Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1384
  Reference Plasmid   NZ_MT039221.1
  Reference Plasmid Size   276248
  Reference Plasmid GC Content   0.53
  Reference Plasmid Mobility Type   non-mobilizable





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
M0116687 DKJJDLAP_00249 275925 3 Skin 0.60 protein_coding upstream_gene_variant MODIFIER -2329A>G None
M0116688 DKJJDLAP_00249 276141 3 Skin 0.60 protein_coding upstream_gene_variant MODIFIER -2545C>T None
M0116689 DKJJDLAP_00249 276144 3 Skin 0.60 protein_coding upstream_gene_variant MODIFIER -2548A>G None
M0116690 DKJJDLAP_00249 276174 3 Skin 0.60 protein_coding upstream_gene_variant MODIFIER -2578G>A 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
DKJJDLAP_00027 VFG049018 RcsAB 94 6.1e-110 1 216 1.0 1 Regulation transcriptional regulator RcsB experiment
DKJJDLAP_00191 VFG048419 Ent 75 3.6e-126 1 280 0.9859 0.9894 Nutritional/Metabolic factor 2,3-dihydro-2,3-dihydroxybenzoate synthetase, isochroismatase experiment
DKJJDLAP_00192 VFG048429 Ent 71 1.7e-225 3 536 0.9852 0.9981 Nutritional/Metabolic factor enterobactin synthase subunit E experiment
DKJJDLAP_00198 VFG000925 Enterobactin 71.3 4.1e-108 9 266 0.9663 0.952 Nutritional/Metabolic factor ferrienterobactin ABC transporter ATPase experiment
DKJJDLAP_00027 VFG049010 RcsAB 94.4 9.2e-110 1 216 1.0 1 Regulation transcriptional regulator RcsB prediction
DKJJDLAP_00085 VFG002901 O-antigen 86 4.6e-104 1 228 1.0 1 Immune modulation histidine ABC transporter permease HisQ prediction
DKJJDLAP_00191 VFG048420 Ent 75.4 1.2e-125 1 280 0.9859 0.9894 Nutritional/Metabolic factor 2,3-dihydro-2,3-dihydroxybenzoate synthetase, isochroismatase prediction
DKJJDLAP_00192 VFG048430 Ent 71.7 2.3e-226 3 536 0.9852 0.9981 Nutritional/Metabolic factor enterobactin synthase subunit E prediction
DKJJDLAP_00198 VFG048486 Ent 70.4 1.1e-107 11 267 0.9625 0.9735 Nutritional/Metabolic factor iron-enterobactin transporter ATP-binding 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
DKJJDLAP_00180 Manganese (Mn), Iron (Fe), Cadmium (Cd), Cobalt (Co), Zinc (Zn) 77.6 8.3e-172 1 410 1.0000 0.9951 experiment
DKJJDLAP_00180 Manganese (Mn), Iron (Fe), Cadmium (Cd), Cobalt (Co), Zinc (Zn) 80 3.7e-173 1 410 1.0000 0.9951 prediction
DKJJDLAP_00233 Cadmium (Cd), Mercury (Hg), Tributyltin (TBT) [class: Organo-tin], Hydrogen Peroxide (H2O2) [class: Peroxides], Hydrochloric acid (HCl) [class: Acid] 87 5.7e-59 1 131 0.9924 0.9924 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
DKJJDLAP_00029 ARO:3003926 82.9 0 1 864 0.9785 0.9841 fluoroquinolone antibiotic fluoroquinolone resistant gyrA antibiotic target alteration
DKJJDLAP_00219 ARO:3003899 87.3 0 1 575 1.0000 1.0000 phosphonic acid antibiotic antibiotic-resistant ptsI phosphotransferase antibiotic target alteration






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
DKJJDLAP_00027 PHI:2499 rcsB 94.9 5e-111 1 215 0.9954 1.0000 eudicots fire blight phosphorelay system loss of pathogenicity
DKJJDLAP_00037 PHI:10648 katA 80.9 1.3e-239 3 478 0.9958 0.9896 rodents opportunistic infection catalase unaffected pathogenicity
DKJJDLAP_00061 PHI:8937 nuoI (PA2644) 85.5 1.4e-87 9 180 0.9556 0.9451 moths nosocomial infection NADH-quinone oxidoreductase unaffected pathogenicity
DKJJDLAP_00069 PHI:5089 RovM 75.6 7.9e-134 1 311 1.0000 1.0000 fleas bubonic plague LysR-type transcriptional regulator reduced virulence
DKJJDLAP_00076 PHI:9843 ackA 70.9 2e-166 3 399 0.9925 0.9925 flies infection acetate kinase unaffected pathogenicity
DKJJDLAP_00077 PHI:123168 pta 87.5 0 10 721 0.9767 0.9958 rodents salmonellosis phosphate acetyltransferase reduced virulence
DKJJDLAP_00088 PHI:8573 purF (Dda3937_02099) 88.9 4.4e-267 1 505 1.0000 1.0000 eudicots soft rot amidophosphoribosyl transferase reduced virulence
DKJJDLAP_00191 PHI:6565 entB 75 9.4e-126 1 280 0.9859 0.9859 rodents pneumonia enterobactin and salmochelin unaffected pathogenicity
DKJJDLAP_00192 PHI:7486 entE (VK055_1924) 71 4.4e-225 3 536 0.9852 0.9963 rodents pneumonia (2,3-dihydroxybenzoyl)adenylate synthase unaffected pathogenicity
DKJJDLAP_00198 PHI:7541 FepC (VK055_1930) 70.4 1.4e-107 11 267 0.9625 0.9735 rodents pneumonia ferric vibriobactin ABC transporter, ATP-binding protein reduced virulence
DKJJDLAP_00218 PHI:9311 ptsH 96.5 2e-39 1 85 1.0000 1.0000 eudicots fire blight phosphocarrier protein HPr reduced virulence
DKJJDLAP_00219 PHI:9312 ptsI 88.3 1.3e-286 1 575 1.0000 1.0000 eudicots fire blight phosphoenolpyruvate-protein phosphotransferase 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
DKJJDLAP_00044 ULG19158.1|GH0|GH94|GT84 100 0 1 2880 1 1
DKJJDLAP_00159 SMZ57817.1|GH103 100 3.93e-269 1 361 1 1
DKJJDLAP_00248 SMZ57900.1|CBM5|GH18 100 0 1 499 1 1
DKJJDLAP_00250 SMZ57902.1|AA10 100 1.61e-145 1 197 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
DKJJDLAP_00035 2.A.42.1.1 79.2 8.1e-165 1 379 1.0000 0.9429 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.42 The Hydroxy/Aromatic Amino Acid Permease (HAAAP) Family
DKJJDLAP_00056 3.D.1.1.1 81.8 5e-220 1 484 0.9979 0.7896 3 Primary Active Transporters 3.D Oxidoreduction-driven transporters 3.D.1 The H+ or Na+-translocating NADH Dehydrogenase (NDH) Family
DKJJDLAP_00057 3.D.1.1.1 87.7 3.1e-260 1 509 1.0000 0.8303 3 Primary Active Transporters 3.D Oxidoreduction-driven transporters 3.D.1 The H+ or Na+-translocating NADH Dehydrogenase (NDH) Family
DKJJDLAP_00058 3.D.1.1.1 84.4 3.6e-295 1 615 1.0000 0.9984 3 Primary Active Transporters 3.D Oxidoreduction-driven transporters 3.D.1 The H+ or Na+-translocating NADH Dehydrogenase (NDH) Family
DKJJDLAP_00063 3.D.1.1.1 79.8 0 4 913 0.9945 1.4780 3 Primary Active Transporters 3.D Oxidoreduction-driven transporters 3.D.1 The H+ or Na+-translocating NADH Dehydrogenase (NDH) Family
DKJJDLAP_00064 3.D.1.1.1 90.4 3.8e-246 2 450 0.9978 0.7259 3 Primary Active Transporters 3.D Oxidoreduction-driven transporters 3.D.1 The H+ or Na+-translocating NADH Dehydrogenase (NDH) Family
DKJJDLAP_00066 3.D.1.1.1 91.3 0 1 598 1.0000 0.9723 3 Primary Active Transporters 3.D Oxidoreduction-driven transporters 3.D.1 The H+ or Na+-translocating NADH Dehydrogenase (NDH) Family
DKJJDLAP_00072 2.A.47.4.8 72.8 3.8e-249 1 610 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.47 The Divalent Anion:Na+ Symporter (DASS) Family
DKJJDLAP_00083 3.A.1.3.29 87.2 1e-123 1 257 1.0000 1.1272 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DKJJDLAP_00084 3.A.1.3.1 85.8 5.8e-113 1 233 0.9957 1.0219 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DKJJDLAP_00085 3.A.1.3.29 80.3 2.3e-98 1 228 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
DKJJDLAP_00086 3.A.1.3.29 75.4 5.1e-110 1 260 1.0000 1.1404 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DKJJDLAP_00089 9.B.160.1.16 86.2 1.7e-71 1 160 0.9639 0.9877 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.160 The Colicin V Production (CvpA) Family
DKJJDLAP_00093 9.B.27.2.3 89.5 1.5e-107 1 219 0.9955 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.27 The Death Effector Domain A (DedA) Family
DKJJDLAP_00102 2.A.80.1.1 81.6 9.1e-157 1 326 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.80 The Tricarboxylate Transporter (TTT) Family
DKJJDLAP_00104 2.A.80.1.1 89.3 4e-244 2 495 0.9763 1.5200 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.80 The Tricarboxylate Transporter (TTT) Family
DKJJDLAP_00130 2.A.102.3.1 71 4.3e-104 4 265 0.9850 0.9740 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.102 The 4-Toluene Sulfonate Uptake Permease (TSUP) Family
DKJJDLAP_00141 3.A.1.27.3 77 5.4e-117 1 252 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
DKJJDLAP_00145 9.B.14.1.3 73 6.7e-276 1 641 0.9771 0.9799 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.14 The Putative Heme Handling Protein (HHP) Family
DKJJDLAP_00148 9.B.14.2.3 77.2 1.8e-112 1 241 0.9837 0.9837 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.14 The Putative Heme Handling Protein (HHP) Family
DKJJDLAP_00149 3.A.1.107.3 75.7 1.8e-84 1 218 0.9954 1.0531 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DKJJDLAP_00158 1.B.1.1.18 81.2 4.9e-194 1 383 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.1 The General Bacterial Porin (GBP) Family
DKJJDLAP_00180 2.A.55.3.1 77.6 3.1e-170 1 410 1.0000 0.9951 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.55 The Metal Ion (Mn2+-iron) Transporter (Nramp) Family
DKJJDLAP_00181 2.A.41.1.1 80.8 3.8e-165 1 394 0.9975 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.41 The Concentrative Nucleoside Transporter (CNT) Family
DKJJDLAP_00198 3.A.1.14.2 71.3 1.4e-107 9 266 0.9663 0.9520 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DKJJDLAP_00212 2.A.28.3.4 77.8 7.6e-135 6 321 0.9576 0.9518 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.28 The Bile Acid:Na+ Symporter (BASS) Family
DKJJDLAP_00216 2.A.121.1.1 77.9 4.2e-109 8 247 0.9486 0.9486 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.121 The Sulfate Transporter (CysZ) Family
DKJJDLAP_00218 8.A.8.1.1 98.8 4e-40 1 85 1.0000 1.0000 8 Accessory Factors Involved in Transport 8.A Auxiliary transport proteins 8.A.8 The Phosphotransferase System HPr (HPr) Family
DKJJDLAP_00219 8.A.7.1.1 87.3 3.9e-280 1 575 1.0000 1.0000 8 Accessory Factors Involved in Transport 8.A Auxiliary transport proteins 8.A.7 The Phosphotransferase System Enzyme I (EI) Family
DKJJDLAP_00220 4.A.3.2.5 97 2.6e-86 1 169 1.0000 1.0000 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.3 The PTS Lactose-N,N'-Diacetylchitobiose-β-glucoside (Lac) Family
DKJJDLAP_00226 3.A.1.6.1 76 1.1e-158 1 362 1.0000 1.3177 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DKJJDLAP_00227 3.A.1.6.1 80.4 3.4e-131 1 291 1.0000 1.0505 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DKJJDLAP_00228 3.A.1.6.1 86.6 6.2e-130 1 277 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
DKJJDLAP_00229 3.A.1.6.1 78.1 8.6e-150 15 338 0.9529 1.1697 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DKJJDLAP_00242 2.A.3.1.10 80.6 2.4e-211 12 460 0.9574 0.9615 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.3 The Amino Acid-Polyamine-Organocation (APC) Family
DKJJDLAP_00245 1.A.136.1.2 77.3 8.4e-42 1 127 1.0000 1.1667 1 Channels/Pores 1.A α-Type Channels 1.A.136 The Type 10 Protein Secretion System (T10SS) Family
DKJJDLAP_00246 1.A.136.1.2 86.5 1.1e-65 1 133 1.0000 1.2315 1 Channels/Pores 1.A α-Type Channels 1.A.136 The Type 10 Protein Secretion System (T10SS) Family
DKJJDLAP_00247 1.A.136.1.2 89.8 2.5e-50 1 108 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.136 The Type 10 Protein Secretion System (T10SS) Family