Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1152
  Reference Plasmid   NZ_CP122654.1
  Reference Plasmid Size   109222
  Reference Plasmid GC Content   0.51
  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
M0197984 NNBMLDCA_00021 21569 12 Gut 0.09 protein_coding missense_variant MODERATE 415A>T Ser139Cys
M0197985 NNBMLDCA_00033 38688 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4557T>A None
M0197986 NNBMLDCA_00033 38693 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4562T>G None
M0197987 NNBMLDCA_00002 1407 58 Gut 0.42 protein_coding upstream_gene_variant MODIFIER -131T>G None
M0197988 NNBMLDCA_00033 38185 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4054A>T None
M0197989 NNBMLDCA_00033 38192 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4061G>T None
M0197990 NNBMLDCA_00001 825 5 Gut 0.04 protein_coding synonymous_variant LOW 825A>T Pro275Pro
M0197991 NNBMLDCA_00007 8189 3 Gut 0.02 protein_coding synonymous_variant LOW 975C>T Gly325Gly
M0197992 NNBMLDCA_00001 424 8 Gut 0.06 protein_coding missense_variant MODERATE 424T>A Cys142Ser
M0197993 NNBMLDCA_00104 95916 4 Gut 0.03 protein_coding synonymous_variant LOW 342C>T Cys114Cys
M0197994 NNBMLDCA_00092 87432 3 Gut 0.02 protein_coding synonymous_variant LOW 6C>T Thr2Thr
M0197995 NNBMLDCA_00001 438 3 Gut 0.02 protein_coding synonymous_variant LOW 438A>G Thr146Thr
M0197996 NNBMLDCA_00001 513 4 Gut 0.03 protein_coding synonymous_variant LOW 513T>C Gly171Gly
M0197997 NNBMLDCA_00120 105055 4 Gut 0.03 protein_coding missense_variant MODERATE 332T>A Phe111Tyr
M0197998 NNBMLDCA_00120 105056 4 Gut 0.03 protein_coding missense_variant MODERATE 333T>A Phe111Leu
M0197999 NNBMLDCA_00120 105057 4 Gut 0.03 protein_coding missense_variant MODERATE 334T>G Tyr112Asp
M0198000 NNBMLDCA_00124 107972 5 Gut 0.04 protein_coding synonymous_variant LOW 771G>A Glu257Glu
M0198001 NNBMLDCA_00126 108400 4 Gut 0.03 protein_coding missense_variant MODERATE 244G>A Asp82Asn
M0198002 NNBMLDCA_00126 108402 4 Gut 0.03 protein_coding missense_variant MODERATE 242A>G Glu81Gly
M0198003 NNBMLDCA_00001 522 6 Gut 0.04 protein_coding synonymous_variant LOW 522C>A Ile174Ile
M0198004 NNBMLDCA_00001 537 6 Gut 0.04 protein_coding synonymous_variant LOW 537G>A Leu179Leu
M0198005 NNBMLDCA_00001 657 5 Gut 0.04 protein_coding synonymous_variant LOW 657T>C Ser219Ser
M0198006 NNBMLDCA_00001 693 4 Gut 0.03 protein_coding synonymous_variant LOW 693C>T Gly231Gly
M0198007 NNBMLDCA_00125 108142 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -61T>A None
M0198008 NNBMLDCA_00125 108143 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -60A>G None
M0198009 NNBMLDCA_00125 108147 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -56A>C None
M0198010 NNBMLDCA_00125 108148 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -55T>A None
M0198011 NNBMLDCA_00125 108151 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -52C>A None
M0198012 NNBMLDCA_00125 108199 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4T>C None
M0198013 NNBMLDCA_00001 66 4 Gut 0.03 protein_coding synonymous_variant LOW 66G>A Val22Val
M0198014 NNBMLDCA_00001 225 5 Gut 0.04 protein_coding missense_variant MODERATE 225A>G Ile75Met
M0198015 NNBMLDCA_00001 231 4 Gut 0.03 protein_coding synonymous_variant LOW 231A>G Lys77Lys
M0198016 NNBMLDCA_00001 232 4 Gut 0.03 protein_coding missense_variant MODERATE 232C>A Pro78Thr
M0198017 NNBMLDCA_00001 405 3 Gut 0.02 protein_coding synonymous_variant LOW 405A>T Thr135Thr
M0198018 NNBMLDCA_00001 408 3 Gut 0.02 protein_coding synonymous_variant LOW 408C>T Phe136Phe
M0198019 NNBMLDCA_00093 88000 3 Gut 0.02 protein_coding missense_variant MODERATE 383A>C Glu128Ala
M0198020 NNBMLDCA_00093 88023 3 Gut 0.02 protein_coding synonymous_variant LOW 360T>C Asp120Asp
M0198021 NNBMLDCA_00093 88024 3 Gut 0.02 protein_coding missense_variant MODERATE 359A>G Asp120Gly






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
NNBMLDCA_00090 VFG043980 Colicin Ib 99.7 0 1 626 1.0 1 Exotoxin colicin-like pore-forming protein prediction
NNBMLDCA_00097 VFG017870 Icm/dot type IVB locus 77.9 1e-89 1 208 0.9905 0.9952 Effector delivery system ParA family 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
NNBMLDCA_00068 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






        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
NNBMLDCA_00067 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
NNBMLDCA_00068 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
NNBMLDCA_00069 ARO:3002601 99.2 2.68e-186 1 259 1.0000 0.9848 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
NNBMLDCA_00070 ARO:3002854 100 9.81e-115 1 157 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
NNBMLDCA_00072 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
NNBMLDCA_00073 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
NNBMLDCA_00074 ARO:3000412 99.6 8.29e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
NNBMLDCA_00078 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM 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
NNBMLDCA_00071 PHI:9804 int 100 4.4e-14 1 37 0.0995 1.0000 rodents gastroenteritis integrase 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
NNBMLDCA_00039 AHF22950.1|GH23 100 5.89e-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
NNBMLDCA_00005 3.A.7.10.1 99.7 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
NNBMLDCA_00006 3.A.7.10.1 99.7 1.2e-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
NNBMLDCA_00007 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
NNBMLDCA_00013 9.B.40.1.2 86.9 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
NNBMLDCA_00024 3.A.7.10.1 99.1 1.5e-183 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
NNBMLDCA_00025 3.A.7.10.1 99.6 3.3e-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
NNBMLDCA_00026 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
NNBMLDCA_00029 3.A.7.10.1 99 4.6e-56 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
NNBMLDCA_00030 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
NNBMLDCA_00031 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
NNBMLDCA_00032 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
NNBMLDCA_00090 1.C.1.1.2 98.7 0 1 626 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
NNBMLDCA_00091 8.B.24.2.1 99.1 3.2e-56 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