Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1418
  Reference Plasmid   NZ_OX441725.1
  Reference Plasmid Size   160836
  Reference Plasmid GC Content   0.33
  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
M0116829 MHGNFBNH_00069 64636 3 Skin 0.33 protein_coding missense_variant MODERATE 85A>G Ile29Val
M0116830 MHGNFBNH_00070 64981 3 Skin 0.33 protein_coding synonymous_variant LOW 493C>T Leu165Leu
M0116831 MHGNFBNH_00070 65209 3 Skin 0.33 protein_coding missense_variant MODERATE 265G>A Val89Ile
M0116832 MHGNFBNH_00070 65353 3 Skin 0.33 protein_coding missense_variant MODERATE 121G>A Val41Ile
M0116833 MHGNFBNH_00070 65456 3 Skin 0.33 protein_coding synonymous_variant LOW 18T>C Val6Val
M0116834 MHGNFBNH_00064 65653 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -4761T>A None
M0116835 MHGNFBNH_00064 65704 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -4812G>T None
M0116836 MHGNFBNH_00065 65956 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -3680A>G None
M0116837 MHGNFBNH_00065 65961 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -3685C>A None
M0116838 MHGNFBNH_00071 66040 3 Skin 0.33 protein_coding stop_lost&splice_region_variant HIGH 517T>C Ter173Glnext*?
M0116839 MHGNFBNH_00071 66112 3 Skin 0.33 protein_coding missense_variant MODERATE 445T>A Leu149Ile
M0116840 MHGNFBNH_00071 66119 3 Skin 0.33 protein_coding synonymous_variant LOW 438G>A Gly146Gly
M0116841 MHGNFBNH_00071 66209 3 Skin 0.33 protein_coding synonymous_variant LOW 348C>T Phe116Phe
M0116842 MHGNFBNH_00071 66290 3 Skin 0.33 protein_coding synonymous_variant LOW 267T>C Asn89Asn
M0116843 MHGNFBNH_00071 66317 3 Skin 0.33 protein_coding synonymous_variant LOW 240C>T Phe80Phe
M0116844 MHGNFBNH_00071 66356 3 Skin 0.33 protein_coding synonymous_variant LOW 201C>T Asn67Asn
M0116845 MHGNFBNH_00071 66368 3 Skin 0.33 protein_coding synonymous_variant LOW 189A>G Glu63Glu
M0116846 MHGNFBNH_00071 66374 3 Skin 0.33 protein_coding synonymous_variant LOW 183T>A Ile61Ile
M0116847 MHGNFBNH_00071 66416 3 Skin 0.33 protein_coding synonymous_variant LOW 141G>A Lys47Lys
M0116848 MHGNFBNH_00071 66446 3 Skin 0.33 protein_coding synonymous_variant LOW 111T>C Phe37Phe
M0116849 MHGNFBNH_00071 66493 3 Skin 0.33 protein_coding missense_variant MODERATE 64C>G Gln22Glu
M0116850 MHGNFBNH_00071 66540 3 Skin 0.33 protein_coding missense_variant MODERATE 17A>G Lys6Arg
M0116851 MHGNFBNH_00065 66575 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -4299A>T None
M0116852 MHGNFBNH_00072 66657 3 Skin 0.33 protein_coding synonymous_variant LOW 579C>T Asn193Asn
M0116853 MHGNFBNH_00072 66717 3 Skin 0.33 protein_coding synonymous_variant LOW 519A>G Val173Val
M0116854 MHGNFBNH_00072 66729 3 Skin 0.33 protein_coding synonymous_variant LOW 507G>A Val169Val






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
MHGNFBNH_00109 VFG001281 SDr 92 0 1 1111 1.0 0.9737 Adherence Ser-Asp rich fibrinogen-binding bone sialoprotein-binding protein experiment
MHGNFBNH_00110 VFG001280 SDr 83.8 0 1 1279 0.9322 0.9495 Adherence Ser-Asp rich fibrinogen-binding bone sialoprotein-binding protein experiment
MHGNFBNH_00111 VFG001279 SDr 91.4 0 1 887 0.8906 0.9288 Adherence Ser-Asp rich fibrinogen-binding bone sialoprotein-binding protein experiment
MHGNFBNH_00124 VFG046465 EF-Tu 74.6 5e-179 1 394 1.0 1 Adherence elongation factor Tu experiment
CKKOLPHL_00109 VFG001281 SDr 92 0 1 1111 1.0 0.9737 Adherence Ser-Asp rich fibrinogen-binding bone sialoprotein-binding protein experiment
CKKOLPHL_00110 VFG001280 SDr 83.8 0 1 1279 0.9322 0.9495 Adherence Ser-Asp rich fibrinogen-binding bone sialoprotein-binding protein experiment
CKKOLPHL_00111 VFG001279 SDr 91.4 0 1 887 0.8906 0.9288 Adherence Ser-Asp rich fibrinogen-binding bone sialoprotein-binding protein experiment
CKKOLPHL_00124 VFG046465 EF-Tu 74.6 5e-179 1 394 1.0 1 Adherence elongation factor Tu experiment
MHGNFBNH_00109 VFG001281 SDr 92 0 1 1111 1.0 0.9737 Adherence Ser-Asp rich fibrinogen-binding bone sialoprotein-binding protein prediction
MHGNFBNH_00110 VFG004596 SDr 88.9 0 1 1372 1.0 0.9906 Adherence Ser-Asp rich fibrinogen-binding bone sialoprotein-binding protein prediction
MHGNFBNH_00111 VFG004603 SDr 90.3 0 1 996 1.0 1.001 Adherence Ser-Asp rich fibrinogen-binding bone sialoprotein-binding protein prediction
MHGNFBNH_00124 VFG046475 EF-Tu 75.6 2.6e-179 1 394 1.0 1 Adherence elongation factor Tu prediction
CKKOLPHL_00109 VFG001281 SDr 92 0 1 1111 1.0 0.9737 Adherence Ser-Asp rich fibrinogen-binding bone sialoprotein-binding protein prediction
CKKOLPHL_00110 VFG004596 SDr 88.9 0 1 1372 1.0 0.9906 Adherence Ser-Asp rich fibrinogen-binding bone sialoprotein-binding protein prediction
CKKOLPHL_00111 VFG004603 SDr 90.3 0 1 996 1.0 1.001 Adherence Ser-Asp rich fibrinogen-binding bone sialoprotein-binding protein prediction
CKKOLPHL_00124 VFG046475 EF-Tu 75.6 2.6e-179 1 394 1.0 1 Adherence elongation factor Tu prediction







        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
MHGNFBNH_00034 ARO:3002704 100 0 1 475 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
MHGNFBNH_00124 ARO:3003438 86.3 2.58e-251 1 392 0.9975 0.9291 elfamycin antibiotic elfamycin resistant EF-Tu antibiotic target alteration
MHGNFBNH_00125 ARO:3003735 100 0 1 693 1.0000 1.0000 fusidane antibiotic antibiotic resistant fusA antibiotic target alteration
MHGNFBNH_00129 ARO:3003291 100 0 1 1207 1.0000 1.0000 peptide antibiotic daptomycin-resistant beta prime subunit of RNA polymerase (rpoC) antibiotic target alteration
MHGNFBNH_00130 ARO:3003285 99.9 0 1 1183 1.0000 1.0000 rifamycin antibiotic rifamycin-resistant beta-subunit of RNA polymerase (rpoB) antibiotic target alteration
CKKOLPHL_00034 ARO:3002704 100 0 1 475 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
CKKOLPHL_00124 ARO:3003438 86.3 2.58e-251 1 392 0.9975 0.9291 elfamycin antibiotic elfamycin resistant EF-Tu antibiotic target alteration
CKKOLPHL_00125 ARO:3003735 100 0 1 693 1.0000 1.0000 fusidane antibiotic antibiotic resistant fusA antibiotic target alteration
CKKOLPHL_00129 ARO:3003291 100 0 1 1207 1.0000 1.0000 peptide antibiotic daptomycin-resistant beta prime subunit of RNA polymerase (rpoC) antibiotic target alteration
CKKOLPHL_00130 ARO:3003285 99.9 0 1 1183 1.0000 1.0000 rifamycin antibiotic rifamycin-resistant beta-subunit of RNA polymerase (rpoB) antibiotic target alteration






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
MHGNFBNH_00010 PHI:10289 nupC 99.5 4.2e-220 1 409 1.0000 1.0000 primates skin infection; food poisoning; respiratory disease nucleoside permease unaffected pathogenicity
MHGNFBNH_00020 PHI:9035 mntR 100 2.9e-119 1 214 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease transcriptional repressor reduced virulence
MHGNFBNH_00043 PHI:7819 MnhA2 94.1 0 1 800 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease multi-subunit Na+/H+ (Mnh) antiporter unaffected pathogenicity
MHGNFBNH_00048 PHI:3305 sarA 100 1.9e-62 1 124 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease production of extracellular proteases reduced virulence
MHGNFBNH_00124 PHI:10282 tufA 100 1.3e-226 1 394 1.0000 1.0000 primates skin infection; food poisoning; respiratory disease elongation factor Tu increased virulence (hypervirulence)
MHGNFBNH_00154 PHI:7075 pdxS 79.7 3.1e-132 1 295 1.0000 1.0000 rodents pleuropneumonia (pig) encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS reduced virulence
CKKOLPHL_00010 PHI:10289 nupC 99.5 4.2e-220 1 409 1.0000 1.0000 primates skin infection; food poisoning; respiratory disease nucleoside permease unaffected pathogenicity
CKKOLPHL_00020 PHI:9035 mntR 100 2.9e-119 1 214 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease transcriptional repressor reduced virulence
CKKOLPHL_00043 PHI:7819 MnhA2 94.1 0 1 800 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease multi-subunit Na+/H+ (Mnh) antiporter unaffected pathogenicity
CKKOLPHL_00048 PHI:3305 sarA 100 1.9e-62 1 124 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease production of extracellular proteases reduced virulence
CKKOLPHL_00124 PHI:10282 tufA 100 1.3e-226 1 394 1.0000 1.0000 primates skin infection; food poisoning; respiratory disease elongation factor Tu increased virulence (hypervirulence)
CKKOLPHL_00154 PHI:7075 pdxS 79.7 3.1e-132 1 295 1.0000 1.0000 rodents pleuropneumonia (pig) encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS 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
MHGNFBNH_00014 ALS69035.1|GT2 100 3.85e-256 1 353 1 1
MHGNFBNH_00018 ATN59787.1|GT26 100 1.2e-182 1 254 1 1
MHGNFBNH_00107 ALS68958.1|GT4 100 0 1 496 1 1
MHGNFBNH_00108 QCW85425.1|GT4 100 0 1 490 1 1
MHGNFBNH_00129 CCO12868.2|GH1 73.1 0 1 1188 0.9843 0.9811
CKKOLPHL_00014 ALS69035.1|GT2 100 3.85e-256 1 353 1 1
CKKOLPHL_00018 ATN59787.1|GT26 100 1.2e-182 1 254 1 1
CKKOLPHL_00107 ALS68958.1|GT4 100 0 1 496 1 1
CKKOLPHL_00108 QCW85425.1|GT4 100 0 1 490 1 1
CKKOLPHL_00129 CCO12868.2|GH1 73.1 0 1 1188 0.9843 0.9811





        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
MHGNFBNH_00001 2.A.120.1.14 99.1 7.2e-181 1 335 0.9853 0.9437 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.120 The Proline/Amino Acid Permease (PAAP) Family
MHGNFBNH_00007 3.A.1.14.7 99.4 1.1e-173 1 334 1.0000 1.2604 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
MHGNFBNH_00008 3.A.1.14.7 100 7.2e-152 1 265 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
MHGNFBNH_00016 3.A.1.104.2 100 1.8e-153 8 277 0.9747 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
MHGNFBNH_00017 3.A.1.104.2 100 8.2e-148 1 264 1.0000 0.9778 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
MHGNFBNH_00021 3.A.1.15.15 100 1.4e-136 1 247 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
MHGNFBNH_00022 3.A.1.15.15 99.6 1.2e-136 1 278 1.0000 1.1255 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
MHGNFBNH_00023 3.A.1.15.15 100 1.7e-176 1 309 1.0000 1.2510 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
MHGNFBNH_00094 3.A.1.134.7 100 2.2e-26 1 55 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
MHGNFBNH_00099 2.A.1.6.14 99.1 2e-258 1 466 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
CKKOLPHL_00001 2.A.120.1.14 99.1 7.2e-181 1 335 0.9853 0.9437 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.120 The Proline/Amino Acid Permease (PAAP) Family
CKKOLPHL_00007 3.A.1.14.7 99.4 1.1e-173 1 334 1.0000 1.2604 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
CKKOLPHL_00008 3.A.1.14.7 100 7.2e-152 1 265 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
CKKOLPHL_00016 3.A.1.104.2 100 1.8e-153 8 277 0.9747 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
CKKOLPHL_00017 3.A.1.104.2 100 8.2e-148 1 264 1.0000 0.9778 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
CKKOLPHL_00021 3.A.1.15.15 100 1.4e-136 1 247 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
CKKOLPHL_00022 3.A.1.15.15 99.6 1.2e-136 1 278 1.0000 1.1255 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
CKKOLPHL_00023 3.A.1.15.15 100 1.7e-176 1 309 1.0000 1.2510 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
CKKOLPHL_00094 3.A.1.134.7 100 2.2e-26 1 55 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
CKKOLPHL_00099 2.A.1.6.14 99.1 2e-258 1 466 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)