Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1175
  Reference Plasmid   NZ_CP128356.1
  Reference Plasmid Size   81646
  Reference Plasmid GC Content   0.30
  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
M0112626 NFPFIOAO_00025 32891 5 Skin 0.14 protein_coding upstream_gene_variant MODIFIER -4480G>A None
M0112627 NFPFIOAO_00025 32892 5 Skin 0.14 protein_coding upstream_gene_variant MODIFIER -4481T>C None
M0112628 NFPFIOAO_00025 32894 4 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -4483T>G None
M0112629 NFPFIOAO_00013 13541 4 Skin 0.11 protein_coding synonymous_variant LOW 921C>T Ser307Ser
M0112630 NFPFIOAO_00013 13825 4 Skin 0.11 protein_coding missense_variant MODERATE 1205A>G His402Arg
M0112631 NFPFIOAO_00013 14306 3 Skin 0.08 protein_coding missense_variant MODERATE 1686G>C Lys562Asn
M0112632 NFPFIOAO_00001 284 9 Skin 0.25 protein_coding downstream_gene_variant MODIFIER *422C>T None
M0112633 NFPFIOAO_00001 592 3 Skin 0.08 protein_coding downstream_gene_variant MODIFIER *114G>A None
M0112634 NFPFIOAO_00001 626 6 Skin 0.17 protein_coding downstream_gene_variant MODIFIER *80T>C None
M0112635 NFPFIOAO_00001 641 3 Skin 0.08 protein_coding downstream_gene_variant MODIFIER *65C>T None
M0112636 NFPFIOAO_00001 2025 5 Skin 0.14 protein_coding missense_variant MODERATE 1321G>T Val441Leu
M0112637 NFPFIOAO_00001 2140 4 Skin 0.11 protein_coding synonymous_variant LOW 1206G>A Leu402Leu
M0112638 NFPFIOAO_00001 2149 4 Skin 0.11 protein_coding synonymous_variant LOW 1197T>C Ala399Ala
M0112639 NFPFIOAO_00001 2853 5 Skin 0.14 protein_coding missense_variant MODERATE 493G>A Ala165Thr
M0112640 NFPFIOAO_00001 3395 3 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -50T>C None
M0112641 NFPFIOAO_00001 3398 3 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -53A>G None
M0112642 NFPFIOAO_00001 3404 3 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -59T>A None
M0112643 NFPFIOAO_00001 3426 3 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -81G>A None
M0112644 NFPFIOAO_00081 80589 7 Skin 0.19 protein_coding synonymous_variant LOW 447T>C Tyr149Tyr
M0112645 NFPFIOAO_00081 80857 7 Skin 0.19 protein_coding missense_variant MODERATE 179G>C Arg60Pro
M0112646 NFPFIOAO_00001 202 4 Skin 0.11 protein_coding downstream_gene_variant MODIFIER *504A>G None
M0112647 NFPFIOAO_00001 404 4 Skin 0.11 protein_coding downstream_gene_variant MODIFIER *302T>C None
M0112648 NFPFIOAO_00001 421 4 Skin 0.11 protein_coding downstream_gene_variant MODIFIER *285A>G None
M0112649 NFPFIOAO_00001 535 3 Skin 0.08 protein_coding downstream_gene_variant MODIFIER *171C>T None
M0112650 NFPFIOAO_00001 594 3 Skin 0.08 protein_coding downstream_gene_variant MODIFIER *112G>A None
M0112651 NFPFIOAO_00001 694 3 Skin 0.08 protein_coding downstream_gene_variant MODIFIER *12A>G None
M0112652 NFPFIOAO_00001 1143 3 Skin 0.08 protein_coding missense_variant MODERATE 2203G>T Ala735Ser
M0112653 NFPFIOAO_00001 1151 3 Skin 0.08 protein_coding missense_variant MODERATE 2195A>G Asn732Ser
M0112654 NFPFIOAO_00001 1233 4 Skin 0.11 protein_coding missense_variant MODERATE 2113A>G Ile705Val
M0112655 NFPFIOAO_00001 1489 3 Skin 0.08 protein_coding synonymous_variant LOW 1857C>T Asp619Asp
M0112656 NFPFIOAO_00001 1578 3 Skin 0.08 protein_coding missense_variant MODERATE 1768G>A Val590Ile
M0112657 NFPFIOAO_00001 1594 3 Skin 0.08 protein_coding synonymous_variant LOW 1752C>T Leu584Leu
M0112658 NFPFIOAO_00001 1752 3 Skin 0.08 protein_coding missense_variant MODERATE 1594G>T Val532Phe
M0112659 NFPFIOAO_00001 2047 4 Skin 0.11 protein_coding synonymous_variant LOW 1299C>T Asp433Asp
M0112660 NFPFIOAO_00001 2298 3 Skin 0.08 protein_coding missense_variant MODERATE 1048C>T Pro350Ser
M0112661 NFPFIOAO_00001 2325 3 Skin 0.08 protein_coding missense_variant MODERATE 1021T>A Ser341Thr
M0112662 NFPFIOAO_00001 2518 3 Skin 0.08 protein_coding synonymous_variant LOW 828T>C Gly276Gly
M0112663 NFPFIOAO_00001 2542 3 Skin 0.08 protein_coding synonymous_variant LOW 804C>T Ile268Ile
M0112664 NFPFIOAO_00001 2653 3 Skin 0.08 protein_coding synonymous_variant LOW 693G>T Thr231Thr
M0112665 NFPFIOAO_00001 2971 3 Skin 0.08 protein_coding synonymous_variant LOW 375C>T Thr125Thr
M0112666 NFPFIOAO_00001 2986 3 Skin 0.08 protein_coding synonymous_variant LOW 360C>T Asn120Asn
M0112667 NFPFIOAO_00001 3169 3 Skin 0.08 protein_coding synonymous_variant LOW 177T>C Ile59Ile
M0112668 NFPFIOAO_00001 3259 3 Skin 0.08 protein_coding synonymous_variant LOW 87C>T Val29Val
M0112669 NFPFIOAO_00001 3513 3 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -168T>G None
M0112670 NFPFIOAO_00081 80479 3 Skin 0.08 protein_coding missense_variant MODERATE 557A>G Tyr186Cys
M0112671 NFPFIOAO_00081 80647 3 Skin 0.08 protein_coding missense_variant MODERATE 389A>C Asp130Ala
M0112672 NFPFIOAO_00081 80765 3 Skin 0.08 protein_coding missense_variant MODERATE 271T>G Cys91Gly
M0112673 NFPFIOAO_00081 80775 3 Skin 0.08 protein_coding synonymous_variant LOW 261T>C Ile87Ile
M0112674 NFPFIOAO_00081 80798 3 Skin 0.08 protein_coding missense_variant MODERATE 238T>C Ser80Pro
M0112675 NFPFIOAO_00081 80846 3 Skin 0.08 protein_coding missense_variant MODERATE 190G>A Ala64Thr
M0112676 NFPFIOAO_00076 81369 5 Skin 0.14 protein_coding upstream_gene_variant MODIFIER -3950T>A None
M0112677 NFPFIOAO_00076 81374 3 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -3955T>A None
M0112678 NFPFIOAO_00082 81388 3 Skin 0.08 protein_coding missense_variant MODERATE 257A>T Asn86Ile
M0112679 NFPFIOAO_00082 81400 5 Skin 0.14 protein_coding missense_variant MODERATE 245A>G Asp82Gly
M0112680 NFPFIOAO_00082 81545 3 Skin 0.08 protein_coding missense_variant MODERATE 100A>G Ile34Val
M0112681 NFPFIOAO_00082 81567 4 Skin 0.11 protein_coding synonymous_variant LOW 78G>A Glu26Glu
M0112682 NFPFIOAO_00082 81578 4 Skin 0.11 protein_coding missense_variant MODERATE 67A>G Asn23Asp
M0112683 NFPFIOAO_00009 14883 3 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -4300G>A None
M0112684 NFPFIOAO_00009 14954 3 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -4371T>G None
M0112685 NFPFIOAO_00009 14961 3 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -4378A>G None
M0112686 NFPFIOAO_00015 15091 3 Skin 0.08 protein_coding missense_variant MODERATE 80A>G Tyr27Cys
M0112687 NFPFIOAO_00001 2841 3 Skin 0.08 protein_coding missense_variant MODERATE 505T>G Ser169Ala
M0112688 NFPFIOAO_00001 2844 3 Skin 0.08 protein_coding missense_variant MODERATE 502A>G Ser168Gly






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
NFPFIOAO_00039 Arsenic (As), Antimony (Sb) 91.6 4.5e-213 2 430 0.9977 1.0000 experiment
NFPFIOAO_00060 Cadmium (Cd), Zinc (Zn) 94.1 2.2e-101 1 205 1.0000 1.0000 experiment
GENALHPE_00039 Arsenic (As), Antimony (Sb) 91.6 4.5e-213 2 430 0.9977 1.0000 experiment
GENALHPE_00060 Cadmium (Cd), Zinc (Zn) 94.1 2.2e-101 1 205 1.0000 1.0000 experiment
NFPFIOAO_00004 Copper (Cu) 100 1.6e-33 1 69 1.0000 1.0000 prediction
NFPFIOAO_00005 Copper (Cu), Silver (Ag) 75.6 0 1 795 1.0000 1.0013 prediction
NFPFIOAO_00039 Arsenic (As), Antimony (Sb) 100 2.6e-225 1 430 1.0000 1.0000 prediction
NFPFIOAO_00060 Cadmium (Cd), Zinc (Zn) 99.5 2.9e-102 1 205 1.0000 1.0000 prediction
GENALHPE_00004 Copper (Cu) 100 1.6e-33 1 69 1.0000 1.0000 prediction
GENALHPE_00005 Copper (Cu), Silver (Ag) 75.6 0 1 795 1.0000 1.0013 prediction
GENALHPE_00039 Arsenic (As), Antimony (Sb) 100 2.6e-225 1 430 1.0000 1.0000 prediction
GENALHPE_00060 Cadmium (Cd), Zinc (Zn) 99.5 2.9e-102 1 205 1.0000 1.0000 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
NFPFIOAO_00012 ARO:3008823 97.9 3.52e-192 1 281 1.0000 1.0000 penicillin beta-lactam BlaZ beta-lactamase antibiotic inactivation
GENALHPE_00012 ARO:3008823 97.9 3.52e-192 1 281 1.0000 1.0000 penicillin beta-lactam BlaZ beta-lactamase antibiotic inactivation






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
NFPFIOAO_00057 PHI:6191 Lqo 81.3 6.5e-247 1 497 0.9960 1.0000 rodents skin infection; food poisoning; respiratory disease L-lactate-quinone oxidoreductases reduced virulence
GENALHPE_00057 PHI:6191 Lqo 81.3 6.5e-247 1 497 0.9960 1.0000 rodents skin infection; food poisoning; respiratory disease L-lactate-quinone oxidoreductases reduced virulence






        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
NFPFIOAO_00005 3.A.3.5.19 73.6 0 4 795 0.9962 0.9888 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
NFPFIOAO_00039 2.A.45.1.1 90.4 6.1e-209 2 430 0.9977 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.45 The Arsenite-Antimonite (ArsB) Efflux Family
NFPFIOAO_00060 2.A.77.1.1 93.7 1.9e-99 1 205 1.0000 0.9809 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.77 The Cadmium Resistance (CadD) Family
NFPFIOAO_00069 2.A.21.2.2 74 8.3e-221 1 512 0.9961 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.21 The Solute:Sodium Symporter (SSS) Family
GENALHPE_00005 3.A.3.5.19 73.6 0 4 795 0.9962 0.9888 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
GENALHPE_00039 2.A.45.1.1 90.4 6.1e-209 2 430 0.9977 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.45 The Arsenite-Antimonite (ArsB) Efflux Family
GENALHPE_00060 2.A.77.1.1 93.7 1.9e-99 1 205 1.0000 0.9809 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.77 The Cadmium Resistance (CadD) Family
GENALHPE_00069 2.A.21.2.2 74 8.3e-221 1 512 0.9961 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.21 The Solute:Sodium Symporter (SSS) Family