Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C752
  Reference Plasmid   NZ_CP055600.1
  Reference Plasmid Size   113051
  Reference Plasmid GC Content   0.50
  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
M0174747 OCHLOLCN_00047 44377 4 Gut 0.80 protein_coding upstream_gene_variant MODIFIER -1795T>C None
M0174748 OCHLOLCN_00047 44421 4 Gut 0.80 protein_coding upstream_gene_variant MODIFIER -1839A>T None
M0174749 OCHLOLCN_00047 44436 4 Gut 0.80 protein_coding upstream_gene_variant MODIFIER -1854G>A None
M0174750 OCHLOLCN_00050 44581 5 Gut 1.00 protein_coding synonymous_variant LOW 84C>T Ala28Ala
M0174751 OCHLOLCN_00050 44647 5 Gut 1.00 protein_coding synonymous_variant LOW 150G>T Leu50Leu
M0174752 OCHLOLCN_00047 44732 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2150G>A None
M0174753 OCHLOLCN_00047 44734 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2152A>G None
M0174754 OCHLOLCN_00047 44756 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2174C>A None
M0174755 OCHLOLCN_00047 44766 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2184G>A None
M0174756 OCHLOLCN_00047 44773 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2191T>A None
M0174757 OCHLOLCN_00051 44910 5 Gut 1.00 protein_coding synonymous_variant LOW 93C>T His31His
M0174758 OCHLOLCN_00051 45598 5 Gut 1.00 protein_coding missense_variant MODERATE 781A>G Thr261Ala






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
OCHLOLCN_00030 VFG043568 OmpD 78.1 1.1e-163 8 370 0.9811 1.0028 Adherence phosphoporin PhoE 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
OCHLOLCN_00030 Methyl Viologen [class: Paraquat] 78.1 2.3e-165 8 370 1.0000 1.0221 experiment
OCHLOLCN_00077 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Pyronin Y [class: Xanthene], Rhodamine 6G [class: Xanthene], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Acridine Orange [class: Acridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Sodium Deoxycholate (SDC) [class: Acid], Crystal Violet [class: Triarylmethane], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)] 100 1.1e-60 1 115 1.0000 1.0000 experiment
OCHLOLCN_00086 Mercury (Hg) 78.2 4.9e-33 1 78 1.0000 1.0000 experiment
OCHLOLCN_00087 Mercury (Hg) 82.6 1.3e-48 1 120 1.0083 1.0000 experiment
OCHLOLCN_00088 Mercury (Hg) 85.3 5e-268 1 564 1.0018 1.0071 experiment
OCHLOLCN_00090 Mercury (Hg) 90.1 7e-39 1 91 1.0000 1.0000 experiment
OCHLOLCN_00091 Mercury (Hg) 100 1.2e-62 1 116 1.0000 1.0000 experiment
OCHLOLCN_00092 Mercury (Hg) 93.8 4e-73 1 144 1.0000 1.0000 experiment
OCHLOLCN_00030 Methyl Viologen [class: Paraquat] 100 1.9e-213 1 370 1.0000 1.0000 prediction
OCHLOLCN_00086 Mercury (Hg) 83.3 2.7e-32 1 78 1.0000 1.0000 prediction
OCHLOLCN_00087 Mercury (Hg) 91.7 5.5e-53 1 120 1.0000 1.0000 prediction
OCHLOLCN_00088 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 0 1 564 1.0000 1.0000 prediction
OCHLOLCN_00090 Mercury (Hg) 100 6.3e-41 1 91 1.0000 0.8835 prediction
OCHLOLCN_00091 Mercury (Hg) 99.1 3.5e-60 1 116 1.0000 1.0000 prediction
OCHLOLCN_00092 Mercury (Hg) 100 4.3e-76 1 144 1.0000 0.7619 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
OCHLOLCN_00076 ARO:3002601 100 2.55e-189 51 313 0.8403 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
OCHLOLCN_00077 ARO:3005010 100 2.01e-78 1 115 1.0000 1.0000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
OCHLOLCN_00078 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul 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
OCHLOLCN_00030 PHI:123435 ompD 78.1 3.9e-164 8 370 0.9811 0.9890 rodents salmonellosis porin OmpD unaffected pathogenicity
OCHLOLCN_00061 PHI:123648 narU 99.4 6.2e-260 1 462 1.0000 1.0000 rodents neonatal meningitis regulatory protein unaffected pathogenicity
OCHLOLCN_00062 PHI:10516 narZ 99 0 1 1246 1.0000 1.0000 rodents urinary tract infection respiratory nitrate reductase 2 alpha chain reduced virulence
OCHLOLCN_00063 PHI:10517 narY 99.4 0 1 514 1.0000 1.0000 rodents urinary tract infection respiratory nitrate reductase 2 beta chain reduced virulence
OCHLOLCN_00064 PHI:10518 narW 96.5 5.9e-126 1 231 1.0000 1.0000 rodents urinary tract infection probable nitrate reductase molybdenum cofactor assembly chaperone reduced virulence
OCHLOLCN_00065 PHI:10519 narV 100 1.2e-128 1 226 1.0000 1.0000 rodents urinary tract infection respiratory nitrate reductase 2 gamma chain 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
OCHLOLCN_00032 BED94841.1|GH24 100 2.66e-150 1 200 1 1
OCHLOLCN_00035 AYL89119.1|GH24 95.8 0 1753 2255 0.2231 0.9031





        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
OCHLOLCN_00022 1.E.4.1.1 100 1.3e-54 1 109 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.4 The LydA Holin (LydA Holin) Family
OCHLOLCN_00030 1.B.1.1.4 81.1 9.3e-174 1 370 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.1 The General Bacterial Porin (GBP) Family
OCHLOLCN_00061 2.A.1.8.10 99.4 1.4e-259 1 462 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
OCHLOLCN_00062 5.A.3.1.2 99 0 1 1246 1.0000 1.0000 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
OCHLOLCN_00086 1.A.72.5.1 100 1.8e-39 1 78 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
OCHLOLCN_00090 1.A.72.3.1 90.1 2.6e-37 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
OCHLOLCN_00091 1.A.72.3.1 87.9 3e-54 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily