Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1166
  Reference Plasmid   NZ_CP125670.1
  Reference Plasmid Size   241357
  Reference Plasmid GC Content   0.37
  Reference Plasmid Mobility Type   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
M0112515 HPKNOADA_00031 25029 5 Skin 0.10 protein_coding missense_variant MODERATE 208G>A Glu70Lys
M0112516 HPKNOADA_00031 25042 5 Skin 0.10 protein_coding missense_variant MODERATE 221T>A Met74Lys
M0112517 HPKNOADA_00026 25052 5 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4523A>G None
M0112518 HPKNOADA_00026 25053 5 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4524C>T None
M0112519 HPKNOADA_00026 25061 5 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4532G>A None
M0112520 HPKNOADA_00026 25065 5 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -4536A>C None
M0112521 HPKNOADA_00032 25176 5 Skin 0.10 protein_coding synonymous_variant LOW 66G>T Arg22Arg
M0112522 HPKNOADA_00032 25179 5 Skin 0.10 protein_coding synonymous_variant LOW 69T>C Ile23Ile
M0112523 HPKNOADA_00032 25197 5 Skin 0.10 protein_coding synonymous_variant LOW 87C>T Tyr29Tyr
M0112524 HPKNOADA_00032 25215 5 Skin 0.10 protein_coding synonymous_variant LOW 105G>C Ser35Ser
M0112525 HPKNOADA_00032 25221 5 Skin 0.10 protein_coding synonymous_variant LOW 111G>T Val37Val
M0112526 HPKNOADA_00032 25236 5 Skin 0.10 protein_coding synonymous_variant LOW 126A>T Thr42Thr
M0112527 HPKNOADA_00032 25239 5 Skin 0.10 protein_coding synonymous_variant LOW 129G>T Leu43Leu
M0112528 HPKNOADA_00032 25245 5 Skin 0.10 protein_coding synonymous_variant LOW 135C>G Arg45Arg
M0112529 HPKNOADA_00032 25251 5 Skin 0.10 protein_coding synonymous_variant LOW 141T>C Phe47Phe
M0112530 HPKNOADA_00032 25254 5 Skin 0.10 protein_coding synonymous_variant LOW 144C>T Leu48Leu
M0112531 HPKNOADA_00032 25272 5 Skin 0.10 protein_coding synonymous_variant LOW 162C>T Asp54Asp
M0112532 HPKNOADA_00032 25275 5 Skin 0.10 protein_coding synonymous_variant LOW 165T>C Pro55Pro
M0112533 HPKNOADA_00032 25293 5 Skin 0.10 protein_coding synonymous_variant LOW 183A>G Glu61Glu
M0112534 HPKNOADA_00032 25302 5 Skin 0.10 protein_coding synonymous_variant LOW 192C>A Pro64Pro
M0112535 HPKNOADA_00032 25308 5 Skin 0.10 protein_coding synonymous_variant LOW 198G>C Thr66Thr
M0112536 HPKNOADA_00032 25329 5 Skin 0.10 protein_coding synonymous_variant LOW 219G>A Gly73Gly
M0112537 HPKNOADA_00032 25446 5 Skin 0.10 protein_coding synonymous_variant LOW 336A>G Leu112Leu
M0112538 HPKNOADA_00032 25476 4 Skin 0.08 protein_coding synonymous_variant LOW 366C>A Ala122Ala
M0112539 HPKNOADA_00032 25527 5 Skin 0.10 protein_coding synonymous_variant LOW 417T>G Gly139Gly
M0112540 HPKNOADA_00032 25637 6 Skin 0.13 protein_coding missense_variant MODERATE 527A>G Glu176Gly
M0112541 HPKNOADA_00032 25640 6 Skin 0.13 protein_coding missense_variant MODERATE 530T>C Val177Ala
M0112542 HPKNOADA_00032 25680 6 Skin 0.13 protein_coding synonymous_variant LOW 570C>A Gly190Gly
M0112543 HPKNOADA_00032 25690 6 Skin 0.13 protein_coding synonymous_variant LOW 580C>A Arg194Arg
M0112544 HPKNOADA_00032 25695 6 Skin 0.13 protein_coding synonymous_variant LOW 585A>C Ala195Ala
M0112545 HPKNOADA_00032 25756 6 Skin 0.13 protein_coding missense_variant MODERATE 646G>A Ala216Thr
M0112546 HPKNOADA_00032 25757 6 Skin 0.13 protein_coding missense_variant MODERATE 647C>T Ala216Val
M0112547 HPKNOADA_00032 25758 6 Skin 0.13 protein_coding synonymous_variant LOW 648A>G Ala216Ala
M0112548 HPKNOADA_00032 25782 6 Skin 0.13 protein_coding synonymous_variant LOW 672C>T Leu224Leu
M0112549 HPKNOADA_00032 25790 6 Skin 0.13 protein_coding missense_variant MODERATE 680G>A Ser227Asn
M0112550 HPKNOADA_00033 25847 6 Skin 0.13 protein_coding synonymous_variant LOW 45T>G Pro15Pro
M0112551 HPKNOADA_00033 25868 6 Skin 0.13 protein_coding synonymous_variant LOW 66T>C Pro22Pro
M0112552 HPKNOADA_00033 25895 6 Skin 0.13 protein_coding synonymous_variant LOW 93G>A Leu31Leu
M0112553 HPKNOADA_00033 25901 6 Skin 0.13 protein_coding synonymous_variant LOW 99A>G Ser33Ser
M0112554 HPKNOADA_00033 25925 6 Skin 0.13 protein_coding synonymous_variant LOW 123A>T Thr41Thr
M0112555 HPKNOADA_00033 25928 6 Skin 0.13 protein_coding synonymous_variant LOW 126T>C Gly42Gly
M0112556 HPKNOADA_00033 25936 6 Skin 0.13 protein_coding missense_variant MODERATE 134A>G Asn45Ser
M0112557 HPKNOADA_00033 25940 6 Skin 0.13 protein_coding synonymous_variant LOW 138T>C Ile46Ile
M0112558 HPKNOADA_00033 25964 6 Skin 0.13 protein_coding synonymous_variant LOW 162G>A Pro54Pro
M0112559 HPKNOADA_00033 25983 6 Skin 0.13 protein_coding missense_variant MODERATE 181C>T His61Tyr
M0112560 HPKNOADA_00033 25997 5 Skin 0.10 protein_coding synonymous_variant LOW 195G>A Glu65Glu
M0112561 HPKNOADA_00033 26051 6 Skin 0.13 protein_coding synonymous_variant LOW 249T>A Arg83Arg
M0112562 HPKNOADA_00033 26633 4 Skin 0.08 protein_coding synonymous_variant LOW 831C>T Ala277Ala
M0112563 HPKNOADA_00033 26702 4 Skin 0.08 protein_coding synonymous_variant LOW 900G>T Ser300Ser
M0112564 HPKNOADA_00033 26945 4 Skin 0.08 protein_coding synonymous_variant LOW 1143C>T Gly381Gly
M0112565 HPKNOADA_00033 27113 5 Skin 0.10 protein_coding synonymous_variant LOW 1311G>A Gly437Gly
M0112566 HPKNOADA_00034 28471 6 Skin 0.13 protein_coding missense_variant MODERATE 783C>A Asp261Glu
M0112567 HPKNOADA_00035 28768 6 Skin 0.13 protein_coding missense_variant MODERATE 209C>A Thr70Lys
M0112568 HPKNOADA_00035 28848 6 Skin 0.13 protein_coding missense_variant MODERATE 289C>T Leu97Phe
M0112569 HPKNOADA_00035 28883 6 Skin 0.13 protein_coding synonymous_variant LOW 324C>T Asn108Asn
M0112570 HPKNOADA_00035 28995 6 Skin 0.13 protein_coding missense_variant MODERATE 436A>G Asn146Asp
M0112571 HPKNOADA_00035 29002 6 Skin 0.13 protein_coding missense_variant MODERATE 443A>G His148Arg
M0112572 HPKNOADA_00035 29042 6 Skin 0.13 protein_coding synonymous_variant LOW 483A>G Gln161Gln
M0112573 HPKNOADA_00035 29111 6 Skin 0.13 protein_coding synonymous_variant LOW 552G>A Glu184Glu
M0112574 HPKNOADA_00035 29172 6 Skin 0.13 protein_coding synonymous_variant LOW 613C>T Leu205Leu
M0112575 HPKNOADA_00035 29175 6 Skin 0.13 protein_coding missense_variant MODERATE 616G>A Glu206Lys
M0112576 HPKNOADA_00035 29300 6 Skin 0.13 protein_coding synonymous_variant LOW 741T>A Ala247Ala
M0112577 HPKNOADA_00035 29393 6 Skin 0.13 protein_coding synonymous_variant LOW 834G>A Arg278Arg
M0112578 HPKNOADA_00035 29429 6 Skin 0.13 protein_coding synonymous_variant LOW 870C>T Pro290Pro
M0112579 HPKNOADA_00035 29567 7 Skin 0.15 protein_coding missense_variant MODERATE 1008G>T Lys336Asn
M0112580 HPKNOADA_00035 29581 7 Skin 0.15 protein_coding missense_variant MODERATE 1022C>A Ala341Asp
M0112581 HPKNOADA_00035 29586 7 Skin 0.15 protein_coding missense_variant MODERATE 1027T>C Phe343Leu
M0112582 HPKNOADA_00035 29618 7 Skin 0.15 protein_coding synonymous_variant LOW 1059C>A Arg353Arg
M0112583 HPKNOADA_00036 29784 6 Skin 0.13 protein_coding synonymous_variant LOW 114G>A Pro38Pro
M0112584 HPKNOADA_00059 49747 8 Skin 0.17 protein_coding missense_variant MODERATE 244T>C Phe82Leu
M0112585 HPKNOADA_00062 52548 7 Skin 0.15 protein_coding synonymous_variant LOW 69A>T Ile23Ile
M0112586 HPKNOADA_00037 31399 5 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -288A>G None
M0112587 HPKNOADA_00038 31423 5 Skin 0.10 protein_coding start_lost HIGH 3G>A Met1?
M0112588 HPKNOADA_00038 31477 4 Skin 0.08 protein_coding synonymous_variant LOW 57T>A Ser19Ser
M0112589 HPKNOADA_00038 31555 5 Skin 0.10 protein_coding synonymous_variant LOW 135C>T Ser45Ser
M0112590 HPKNOADA_00038 31561 5 Skin 0.10 protein_coding synonymous_variant LOW 141A>G Gly47Gly
M0112591 HPKNOADA_00038 31569 5 Skin 0.10 protein_coding missense_variant MODERATE 149G>C Cys50Ser
M0112592 HPKNOADA_00038 31771 5 Skin 0.10 protein_coding synonymous_variant LOW 351G>A Leu117Leu
M0112593 HPKNOADA_00038 31780 5 Skin 0.10 protein_coding synonymous_variant LOW 360C>T Ser120Ser
M0112594 HPKNOADA_00038 31828 5 Skin 0.10 protein_coding synonymous_variant LOW 408C>T Gly136Gly
M0112595 HPKNOADA_00038 31879 5 Skin 0.10 protein_coding synonymous_variant LOW 459A>G Val153Val
M0112596 HPKNOADA_00037 31949 4 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -838C>A None
M0112597 HPKNOADA_00039 31959 4 Skin 0.08 protein_coding synonymous_variant LOW 9A>G Gln3Gln
M0112598 HPKNOADA_00039 32433 6 Skin 0.13 protein_coding synonymous_variant LOW 483C>T Asn161Asn
M0112599 HPKNOADA_00039 32553 5 Skin 0.10 protein_coding synonymous_variant LOW 603C>G Thr201Thr
M0112600 HPKNOADA_00039 32559 5 Skin 0.10 protein_coding synonymous_variant LOW 609A>T Gly203Gly
M0112601 HPKNOADA_00039 32566 5 Skin 0.10 protein_coding synonymous_variant LOW 616T>C Leu206Leu
M0112602 HPKNOADA_00040 32758 5 Skin 0.10 protein_coding synonymous_variant LOW 924C>T Asn308Asn
M0112603 HPKNOADA_00040 33262 5 Skin 0.10 protein_coding synonymous_variant LOW 420T>C Arg140Arg
M0112604 HPKNOADA_00040 33406 5 Skin 0.10 protein_coding synonymous_variant LOW 276A>G Leu92Leu
M0112605 HPKNOADA_00036 30262 5 Skin 0.10 protein_coding missense_variant MODERATE 592G>A Val198Ile
M0112606 HPKNOADA_00036 30267 5 Skin 0.10 protein_coding synonymous_variant LOW 597T>C Asn199Asn
M0112607 HPKNOADA_00036 30302 5 Skin 0.10 protein_coding missense_variant MODERATE 632A>G Asn211Ser
M0112608 HPKNOADA_00037 31187 4 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -76C>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
HPKNOADA_00062 Gold (Au) 70.5 1.9e-49 1 129 0.8487 0.8377 experiment
HPKNOADA_00063 Copper (Cu), Gold (Au) 75.8 0 79 823 0.8998 0.9777 experiment
HPKNOADA_00068 Gold (Au), Methylene Blue [class: Thiazinium], Crystal Violet [class: Triarylmethane] 75 0 4 1043 0.9905 0.9896 experiment
HPKNOADA_00055 Nickel (Ni), Cobalt (Co) 83.2 1e-197 1 435 1.0000 1.0000 prediction
HPKNOADA_00062 Gold (Au) 71.3 6.8e-48 1 129 0.8487 0.8377 prediction
HPKNOADA_00063 Copper (Cu), Gold (Au) 100 0 1 828 1.0000 1.0000 prediction
HPKNOADA_00068 Gold (Au), Methylene Blue [class: Thiazinium], Crystal Violet [class: Triarylmethane] 76 0 4 1043 0.9896 0.9858 prediction






        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
HPKNOADA_00062 ARO:3000504 70.5 2.2e-61 1 129 0.8487 0.8377 monobactam resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
HPKNOADA_00068 ARO:3000790 74.9 0 3 1043 0.9915 0.9905 monobactam resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux






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
HPKNOADA_00063 PHI:8812 CopA (ABUW_2707) 70.9 0 15 823 0.9771 0.9818 rodents nosocomial infection copper-translocating P-type ATPase 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
HPKNOADA_00025 WHP07741.1|GH23 100 2.52e-193 1 272 1 1
HPKNOADA_00131 WHP07827.1|GH23 100 0 1 622 1 1
HPKNOADA_00197 WHP07827.1|GH23 100 0 1 622 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
HPKNOADA_00063 3.A.3.5.20 75.8 0 79 823 0.8998 0.9764 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
HPKNOADA_00068 2.A.6.2.25 75 0 4 1043 0.9867 2.0736 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily