000 penicillin beta-lactam methicillin resistant PBP2 antibiotic target replacement
IICPEKDE_00049 ARO:3000617 99.7 0 1 668 1.0000 1.0000 penicillin beta-lactam methicillin resistant PBP2 antibiotic target replacement
HFLCKLGD_00019 ARO:3000521 99.5 0 1 1024 1.0000 1.0000 mupirocin-like antibiotic antibiotic-resistant isoleucyl-tRNA synthetase (ileS) antibiotic target alteration
HFLCKLGD_00022 ARO:3002623 99.2 2.96e-189 4 256 0.9883 1.0000 aminoglycoside antibiotic ANT(4') antibiotic inactivation
HFLCKLGD_00047 ARO:3000124 100 8.56e-86 1 123 1.0000 1.0000 penicillin beta-lactam methicillin resistant PBP2 antibiotic target replacement
HFLCKLGD_00048 ARO:3000215 100 0 1 585 1.0000 1.0000 penicillin beta-lactam methicillin resistant PBP2 antibiotic target replacement
HFLCKLGD_00049 ARO:3000617 99.7 0 1 668 1.0000 1.0000 penicillin beta-lactam methicillin resistant PBP2 antibiotic target replacement






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
IICPEKDE_00049 PHI:6884 MecA 99.9 0 1 668 1.0000 1.0000 rodents pneumonia penicillin-binding protein unaffected pathogenicity
HFLCKLGD_00049 PHI:6884 MecA 99.9 0 1 668 1.0000 1.0000 rodents pneumonia penicillin-binding protein unaffected pathogenicity






        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
IICPEKDE_00010 AVG65317.1|GH73 100 2.94e-258 1 358 1 1
HFLCKLGD_00010 AVG65317.1|GH73 100 2.94e-258 1 358 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
IICPEKDE_00003 3.A.7.7.1 100 5.2e-29 1 62 1.0000 1.1273 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IICPEKDE_00004 3.A.7.7.1 100 5.6e-175 1 324 1.0000 5.8909 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IICPEKDE_00005 3.A.7.7.1 100 2.1e-54 1 105 1.0000 1.9091 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IICPEKDE_00006 3.A.7.7.1 100 1.8e-66 1 135 1.0000 2.4545 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IICPEKDE_00007 3.A.7.7.1 100 1.5e-126 1 227 1.0000 4.1273 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IICPEKDE_00008 3.A.7.7.1 100 0 1 670 1.0000 12.1818 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IICPEKDE_00009 3.A.7.7.1 100 6e-233 1 426 1.0000 7.7455 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IICPEKDE_00010 3.A.7.7.1 99.7 4e-206 1 358 1.0000 6.5091 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IICPEKDE_00011 3.A.7.7.1 100 3.3e-83 1 161 1.0000 2.9273 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IICPEKDE_00012 3.A.7.7.1 100 0 1 700 1.0000 12.7273 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IICPEKDE_00013 3.A.7.7.1 100 1.9e-80 1 154 1.0000 2.8000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IICPEKDE_00014 3.A.7.7.1 100 2.5e-300 1 546 1.0000 9.9273 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IICPEKDE_00015 3.A.7.7.1 100 1e-162 1 305 1.0000 5.5455 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IICPEKDE_00016 3.A.7.7.1 100 8.3e-69 1 130 1.0000 2.3636 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IICPEKDE_00017 3.A.7.7.1 100 1.3e-23 1 55 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00003 3.A.7.7.1 100 5.2e-29 1 62 1.0000 1.1273 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00004 3.A.7.7.1 100 5.6e-175 1 324 1.0000 5.8909 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00005 3.A.7.7.1 100 2.1e-54 1 105 1.0000 1.9091 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00006 3.A.7.7.1 100 1.8e-66 1 135 1.0000 2.4545 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00007 3.A.7.7.1 100 1.5e-126 1 227 1.0000 4.1273 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00008 3.A.7.7.1 100 0 1 670 1.0000 12.1818 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00009 3.A.7.7.1 100 6e-233 1 426 1.0000 7.7455 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00010 3.A.7.7.1 99.7 4e-206 1 358 1.0000 6.5091 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00011 3.A.7.7.1 100 3.3e-83 1 161 1.0000 2.9273 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00012 3.A.7.7.1 100 0 1 700 1.0000 12.7273 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00013 3.A.7.7.1 100 1.9e-80 1 154 1.0000 2.8000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00014 3.A.7.7.1 100 2.5e-300 1 546 1.0000 9.9273 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00015 3.A.7.7.1 100 1e-162 1 305 1.0000 5.5455 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00016 3.A.7.7.1 100 8.3e-69 1 130 1.0000 2.3636 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
HFLCKLGD_00017 3.A.7.7.1 100 1.3e-23 1 55 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family