Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1369
  Reference Plasmid   NZ_LT985321.1
  Reference Plasmid Size   117804
  Reference Plasmid GC Content   0.52
  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
M0208327 NHIPIFPM_00027 24657 3 Gut 1.00 protein_coding missense_variant MODERATE 208C>T Leu70Phe
M0208328 NHIPIFPM_00027 24672 3 Gut 1.00 protein_coding missense_variant MODERATE 193A>G Thr65Ala
M0208329 NHIPIFPM_00028 25439 3 Gut 1.00 protein_coding missense_variant MODERATE 563A>G Gln188Arg
M0208330 NHIPIFPM_00028 25452 3 Gut 1.00 protein_coding synonymous_variant LOW 576G>T Val192Val
M0208331 NHIPIFPM_00030 26912 3 Gut 1.00 protein_coding missense_variant MODERATE 161C>T Thr54Met
M0208332 NHIPIFPM_00030 26945 3 Gut 1.00 protein_coding missense_variant MODERATE 194T>C Val65Ala
M0208333 NHIPIFPM_00030 26957 3 Gut 1.00 protein_coding missense_variant MODERATE 206C>T Thr69Ile






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
NHIPIFPM_00028 VFG043980 Colicin Ib 98.7 4.5e-247 1 463 1.0 0.7396 Exotoxin colicin-like pore-forming protein 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
NHIPIFPM_00007 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
NHIPIFPM_00015 Mercury (Hg) 78.2 4.9e-33 1 78 1.0000 1.0000 experiment
NHIPIFPM_00016 Mercury (Hg) 82.6 1.3e-48 1 120 1.0083 1.0000 experiment
NHIPIFPM_00017 Mercury (Hg) 85.3 5e-268 1 564 1.0018 1.0071 experiment
NHIPIFPM_00019 Mercury (Hg) 90.1 7e-39 1 91 1.0000 1.0000 experiment
NHIPIFPM_00020 Mercury (Hg) 100 1.3e-62 19 134 0.8657 1.0000 experiment
NHIPIFPM_00021 Mercury (Hg) 93.8 4e-73 1 144 1.0000 1.0000 experiment
NHIPIFPM_00015 Mercury (Hg) 83.3 2.7e-32 1 78 1.0000 1.0000 prediction
NHIPIFPM_00016 Mercury (Hg) 91.7 5.5e-53 1 120 1.0000 1.0000 prediction
NHIPIFPM_00017 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 0 1 564 1.0000 1.0000 prediction
NHIPIFPM_00019 Mercury (Hg) 100 6.3e-41 1 91 1.0000 0.8835 prediction
NHIPIFPM_00020 Mercury (Hg) 90.3 1.2e-64 1 134 1.0000 1.0000 prediction
NHIPIFPM_00021 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
NHIPIFPM_00006 ARO:3002601 100 6.32e-189 74 336 0.7827 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
NHIPIFPM_00007 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
NHIPIFPM_00008 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
NHIPIFPM_00024 ARO:3000165 99.7 7.17e-278 1 390 0.9774 0.9198 tetracycline antibiotic major facilitator superfamily (MFS) 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






        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
NHIPIFPM_00116 CCE57598.2|GH23 100 2.92e-138 1 186 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
NHIPIFPM_00015 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
NHIPIFPM_00019 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
NHIPIFPM_00020 1.A.72.3.1 87.9 3.5e-54 19 134 0.8657 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
NHIPIFPM_00024 2.A.1.2.4 100 2.4e-223 1 399 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
NHIPIFPM_00025 2.A.7.3.67 100 1.8e-159 1 294 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
NHIPIFPM_00028 1.C.1.1.2 98.9 3.5e-247 1 463 1.0000 0.7396 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
NHIPIFPM_00029 8.B.24.2.1 97.3 1.2e-55 1 110 0.9565 0.8661 8 Accessory Factors Involved in Transport 8.B Ribosomally synthesized protein/peptide toxins/agonists that target channels and carriers 8.B.24 The Colicin Immunity Protein (ColIP) Functional Family
NHIPIFPM_00063 3.A.7.10.1 99.6 0 1 763 1.0000 7.9479 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
NHIPIFPM_00064 3.A.7.10.1 99.2 6.1e-207 1 356 1.0000 3.7083 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
NHIPIFPM_00065 3.A.7.10.1 100 2.4e-244 1 402 1.0000 4.1875 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
NHIPIFPM_00089 9.B.40.1.2 97.6 0 1 722 1.0000 0.9691 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.40 The DotA/TraY (DotA/TraY) Family
NHIPIFPM_00100 3.A.7.10.1 99.1 6.7e-184 1 327 1.0000 3.4063 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
NHIPIFPM_00101 3.A.7.10.1 99.1 7.4e-129 1 230 1.0000 2.3958 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
NHIPIFPM_00102 3.A.7.10.1 100 1.3e-57 1 115 1.0000 1.1979 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
NHIPIFPM_00105 3.A.7.10.1 97.9 1.3e-55 1 96 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
NHIPIFPM_00106 3.A.7.10.1 100 3.3e-222 1 382 1.0000 3.9792 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
NHIPIFPM_00107 3.A.7.10.1 99.6 7.3e-160 1 272 1.0000 2.8333 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
NHIPIFPM_00108 3.A.7.10.1 100 6e-87 1 152 1.0000 1.5833 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