Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C589
  Reference Plasmid   NZ_CP035287.1
  Reference Plasmid Size   1740310
  Reference Plasmid GC Content   0.68
  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
M0095632 LGFFOHBC_00364 371823 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -3743A>C 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
LGFFOHBC_01040 VFG048885 Capsule 74.4 2.1e-170 55 425 0.8689 0.992 Immune modulation GDP-mannose 4,6-dehydratase experiment
LGFFOHBC_01040 VFG048885 Capsule 74.4 1.6e-169 55 425 0.8689 0.992 Immune modulation GDP-mannose 4,6-dehydratase prediction
LGFFOHBC_01081 VFG013051 Ferrous iron transport 73.9 1.3e-111 2 284 0.9895 0.993 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitC prediction
LGFFOHBC_01291 VFG043535 SP41 71.2 2e-177 8 428 0.9768 0.9723 Adherence sn-glycerol-3-phosphate ABC transporter substrate-binding protein UgpB 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
LGFFOHBC_00444 Arsenic (As) 70.1 2e-82 27 230 0.8681 0.8793 experiment
LGFFOHBC_01081 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 74.5 2.7e-113 5 279 0.9615 0.9615 experiment
LGFFOHBC_00323 Mercury (Hg) 100 1.2e-78 1 146 1.0000 1.0000 prediction
LGFFOHBC_00327 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 0 1 745 1.0000 1.0000 prediction
LGFFOHBC_00365 Arsenic (As) 100 6.3e-133 1 238 1.0000 1.0000 prediction
LGFFOHBC_00366 Arsenic (As) 89.7 2.3e-171 1 348 0.9613 0.9803 prediction
LGFFOHBC_00419 Copper (Cu) 100 1.4e-305 1 519 1.0000 1.0000 prediction
LGFFOHBC_00444 Arsenic (As) 77.1 9.7e-102 2 235 1.0043 0.9916 prediction
LGFFOHBC_00445 Arsenic (As) 82.7 1.7e-161 1 352 0.9860 0.9915 prediction
LGFFOHBC_00626 Tellurium (Te), Copper (Cu) 78.7 8.1e-164 1 364 1.0055 0.9919 prediction
LGFFOHBC_00655 Cobalt (Co), Cadmium (Cd), Nickel (Ni) 100 7.7e-179 1 317 1.0000 1.0000 prediction
LGFFOHBC_01081 Iron (Fe), Manganese (Mn) 80 7.9e-122 1 285 0.9965 0.9965 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
LGFFOHBC_00457 ARO:3002534 77.2 1.98e-147 6 268 0.9359 0.9777 aminoglycoside antibiotic AAC(3) 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
LGFFOHBC_00879 PHI:11744 ppk2A (PA14_01730) 74.3 1.5e-114 54 310 0.7764 0.8624 nematodes opportunistic infection polyphosphate kinase reduced virulence
LGFFOHBC_01073 PHI:124329 ClpP 70.8 2.8e-79 1 202 0.9665 0.9617 rodents brucellosis protease reduced virulence
LGFFOHBC_01081 PHI:10084 STM14_RS15355 74.5 4.6e-112 5 279 0.9615 0.9615 eudicots infection iron ABC transporter permease unaffected pathogenicity
LGFFOHBC_01224 PHI:10271 hfq 75.3 3.8e-29 1 77 1.0000 0.9625 eudicots tumor RNA-binding protein reduced virulence
LGFFOHBC_01326 PHI:10517 narY 70.1 2.3e-223 1 488 0.9663 0.9514 rodents urinary tract infection respiratory nitrate reductase 2 beta chain reduced virulence
LGFFOHBC_01511 PHI:7214 STM14_1005 77 7.2e-177 7 388 0.9845 1.0000 rodents salmonellosis putative acyl-CoA dehydrogenase 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
LGFFOHBC_00163 WGR56302.1|GH0 95.5 0 1 1295 1 1
LGFFOHBC_00358 AIK42326.1|GH23 100 7.44e-177 1 254 1 1
LGFFOHBC_00673 WEJ81487.1|GT2 100 7.48e-184 1 259 1 1
LGFFOHBC_00674 WGR55133.1|GT83 98.7 0 1 521 1 1
LGFFOHBC_00843 WEJ81643.1|GH3 100 3.7e-230 1 328 1 1
LGFFOHBC_00856 WGR55311.1|GT14 100 0 5 529 0.9924 1
LGFFOHBC_00898 WEJ81693.1|GT51 100 0 1 845 1 1
LGFFOHBC_00909 WEJ81704.1|GT4 100 2.35e-306 1 405 1 1
LGFFOHBC_00925 WEJ81719.1|GH103 100 5.87000000000043e-312 1 424 1 1
LGFFOHBC_01043 WEJ81822.1|CE2 100 3.34e-286 1 388 1 1
LGFFOHBC_01363 WEJ82111.1|GH108 100 5.76e-142 1 203 1 1
LGFFOHBC_01439 WEJ82183.1|GH77 100 0 1 611 1 1
LGFFOHBC_01440 WEJ82184.1|CBM48|GH13_11 100 0 1 697 1 1
LGFFOHBC_01441 WEJ82185.1|GT5 100 0 1 467 1 1
LGFFOHBC_01443 WEJ82187.1|CBM48|GH13_9 100 0 1 733 1 1
LGFFOHBC_01444 WEJ82188.1|GT35 100 0 1 798 1 1
LGFFOHBC_01574 WEJ82312.1|CE4 100 0 1 470 1 1
LGFFOHBC_01637 WEJ82369.1|CE11 100 4.28e-221 1 312 1 1
LGFFOHBC_01647 WEJ82379.1|GT28 100 1.74e-250 1 367 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
LGFFOHBC_00170 1.A.77.2.16 92 1.9e-53 1 113 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.77 The Mg2+/Ca2+ Uniporter (MCU) Family
LGFFOHBC_00171 3.A.2.1.7 98.4 1.3e-131 1 248 1.0000 1.6757 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.2 The H+- or Na+-translocating F-type, V-type and A-type ATPase (F-ATPase) Superfamily
LGFFOHBC_00173 3.A.2.1.7 94.5 4.5e-99 1 219 1.0000 1.4527 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.2 The H+- or Na+-translocating F-type, V-type and A-type ATPase (F-ATPase) Superfamily
LGFFOHBC_00174 3.A.2.1.7 93.5 2.4e-82 1 184 1.0000 1.2432 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.2 The H+- or Na+-translocating F-type, V-type and A-type ATPase (F-ATPase) Superfamily
LGFFOHBC_00238 2.A.98.1.1 94.1 6.1e-164 1 338 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.98 The Putative Sulfate Exporter (PSE) Family
LGFFOHBC_00430 3.A.3.5.39 71.1 7.2e-309 3 783 0.9974 0.9571 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
LGFFOHBC_00470 2.A.118.1.2 81 2e-213 11 477 0.9790 0.9791 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.118 The Basic Amino Acid Antiporter (ArcD) Family
LGFFOHBC_00655 2.A.4.3.13 74.2 1.1e-127 11 315 0.9621 0.9657 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.4 The Cation Diffusion Facilitator (CDF) Family
LGFFOHBC_00752 3.D.4.6.2 70.8 1.4e-118 1 274 1.0000 1.0000 3 Primary Active Transporters 3.D Oxidoreduction-driven transporters 3.D.4 The Proton-translocating Cytochrome Oxidase (COX) Superfamily
LGFFOHBC_01050 2.A.63.1.1 71.4 8.1e-36 1 112 0.9825 0.9256 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.63 The Monovalent Cation (K+ or Na+):Proton Antiporter-3 (CPA3) Family
LGFFOHBC_01080 3.A.1.15.9 72.4 5.8e-115 6 288 0.9826 0.9402 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
LGFFOHBC_01081 3.A.1.15.9 78.9 7.8e-120 1 285 0.9965 0.9468 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
LGFFOHBC_01248 5.A.1.2.7 72.5 3.9e-96 1 244 0.9959 0.9959 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.1 The Disulfide Bond Oxidoreductase D (DsbD) Family
LGFFOHBC_01278 3.A.1.1.5 74.1 1e-139 1 332 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
LGFFOHBC_01279 3.A.1.1.5 77.5 3.2e-118 1 276 1.0000 0.8313 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
LGFFOHBC_01280 3.A.1.1.5 75.1 5.6e-118 1 289 1.0000 0.8705 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
LGFFOHBC_01302 2.A.21.7.5 80 1.6e-244 7 571 0.9895 0.9862 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.21 The Solute:Sodium Symporter (SSS) Family
LGFFOHBC_01310 3.D.4.2.2 90.4 0 1 653 1.0000 1.0000 3 Primary Active Transporters 3.D Oxidoreduction-driven transporters 3.D.4 The Proton-translocating Cytochrome Oxidase (COX) Superfamily
LGFFOHBC_01328 2.A.1.8.11 98.3 0 1 905 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
LGFFOHBC_01340 9.B.29.2.12 85.5 1.5e-119 1 249 0.9920 0.9920 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.29 The 4-5 TMS Putative Chaperone (4-5PC) Family
LGFFOHBC_01361 9.B.14.1.1 73.1 3.8e-279 1 648 0.9923 0.9908 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.14 The Putative Heme Handling Protein (HHP) Family
LGFFOHBC_01391 2.A.28.3.3 93.8 5.5e-160 27 348 0.9253 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.28 The Bile Acid:Na+ Symporter (BASS) Family
LGFFOHBC_01400 3.A.1.1.35 75.3 3.9e-264 8 573 0.9878 0.9947 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
LGFFOHBC_01456 3.A.1.1.17 72 1.3e-128 1 316 0.9875 0.7683 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily