Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C786
  Reference Plasmid   NZ_CP062915.1
  Reference Plasmid Size   151873
  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
M0183634 GKMCEMGI_00031 32754 7 Gut 0.58 protein_coding synonymous_variant LOW 1095G>T Val365Val
M0183635 GKMCEMGI_00033 34947 7 Gut 0.58 protein_coding missense_variant MODERATE 1206T>A Ser402Arg
M0183636 GKMCEMGI_00033 35061 7 Gut 0.58 protein_coding synonymous_variant LOW 1092C>T Gly364Gly
M0183637 GKMCEMGI_00033 35121 6 Gut 0.50 protein_coding synonymous_variant LOW 1032G>A Gly344Gly
M0183638 GKMCEMGI_00033 35310 6 Gut 0.50 protein_coding synonymous_variant LOW 843A>G Gln281Gln
M0183639 GKMCEMGI_00033 35353 6 Gut 0.50 protein_coding missense_variant MODERATE 800C>T Ala267Val
M0183640 GKMCEMGI_00033 35528 5 Gut 0.42 protein_coding missense_variant MODERATE 625A>G Asn209Asp
M0183641 GKMCEMGI_00033 35580 5 Gut 0.42 protein_coding missense_variant MODERATE 573T>A Asp191Glu
M0183642 GKMCEMGI_00033 35598 5 Gut 0.42 protein_coding synonymous_variant LOW 555T>C Asn185Asn
M0183643 GKMCEMGI_00033 35673 5 Gut 0.42 protein_coding synonymous_variant LOW 480A>C Ala160Ala
M0183644 GKMCEMGI_00033 35775 5 Gut 0.42 protein_coding synonymous_variant LOW 378A>G Gly126Gly
M0183645 GKMCEMGI_00033 35880 5 Gut 0.42 protein_coding synonymous_variant LOW 273C>T Asn91Asn
M0183646 GKMCEMGI_00033 35919 5 Gut 0.42 protein_coding synonymous_variant LOW 234C>T Val78Val
M0183647 GKMCEMGI_00033 35922 5 Gut 0.42 protein_coding synonymous_variant LOW 231C>T Gly77Gly
M0183648 GKMCEMGI_00030 29291 3 Gut 0.25 protein_coding synonymous_variant LOW 1395T>C Ile465Ile
M0183649 GKMCEMGI_00030 29423 4 Gut 0.33 protein_coding synonymous_variant LOW 1527T>C Thr509Thr
M0183650 GKMCEMGI_00030 29528 5 Gut 0.42 protein_coding synonymous_variant LOW 1632A>G Thr544Thr
M0183651 GKMCEMGI_00030 29834 6 Gut 0.50 protein_coding synonymous_variant LOW 1938G>A Ala646Ala
M0183652 GKMCEMGI_00030 29879 5 Gut 0.42 protein_coding synonymous_variant LOW 1983G>A Ala661Ala
M0183653 GKMCEMGI_00030 29894 6 Gut 0.50 protein_coding synonymous_variant LOW 1998A>G Val666Val
M0183654 GKMCEMGI_00030 29950 6 Gut 0.50 protein_coding missense_variant MODERATE 2054T>C Ile685Thr
M0183655 GKMCEMGI_00030 29984 5 Gut 0.42 protein_coding synonymous_variant LOW 2088G>A Leu696Leu
M0183656 GKMCEMGI_00030 30071 5 Gut 0.42 protein_coding synonymous_variant LOW 2175C>T Arg725Arg
M0183657 GKMCEMGI_00030 30110 5 Gut 0.42 protein_coding synonymous_variant LOW 2214T>C His738His
M0183658 GKMCEMGI_00030 30134 6 Gut 0.50 protein_coding synonymous_variant LOW 2238T>G Leu746Leu
M0183659 GKMCEMGI_00030 30255 6 Gut 0.50 protein_coding missense_variant MODERATE 2359T>A Phe787Ile
M0183660 GKMCEMGI_00030 30344 5 Gut 0.42 protein_coding synonymous_variant LOW 2448G>A Gln816Gln
M0183661 GKMCEMGI_00030 30395 6 Gut 0.50 protein_coding synonymous_variant LOW 2499T>C Ser833Ser
M0183662 GKMCEMGI_00030 30554 6 Gut 0.50 protein_coding synonymous_variant LOW 2658T>C Ala886Ala
M0183663 GKMCEMGI_00033 36076 4 Gut 0.33 protein_coding missense_variant MODERATE 77C>A Ser26Tyr
M0183664 GKMCEMGI_00033 36111 4 Gut 0.33 protein_coding synonymous_variant LOW 42G>A Leu14Leu
M0183665 GKMCEMGI_00033 36153 4 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -1T>A None
M0183666 GKMCEMGI_00033 36221 4 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -69A>G None
M0183667 GKMCEMGI_00033 36276 4 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -124T>C None
M0183668 GKMCEMGI_00033 36303 4 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -151T>G None
M0183669 GKMCEMGI_00033 36307 4 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -155G>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
GKMCEMGI_00029 VFG012513 Salmochelin siderophore 99.5 6.1e-219 1 371 1.0 1 Nutritional/Metabolic factor glucosyltransferase IroB experiment
GKMCEMGI_00030 VFG012509 Salmochelin siderophore 99.7 0 1 1219 1.0 1 Nutritional/Metabolic factor ATP binding cassette transporter experiment
GKMCEMGI_00031 VFG012505 Salmochelin siderophore 100 7.9e-244 1 409 1.0 1 Nutritional/Metabolic factor esterase experiment
GKMCEMGI_00032 VFG012501 Salmochelin siderophore 100 6.7e-190 1 318 1.0 1 Nutritional/Metabolic factor esterase experiment
GKMCEMGI_00033 VFG000935 Salmochelin siderophore 99.3 0 1 725 1.0 1 Nutritional/Metabolic factor salmochelin receptor IroN experiment
GKMCEMGI_00144 VFG048621 Aerobactin 99.6 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor IutA experiment
GKMCEMGI_00145 VFG000937 Aerobactin 97.9 1.3e-252 1 425 1.0 0.9551 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD experiment
GKMCEMGI_00146 VFG000938 Aerobactin 97.6 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC experiment
GKMCEMGI_00147 VFG000939 Aerobactin 95.9 6.6e-190 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB experiment
GKMCEMGI_00148 VFG000940 Aerobactin 94.9 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD experiment
GKMCEMGI_00029 VFG012515 Salmochelin siderophore 100 9.2e-219 1 371 1.0 1 Nutritional/Metabolic factor glucosyltransferase IroB prediction
GKMCEMGI_00030 VFG033929 Salmochelin siderophore 100 0 1 1219 1.0 1 Nutritional/Metabolic factor ATP binding cassette transporter prediction
GKMCEMGI_00031 VFG012505 Salmochelin siderophore 100 5.9e-243 1 409 1.0 1 Nutritional/Metabolic factor esterase prediction
GKMCEMGI_00032 VFG012501 Salmochelin siderophore 100 5e-189 1 318 1.0 1 Nutritional/Metabolic factor esterase prediction
GKMCEMGI_00033 VFG012499 Salmochelin siderophore 99.7 0 1 725 1.0 1 Nutritional/Metabolic factor salmochelin receptor IroN prediction
GKMCEMGI_00144 VFG012518 Aerobactin 100 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor precusor IutA prediction
GKMCEMGI_00145 VFG033958 Aerobactin 100 3.7e-256 1 425 1.0 1 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD prediction
GKMCEMGI_00146 VFG012522 Aerobactin 100 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC prediction
GKMCEMGI_00147 VFG012524 Aerobactin 100 1.1e-196 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB prediction
GKMCEMGI_00148 VFG012526 Aerobactin 100 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD prediction
GKMCEMGI_00153 VFG012590 Iron/manganese transport 100 3.8e-148 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitD prediction
GKMCEMGI_00154 VFG012585 Iron/manganese transport 99.6 3e-153 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitC prediction
GKMCEMGI_00155 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
GKMCEMGI_00156 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
GKMCEMGI_00154 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87 6.9e-133 1 277 0.9719 0.9685 experiment
GKMCEMGI_00155 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 77.7 3.7e-115 2 266 0.9636 0.9707 experiment
GKMCEMGI_00156 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 75.8 1.1e-133 8 304 0.9770 0.9738 experiment
GKMCEMGI_00154 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87.8 2.6e-133 1 279 0.9789 0.9789 prediction
GKMCEMGI_00155 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 81.1 2.3e-118 2 266 0.9636 0.9707 prediction
GKMCEMGI_00156 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
GKMCEMGI_00059 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
GKMCEMGI_00060 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
GKMCEMGI_00069 ARO:3000166 99.3 3.06e-283 1 401 1.0000 1.0000 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
GKMCEMGI_00070 ARO:3003479 100 1.46e-152 1 207 1.0000 0.9952 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump 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
GKMCEMGI_00005 PHI:6531 HlyF 100 2.6e-216 1 369 1.0000 1.0000 birds colibacillosis hemolysin reduced virulence
GKMCEMGI_00029 PHI:6564 iroB 90.6 1.5e-200 1 371 1.0000 1.0000 rodents pneumonia salmochelin unaffected pathogenicity
GKMCEMGI_00030 PHI:9461 iroC 80.1 0 1 1205 0.9885 0.9926 primates salmonellosis putative ABC transporter protein reduced virulence
GKMCEMGI_00031 PHI:4860 IroD 99.5 1.8e-242 1 409 1.0000 1.0000 birds respiratory disease (poultry); systemic disease (poultry) catecholate siderophore esterases reduced virulence
GKMCEMGI_00032 PHI:4861 IroE 99.1 7.4e-188 1 318 1.0000 1.0000 birds respiratory disease (poultry); systemic disease (poultry) catecholate siderophore esterases unaffected pathogenicity
GKMCEMGI_00033 PHI:9464 iroN 82.1 0 1 725 1.0000 0.9972 primates salmonellosis TonB-dependent outer membrane siderophore receptor protein reduced virulence
GKMCEMGI_00144 PHI:3611 iutA 99.7 0 1 732 1.0000 0.9986 birds colibacillosis aerobactin reduced virulence
GKMCEMGI_00145 PHI:3610 iucD 100 1.3e-256 1 425 1.0000 1.0000 birds colibacillosis aerobactin reduced virulence
GKMCEMGI_00146 PHI:124069 iucC (PAGR_g3925) 83.9 9.1e-301 1 577 0.9948 0.9983 monocots None aerobactin siderophores unaffected pathogenicity
GKMCEMGI_00147 PHI:124068 iucB (PAGR_g3926) 80 1.2e-158 1 315 1.0000 1.0000 monocots None aerobactin siderophores unaffected pathogenicity
GKMCEMGI_00148 PHI:124067 iucA (PAGR_g3927) 78.5 5.7e-271 1 573 0.9983 0.9598 monocots None aerobactin siderophores unaffected pathogenicity
GKMCEMGI_00154 PHI:10084 STM14_RS15355 87 1.2e-131 1 277 0.9719 0.9685 eudicots infection iron ABC transporter permease unaffected pathogenicity
GKMCEMGI_00155 PHI:10083 STM14_RS15350 77.7 6.1e-114 2 266 0.9636 0.9707 eudicots infection iron ABC transporter permease unaffected pathogenicity
GKMCEMGI_00156 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






        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
GKMCEMGI_00029 QBC88968.1|GT1 100 1.38e-274 1 371 1 1
GKMCEMGI_00114 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
GKMCEMGI_00006 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
GKMCEMGI_00030 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
GKMCEMGI_00033 1.B.14.1.3 82 0 1 725 1.0000 0.9972 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
GKMCEMGI_00041 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
GKMCEMGI_00042 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
GKMCEMGI_00049 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
GKMCEMGI_00069 2.A.1.2.68 99.8 6.4e-221 1 401 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
GKMCEMGI_00074 2.A.27.1.4 99.8 1.5e-214 1 401 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.27 The Glutamate:Na+ Symporter (ESS) Family
GKMCEMGI_00154 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
GKMCEMGI_00155 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
GKMCEMGI_00156 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