Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1109
  Reference Plasmid   NZ_CP116111.1
  Reference Plasmid Size   159559
  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
M0196206 ELOEOCLA_00074 76409 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2130T>G None
M0196207 ELOEOCLA_00074 76416 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2137A>T None
M0196208 ELOEOCLA_00074 76421 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2142A>T None






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
ELOEOCLA_00015 VFG012513 Salmochelin siderophore 99.5 6.1e-219 1 371 1.0 1 Nutritional/Metabolic factor glucosyltransferase IroB experiment
ELOEOCLA_00016 VFG012509 Salmochelin siderophore 99.5 0 1 1219 1.0 1 Nutritional/Metabolic factor ATP binding cassette transporter experiment
ELOEOCLA_00017 VFG012505 Salmochelin siderophore 99.5 6.7e-243 1 409 1.0 1 Nutritional/Metabolic factor esterase experiment
ELOEOCLA_00018 VFG012501 Salmochelin siderophore 98.7 8.2e-188 1 318 1.0 1 Nutritional/Metabolic factor esterase experiment
ELOEOCLA_00019 VFG000935 Salmochelin siderophore 99 0 1 725 1.0 1 Nutritional/Metabolic factor salmochelin receptor IroN experiment
ELOEOCLA_00136 VFG048621 Aerobactin 99.6 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor IutA experiment
ELOEOCLA_00137 VFG000937 Aerobactin 97.9 1.3e-252 1 425 1.0 0.9551 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD experiment
ELOEOCLA_00138 VFG000938 Aerobactin 97.6 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC experiment
ELOEOCLA_00139 VFG000939 Aerobactin 95.9 5.1e-190 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB experiment
ELOEOCLA_00140 VFG000940 Aerobactin 94.9 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD experiment
ELOEOCLA_00015 VFG012515 Salmochelin siderophore 100 9.2e-219 1 371 1.0 1 Nutritional/Metabolic factor glucosyltransferase IroB prediction
ELOEOCLA_00016 VFG012509 Salmochelin siderophore 99.5 0 1 1219 1.0 1 Nutritional/Metabolic factor ATP binding cassette transporter prediction
ELOEOCLA_00017 VFG012508 Salmochelin siderophore 100 4.5e-243 1 409 1.0 1 Nutritional/Metabolic factor esterase prediction
ELOEOCLA_00018 VFG012504 Salmochelin siderophore 99.7 8.5e-189 1 318 1.0 1 Nutritional/Metabolic factor esterase prediction
ELOEOCLA_00019 VFG012499 Salmochelin siderophore 100 0 1 725 1.0 1 Nutritional/Metabolic factor salmochelin receptor IroN prediction
ELOEOCLA_00136 VFG033944 Aerobactin 99.9 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor precusor IutA prediction
ELOEOCLA_00137 VFG033958 Aerobactin 100 3.7e-256 1 425 1.0 1 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD prediction
ELOEOCLA_00138 VFG012522 Aerobactin 100 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC prediction
ELOEOCLA_00139 VFG033993 Aerobactin 100 1.1e-196 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB prediction
ELOEOCLA_00140 VFG012526 Aerobactin 100 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD prediction
ELOEOCLA_00145 VFG012590 Iron/manganese transport 100 3.8e-148 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitD prediction
ELOEOCLA_00146 VFG012585 Iron/manganese transport 100 1.4e-153 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitC prediction
ELOEOCLA_00147 VFG034214 Iron/manganese transport 100 5.5e-152 1 275 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter ATP-binding protein SitB prediction
ELOEOCLA_00148 VFG012575 Iron/manganese transport 100 7.4e-174 1 304 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter substrate-binding protein SitA 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
ELOEOCLA_00049 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Clorine Dioxide (ClO2) [class: Halogens], Triclosan [class: Phenolic compounds], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine] 99 4.4e-215 1 394 1.0000 1.0077 experiment
ELOEOCLA_00050 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Clorine Dioxide (ClO2) [class: Halogens], Triclosan [class: Phenolic compounds], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine] 99.9 0 1 1050 1.0000 1.0000 experiment
ELOEOCLA_00063 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
ELOEOCLA_00146 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87 9e-133 1 277 0.9719 0.9685 experiment
ELOEOCLA_00147 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 77.7 3.7e-115 2 266 0.9636 0.9707 experiment
ELOEOCLA_00148 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 75.8 1.1e-133 8 304 0.9770 0.9738 experiment
ELOEOCLA_00049 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Clorine Dioxide (ClO2) [class: Halogens], Triclosan [class: Phenolic compounds], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine] 99.2 7.8e-213 1 394 1.0000 1.0077 prediction
ELOEOCLA_00050 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Clorine Dioxide (ClO2) [class: Halogens], Triclosan [class: Phenolic compounds], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine] 100 0 1 1050 1.0000 1.0000 prediction
ELOEOCLA_00146 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87.8 3.4e-133 1 279 0.9789 0.9789 prediction
ELOEOCLA_00147 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 81.1 2.3e-118 2 266 0.9636 0.9707 prediction
ELOEOCLA_00148 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 76.4 4e-132 8 304 0.9770 0.9738 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
ELOEOCLA_00041 ARO:3000165 99.7 7.17e-278 1 390 0.9774 0.9198 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
ELOEOCLA_00049 ARO:3003922 99 2.02e-270 1 394 1.0000 1.0077 fluoroquinolone antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
ELOEOCLA_00050 ARO:3003923 99.9 0 1 1050 1.0000 1.0000 fluoroquinolone antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
ELOEOCLA_00054 ARO:3004621 99 6.49e-211 1 286 1.0000 1.0000 aminoglycoside antibiotic AAC(3) antibiotic inactivation
ELOEOCLA_00056 ARO:3000316 100 1e-217 1 301 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
ELOEOCLA_00057 ARO:3003839 98.5 3.05e-268 1 412 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
ELOEOCLA_00062 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
ELOEOCLA_00063 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
ELOEOCLA_00064 ARO:3002605 100 9.47e-192 1 262 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
ELOEOCLA_00065 ARO:3002860 99.4 1.04e-111 43 199 0.7889 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
ELOEOCLA_00073 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
ELOEOCLA_00015 PHI:6564 iroB 90.6 1.5e-200 1 371 1.0000 1.0000 rodents pneumonia salmochelin unaffected pathogenicity
ELOEOCLA_00016 PHI:9461 iroC 80.1 0 1 1205 0.9885 0.9926 primates salmonellosis putative ABC transporter protein reduced virulence
ELOEOCLA_00017 PHI:4860 IroD 100 1.6e-243 1 409 1.0000 1.0000 birds respiratory disease (poultry); systemic disease (poultry) catecholate siderophore esterases reduced virulence
ELOEOCLA_00018 PHI:4861 IroE 99.7 3e-189 1 318 1.0000 1.0000 birds respiratory disease (poultry); systemic disease (poultry) catecholate siderophore esterases unaffected pathogenicity
ELOEOCLA_00019 PHI:9464 iroN 82.3 0 1 725 1.0000 0.9972 primates salmonellosis TonB-dependent outer membrane siderophore receptor protein reduced virulence
ELOEOCLA_00049 PHI:6448 oqxA 98.7 2.8e-213 1 394 1.0000 1.0000 nematodes pneumonia RND family efflux transporter reduced virulence
ELOEOCLA_00050 PHI:6449 oqxB 99.6 0 1 1050 1.0000 1.0000 nematodes pneumonia multidrug efflux pump reduced virulence
ELOEOCLA_00066 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
ELOEOCLA_00136 PHI:6563 iucA 99.6 0 1 732 1.0000 0.9986 rodents pneumonia aerobactin reduced virulence
ELOEOCLA_00137 PHI:3610 iucD 100 1.3e-256 1 425 1.0000 1.0000 birds colibacillosis aerobactin reduced virulence
ELOEOCLA_00138 PHI:124069 iucC (PAGR_g3925) 83.9 9.1e-301 1 577 0.9948 0.9983 monocots None aerobactin siderophores unaffected pathogenicity
ELOEOCLA_00139 PHI:124068 iucB (PAGR_g3926) 79.7 3.6e-158 1 315 1.0000 1.0000 monocots None aerobactin siderophores unaffected pathogenicity
ELOEOCLA_00140 PHI:124067 iucA (PAGR_g3927) 78.5 5.7e-271 1 573 0.9983 0.9598 monocots None aerobactin siderophores unaffected pathogenicity
ELOEOCLA_00146 PHI:10084 STM14_RS15355 87 1.5e-131 1 277 0.9719 0.9685 eudicots infection iron ABC transporter permease unaffected pathogenicity
ELOEOCLA_00147 PHI:10083 STM14_RS15350 77.7 6.1e-114 2 266 0.9636 0.9707 eudicots infection iron ABC transporter permease unaffected pathogenicity
ELOEOCLA_00148 PHI:10082 STM14_RS15345 75.8 1.9e-132 8 304 0.9770 0.9705 eudicots infection manganese/iron ABC transporter ATP-binding protein unaffected pathogenicity
ELOEOCLA_00158 PHI:6531 HlyF 98.8 8.8e-195 1 339 0.9941 0.9187 birds colibacillosis hemolysin 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
ELOEOCLA_00015 QBC88968.1|GT1 100 1.38e-274 1 371 1 1
ELOEOCLA_00121 QAZ75040.1|GH23 100 4.96e-124 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
ELOEOCLA_00016 3.A.1.106.7 79.9 0 1 1205 0.9885 0.9926 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
ELOEOCLA_00019 1.B.14.1.3 82.2 0 1 725 1.0000 0.9972 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
ELOEOCLA_00029 8.B.24.3.1 99.1 3.2e-64 1 117 1.0000 0.8298 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
ELOEOCLA_00040 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
ELOEOCLA_00041 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)
ELOEOCLA_00050 2.A.6.2.47 99.6 0 1 1050 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
ELOEOCLA_00061 2.A.51.1.7 99.2 3.3e-209 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
ELOEOCLA_00081 1.E.53.1.11 98.5 1.1e-32 1 68 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
ELOEOCLA_00146 3.A.1.15.7 87 3.4e-131 1 277 0.9719 0.9082 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
ELOEOCLA_00147 3.A.1.15.7 77.7 1.4e-113 2 266 0.9636 0.8689 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
ELOEOCLA_00148 3.A.1.15.7 75.8 4.2e-132 8 304 0.9770 0.9705 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
ELOEOCLA_00159 9.B.50.1.1 73.2 3.9e-144 1 317 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.50 The Outer Membrane Beta-barrel Endoprotease, Omptin (Omptin) Family