Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C367
  Reference Plasmid   NZ_AP022208.1
  Reference Plasmid Size   214586
  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
M0156905 JEEKABFE_00061 44977 3 Gut 0.50 protein_coding missense_variant MODERATE 203A>C Asn68Thr
M0156906 JEEKABFE_00092 67011 3 Gut 0.50 protein_coding missense_variant MODERATE 73G>A Ala25Thr
M0156907 JEEKABFE_00092 67012 3 Gut 0.50 protein_coding missense_variant MODERATE 74C>A Ala25Glu
M0156908 JEEKABFE_00092 67109 3 Gut 0.50 protein_coding synonymous_variant LOW 171T>A Ala57Ala
M0156909 JEEKABFE_00092 67355 3 Gut 0.50 protein_coding synonymous_variant LOW 417A>G Thr139Thr
M0156910 JEEKABFE_00184 139544 3 Gut 0.50 protein_coding synonymous_variant LOW 624T>C Tyr208Tyr
M0156911 JEEKABFE_00184 140510 3 Gut 0.50 protein_coding synonymous_variant LOW 1590A>G Thr530Thr
M0156912 JEEKABFE_00184 140588 3 Gut 0.50 protein_coding synonymous_variant LOW 1668A>C Val556Val
M0156913 JEEKABFE_00184 140597 3 Gut 0.50 protein_coding synonymous_variant LOW 1677C>T Ser559Ser
M0156914 JEEKABFE_00184 140690 3 Gut 0.50 protein_coding synonymous_variant LOW 1770T>C Ala590Ala






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
JEEKABFE_00059 VFG001445 TraJ 100 6e-116 1 200 0.8772 0.995 Invasion unknown protein experiment
JEEKABFE_00257 VFG001827 ShET2 99.7 7.9e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
JEEKABFE_00059 VFG001445 TraJ 100 4.5e-115 1 200 0.8772 0.995 Invasion unknown protein prediction
JEEKABFE_00257 VFG036084 Enterotoxin SenB/TieB 100 1.2e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB 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
JEEKABFE_00208 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
JEEKABFE_00200 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
JEEKABFE_00202 ARO:3004623 100 4.76e-213 1 286 1.0000 1.0000 aminoglycoside antibiotic AAC(3) antibiotic inactivation
JEEKABFE_00206 ARO:3002860 99.4 5.26e-112 26 182 0.8626 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
JEEKABFE_00207 ARO:3002605 100 9.47e-192 1 262 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
JEEKABFE_00208 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
JEEKABFE_00209 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
JEEKABFE_00214 ARO:3003839 100 4.74e-272 1 412 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
JEEKABFE_00215 ARO:3000316 100 1e-217 1 301 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
JEEKABFE_00217 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
JEEKABFE_00218 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
JEEKABFE_00219 ARO:3002660 99.3 4.37e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
JEEKABFE_00221 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
JEEKABFE_00205 PHI:9804 int 100 3e-14 1 37 0.1462 1.0000 rodents gastroenteritis integrase reduced virulence
JEEKABFE_00257 PHI:10795 senB 100 4.2e-225 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
JEEKABFE_00258 PHI:10794 cjrC 100 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
JEEKABFE_00259 PHI:10793 cjrB 100 1.7e-137 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
JEEKABFE_00260 PHI:10792 cjrA 100 5.6e-166 1 291 1.0000 1.0000 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)






        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
JEEKABFE_00057 AML12690.1|GH23 100 7.04e-124 1 169 1 1
JEEKABFE_00148 AXI38019.1|GH23 100 2.02e-123 1 169 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
JEEKABFE_00016 2.A.108.2.10 100 5e-101 3 175 0.9886 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
JEEKABFE_00017 2.A.108.2.10 99.8 0 1 646 1.0000 3.7341 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
JEEKABFE_00107 1.E.53.1.11 100 1.1e-21 1 49 1.0000 0.7206 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
JEEKABFE_00114 3.A.1.116.1 95 7.1e-130 1 238 0.9794 0.9636 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
JEEKABFE_00115 3.A.1.116.1 99.6 3.6e-126 1 241 1.0000 0.9757 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
JEEKABFE_00210 2.A.51.1.7 99.5 5.1e-210 1 376 0.9377 0.9666 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.51 The Chromate Ion Transporter (CHR) Family
JEEKABFE_00221 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)
JEEKABFE_00222 2.A.7.3.67 100 2.7e-123 1 232 1.0000 0.7891 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
JEEKABFE_00258 1.B.14.7.1 100 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
JEEKABFE_00259 2.C.1.1.3 100 3.7e-137 1 258 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.C Ion-gradient-driven energizers 2.C.1 The TonB-ExbB-ExbD/TolA-TolQ-TolR Outer Membrane Receptor Energizers and Stabilizers (TonB/TolA) Family