Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1274
  Reference Plasmid   NZ_CP146664.1
  Reference Plasmid Size   130826
  Reference Plasmid GC Content   0.49
  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
M0205231 ABEKFOIE_00108 101401 3 Gut 1.00 protein_coding synonymous_variant LOW 222C>G Gly74Gly
M0205232 ABEKFOIE_00108 101410 3 Gut 1.00 protein_coding synonymous_variant LOW 213T>G Arg71Arg
M0205233 ABEKFOIE_00108 101417 3 Gut 1.00 protein_coding missense_variant MODERATE 206C>T Ala69Val
M0205234 ABEKFOIE_00108 101497 3 Gut 1.00 protein_coding synonymous_variant LOW 126C>A Arg42Arg
M0205235 ABEKFOIE_00108 101503 3 Gut 1.00 protein_coding missense_variant MODERATE 120G>T Gln40His
M0205236 ABEKFOIE_00108 101554 3 Gut 1.00 protein_coding synonymous_variant LOW 69T>C Ala23Ala
M0205237 ABEKFOIE_00108 101560 3 Gut 1.00 protein_coding synonymous_variant LOW 63C>T Ala21Ala
M0205238 ABEKFOIE_00108 101563 3 Gut 1.00 protein_coding missense_variant MODERATE 60T>A His20Gln
M0205239 ABEKFOIE_00108 101568 3 Gut 1.00 protein_coding missense_variant MODERATE 55A>G Lys19Glu
M0205240 ABEKFOIE_00108 101578 3 Gut 1.00 protein_coding synonymous_variant LOW 45T>C Pro15Pro
M0205241 ABEKFOIE_00108 101580 3 Gut 1.00 protein_coding missense_variant MODERATE 43C>T Pro15Ser
M0205242 ABEKFOIE_00108 101581 3 Gut 1.00 protein_coding synonymous_variant LOW 42T>C Gly14Gly
M0205243 ABEKFOIE_00109 101650 3 Gut 1.00 protein_coding missense_variant MODERATE 481T>A Cys161Ser
M0205244 ABEKFOIE_00109 101657 3 Gut 1.00 protein_coding synonymous_variant LOW 474T>C Ala158Ala
M0205245 ABEKFOIE_00109 101669 3 Gut 1.00 protein_coding synonymous_variant LOW 462T>A Thr154Thr
M0205246 ABEKFOIE_00109 101711 3 Gut 1.00 protein_coding missense_variant MODERATE 420C>G Asp140Glu
M0205247 ABEKFOIE_00109 101716 3 Gut 1.00 protein_coding missense_variant MODERATE 415A>G Ser139Gly
M0205248 ABEKFOIE_00109 101824 3 Gut 1.00 protein_coding missense_variant MODERATE 307T>C Ser103Pro
M0205249 ABEKFOIE_00109 101844 3 Gut 1.00 protein_coding missense_variant MODERATE 287G>C Gly96Ala
M0205250 ABEKFOIE_00109 101866 3 Gut 1.00 protein_coding missense_variant MODERATE 265G>A Ala89Thr
M0205251 ABEKFOIE_00109 101874 3 Gut 1.00 protein_coding missense_variant MODERATE 257T>C Val86Ala
M0205252 ABEKFOIE_00109 101999 3 Gut 1.00 protein_coding synonymous_variant LOW 132C>T Arg44Arg
M0205253 ABEKFOIE_00109 102014 3 Gut 1.00 protein_coding synonymous_variant LOW 117A>T Ala39Ala
M0205254 ABEKFOIE_00109 102020 3 Gut 1.00 protein_coding synonymous_variant LOW 111A>G Glu37Glu
M0205255 ABEKFOIE_00109 102047 3 Gut 1.00 protein_coding synonymous_variant LOW 84T>C Arg28Arg
M0205256 ABEKFOIE_00109 102059 3 Gut 1.00 protein_coding synonymous_variant LOW 72A>G Thr24Thr
M0205257 ABEKFOIE_00109 102081 3 Gut 1.00 protein_coding missense_variant MODERATE 50C>T Thr17Met
M0205258 ABEKFOIE_00109 102092 3 Gut 1.00 protein_coding synonymous_variant LOW 39T>C Arg13Arg
M0205259 ABEKFOIE_00109 102104 3 Gut 1.00 protein_coding synonymous_variant LOW 27A>T Ser9Ser
M0205260 ABEKFOIE_00109 102107 3 Gut 1.00 protein_coding synonymous_variant LOW 24A>G Thr8Thr
M0205261 ABEKFOIE_00104 102176 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4232C>A None
M0205262 ABEKFOIE_00110 102343 3 Gut 1.00 protein_coding synonymous_variant LOW 1884T>C Ser628Ser
M0205263 ABEKFOIE_00110 102390 3 Gut 1.00 protein_coding synonymous_variant LOW 1837C>T Leu613Leu






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
ABEKFOIE_00037 VFG012513 Salmochelin siderophore 99.5 6.1e-219 1 371 1.0 1 Nutritional/Metabolic factor glucosyltransferase IroB experiment
ABEKFOIE_00038 VFG012509 Salmochelin siderophore 99.5 0 1 1219 1.0 1 Nutritional/Metabolic factor ATP binding cassette transporter experiment
ABEKFOIE_00039 VFG012505 Salmochelin siderophore 99.3 1.7e-241 1 409 1.0 1 Nutritional/Metabolic factor esterase experiment
ABEKFOIE_00040 VFG012501 Salmochelin siderophore 99.4 7.4e-189 1 318 1.0 1 Nutritional/Metabolic factor esterase experiment
ABEKFOIE_00041 VFG000935 Salmochelin siderophore 98.9 0 1 725 1.0 1 Nutritional/Metabolic factor salmochelin receptor IroN experiment
ABEKFOIE_00128 VFG048621 Aerobactin 99.6 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor IutA experiment
ABEKFOIE_00129 VFG000937 Aerobactin 97.9 1.3e-252 1 425 1.0 0.9551 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD experiment
ABEKFOIE_00130 VFG000938 Aerobactin 97.6 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC experiment
ABEKFOIE_00131 VFG000939 Aerobactin 95.9 6.6e-190 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB experiment
ABEKFOIE_00132 VFG000940 Aerobactin 94.9 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD experiment
ABEKFOIE_00003 VFG012590 Iron/manganese transport 100 3.8e-148 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitD prediction
ABEKFOIE_00004 VFG012585 Iron/manganese transport 99.6 3e-153 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitC prediction
ABEKFOIE_00005 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
ABEKFOIE_00006 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
ABEKFOIE_00037 VFG012515 Salmochelin siderophore 100 9.2e-219 1 371 1.0 1 Nutritional/Metabolic factor glucosyltransferase IroB prediction
ABEKFOIE_00038 VFG012511 Salmochelin siderophore 99.9 0 1 1219 1.0 1 Nutritional/Metabolic factor ATP binding cassette transporter prediction
ABEKFOIE_00039 VFG012507 Salmochelin siderophore 100 1.7e-242 1 409 1.0 1 Nutritional/Metabolic factor esterase prediction
ABEKFOIE_00040 VFG012503 Salmochelin siderophore 100 6.5e-189 1 318 1.0 1 Nutritional/Metabolic factor esterase prediction
ABEKFOIE_00041 VFG012499 Salmochelin siderophore 99.9 0 1 725 1.0 1 Nutritional/Metabolic factor salmochelin receptor IroN prediction
ABEKFOIE_00059 VFG044067 Colicin Ia 100 0 1 626 1.0 1 Exotoxin colicin-like pore-forming protein prediction
ABEKFOIE_00128 VFG012518 Aerobactin 100 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor precusor IutA prediction
ABEKFOIE_00129 VFG033958 Aerobactin 100 3.7e-256 1 425 1.0 1 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD prediction
ABEKFOIE_00130 VFG012522 Aerobactin 100 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC prediction
ABEKFOIE_00131 VFG012524 Aerobactin 100 1.1e-196 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB prediction
ABEKFOIE_00132 VFG012526 Aerobactin 100 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD 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
ABEKFOIE_00004 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87 6.9e-133 1 277 0.9719 0.9685 experiment
ABEKFOIE_00005 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 77.7 3.7e-115 2 266 0.9636 0.9707 experiment
ABEKFOIE_00006 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 75.8 1.1e-133 8 304 0.9770 0.9738 experiment
ABEKFOIE_00004 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87.8 2.6e-133 1 279 0.9789 0.9789 prediction
ABEKFOIE_00005 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 81.1 2.3e-118 2 266 0.9636 0.9707 prediction
ABEKFOIE_00006 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






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
ABEKFOIE_00004 PHI:10084 STM14_RS15355 87 1.2e-131 1 277 0.9719 0.9685 eudicots infection iron ABC transporter permease unaffected pathogenicity
ABEKFOIE_00005 PHI:10083 STM14_RS15350 77.7 6.1e-114 2 266 0.9636 0.9707 eudicots infection iron ABC transporter permease unaffected pathogenicity
ABEKFOIE_00006 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
ABEKFOIE_00015 PHI:6531 HlyF 100 2.6e-216 1 369 1.0000 1.0000 birds colibacillosis hemolysin reduced virulence
ABEKFOIE_00037 PHI:6564 iroB 90.6 1.5e-200 1 371 1.0000 1.0000 rodents pneumonia salmochelin unaffected pathogenicity
ABEKFOIE_00038 PHI:9461 iroC 79.9 0 1 1205 0.9885 0.9926 primates salmonellosis putative ABC transporter protein reduced virulence
ABEKFOIE_00039 PHI:4860 IroD 99.8 3.9e-242 1 409 1.0000 1.0000 birds respiratory disease (poultry); systemic disease (poultry) catecholate siderophore esterases reduced virulence
ABEKFOIE_00040 PHI:4861 IroE 99.7 8.8e-189 1 318 1.0000 1.0000 birds respiratory disease (poultry); systemic disease (poultry) catecholate siderophore esterases unaffected pathogenicity
ABEKFOIE_00041 PHI:9464 iroN 82.3 0 1 725 1.0000 0.9972 primates salmonellosis TonB-dependent outer membrane siderophore receptor protein reduced virulence
ABEKFOIE_00128 PHI:3611 iutA 99.7 0 1 732 1.0000 0.9986 birds colibacillosis aerobactin reduced virulence
ABEKFOIE_00129 PHI:3610 iucD 100 1.3e-256 1 425 1.0000 1.0000 birds colibacillosis aerobactin reduced virulence
ABEKFOIE_00130 PHI:124069 iucC (PAGR_g3925) 83.9 9.1e-301 1 577 0.9948 0.9983 monocots None aerobactin siderophores unaffected pathogenicity
ABEKFOIE_00131 PHI:124068 iucB (PAGR_g3926) 80 1.2e-158 1 315 1.0000 1.0000 monocots None aerobactin siderophores unaffected pathogenicity
ABEKFOIE_00132 PHI:124067 iucA (PAGR_g3927) 78.5 5.7e-271 1 573 0.9983 0.9598 monocots None aerobactin siderophores unaffected pathogenicity






        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
ABEKFOIE_00037 QBC88968.1|GT1 100 1.38e-274 1 371 1 1
ABEKFOIE_00101 QBQ68813.1|GH23 100 5.79e-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
ABEKFOIE_00004 3.A.1.15.7 87 2.6e-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
ABEKFOIE_00005 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
ABEKFOIE_00006 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
ABEKFOIE_00016 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
ABEKFOIE_00038 3.A.1.106.7 79.8 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
ABEKFOIE_00041 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
ABEKFOIE_00048 3.A.1.112.12 100 0 1 698 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
ABEKFOIE_00049 1.C.31.1.1 100 4.6e-54 1 103 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.31 The Channel-forming Colicin V (Colicin V) Family
ABEKFOIE_00052 2.A.123.2.16 100 1.7e-41 1 89 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.123 The Sweet; PQ-loop; Saliva; MtN3 (Sweet) Family
ABEKFOIE_00059 1.C.1.1.1 98.9 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