Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C731
  Reference Plasmid   NZ_CP053298.1
  Reference Plasmid Size   119964
  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
M0173703 AEPONOFB_00075 62986 37 Gut 0.90 protein_coding missense_variant MODERATE 167T>C Met56Thr
M0173704 AEPONOFB_00076 63395 37 Gut 0.90 protein_coding synonymous_variant LOW 324A>G Leu108Leu
M0173705 AEPONOFB_00076 63505 38 Gut 0.93 protein_coding missense_variant MODERATE 214A>G Thr72Ala
M0173706 AEPONOFB_00076 63513 36 Gut 0.88 protein_coding missense_variant MODERATE 206G>T Gly69Val
M0173707 AEPONOFB_00076 63668 38 Gut 0.93 protein_coding synonymous_variant LOW 51G>A Gly17Gly
M0173708 AEPONOFB_00077 64170 40 Gut 0.98 protein_coding synonymous_variant LOW 324G>A Arg108Arg
M0173709 AEPONOFB_00078 64275 38 Gut 0.93 protein_coding missense_variant MODERATE 530A>C Gln177Pro
M0173710 AEPONOFB_00078 64324 40 Gut 0.98 protein_coding missense_variant MODERATE 481A>T Arg161Trp
M0173711 AEPONOFB_00078 64683 40 Gut 0.98 protein_coding missense_variant MODERATE 122A>G Asn41Ser
M0173712 AEPONOFB_00079 64908 40 Gut 0.98 protein_coding missense_variant MODERATE 154A>G Thr52Ala
M0173713 AEPONOFB_00079 64988 40 Gut 0.98 protein_coding missense_variant MODERATE 74A>G Tyr25Cys
M0173714 AEPONOFB_00073 65066 40 Gut 0.98 protein_coding upstream_gene_variant MODIFIER -3658A>G None
M0173715 AEPONOFB_00080 65307 37 Gut 0.90 protein_coding missense_variant MODERATE 148T>C Trp50Arg
M0173716 AEPONOFB_00080 65426 36 Gut 0.88 protein_coding synonymous_variant LOW 267T>C Ile89Ile
M0173717 AEPONOFB_00080 65465 36 Gut 0.88 protein_coding synonymous_variant LOW 306C>T Phe102Phe
M0173718 AEPONOFB_00081 65627 36 Gut 0.88 protein_coding missense_variant MODERATE 145A>G Asn49Asp
M0173719 AEPONOFB_00081 65773 35 Gut 0.85 protein_coding synonymous_variant LOW 291T>C Ala97Ala
M0173720 AEPONOFB_00081 66148 29 Gut 0.71 protein_coding synonymous_variant LOW 666C>T Gly222Gly
M0173721 AEPONOFB_00081 66172 29 Gut 0.71 protein_coding synonymous_variant LOW 690G>A Ala230Ala
M0173722 AEPONOFB_00081 66177 31 Gut 0.76 protein_coding missense_variant MODERATE 695A>T Asn232Ile
M0173723 AEPONOFB_00081 66184 29 Gut 0.71 protein_coding missense_variant MODERATE 702T>G Asn234Lys
M0173724 AEPONOFB_00081 66187 29 Gut 0.71 protein_coding synonymous_variant LOW 705T>C Gly235Gly
M0173725 AEPONOFB_00081 66232 29 Gut 0.71 protein_coding synonymous_variant LOW 750T>G Arg250Arg
M0173726 AEPONOFB_00081 66233 29 Gut 0.71 protein_coding missense_variant MODERATE 751G>A Ala251Thr
M0173727 AEPONOFB_00081 66244 29 Gut 0.71 protein_coding synonymous_variant LOW 762A>G Glu254Glu
M0173728 AEPONOFB_00081 66349 31 Gut 0.76 protein_coding synonymous_variant LOW 867A>C Ile289Ile
M0173729 AEPONOFB_00101 83942 29 Gut 0.71 protein_coding synonymous_variant LOW 51G>A Lys17Lys
M0173730 AEPONOFB_00101 84078 29 Gut 0.71 protein_coding missense_variant MODERATE 187A>C Asn63His
M0173731 AEPONOFB_00101 84080 29 Gut 0.71 protein_coding missense_variant MODERATE 189C>G Asn63Lys
M0173732 AEPONOFB_00101 84083 29 Gut 0.71 protein_coding missense_variant MODERATE 192T>A Asp64Glu
M0173733 AEPONOFB_00101 84143 29 Gut 0.71 protein_coding synonymous_variant LOW 252G>A Glu84Glu
M0173734 AEPONOFB_00101 84146 29 Gut 0.71 protein_coding synonymous_variant LOW 255G>T Val85Val
M0173735 AEPONOFB_00101 84158 29 Gut 0.71 protein_coding synonymous_variant LOW 267G>A Ala89Ala
M0173736 AEPONOFB_00101 84209 29 Gut 0.71 protein_coding synonymous_variant LOW 318C>A Ile106Ile
M0173737 AEPONOFB_00101 84210 29 Gut 0.71 protein_coding missense_variant MODERATE 319A>C Ile107Leu
M0173738 AEPONOFB_00101 84227 29 Gut 0.71 protein_coding synonymous_variant LOW 336T>A Ala112Ala
M0173739 AEPONOFB_00101 84230 29 Gut 0.71 protein_coding synonymous_variant LOW 339G>A Val113Val
M0173740 AEPONOFB_00101 84237 29 Gut 0.71 protein_coding missense_variant MODERATE 346A>T Thr116Ser
M0173741 AEPONOFB_00101 84239 29 Gut 0.71 protein_coding synonymous_variant LOW 348C>T Thr116Thr
M0173742 AEPONOFB_00101 84242 29 Gut 0.71 protein_coding synonymous_variant LOW 351C>T Val117Val
M0173743 AEPONOFB_00101 84244 29 Gut 0.71 protein_coding missense_variant MODERATE 353T>C Val118Ala
M0173744 AEPONOFB_00101 84245 29 Gut 0.71 protein_coding synonymous_variant LOW 354T>C Val118Val
M0173745 AEPONOFB_00101 84248 29 Gut 0.71 protein_coding synonymous_variant LOW 357C>A Gly119Gly
M0173746 AEPONOFB_00101 84249 29 Gut 0.71 protein_coding missense_variant MODERATE 358C>T Leu120Phe
M0173747 AEPONOFB_00102 84273 29 Gut 0.71 protein_coding missense_variant MODERATE 5C>T Ser2Leu
M0173748 AEPONOFB_00103 84695 28 Gut 0.68 protein_coding missense_variant MODERATE 94G>C Val32Leu
M0173749 AEPONOFB_00103 84721 29 Gut 0.71 protein_coding synonymous_variant LOW 120C>T Arg40Arg
M0173750 AEPONOFB_00103 84751 29 Gut 0.71 protein_coding synonymous_variant LOW 150G>C Thr50Thr
M0173751 AEPONOFB_00113 92173 29 Gut 0.71 protein_coding synonymous_variant LOW 1425G>A Gly475Gly
M0173752 AEPONOFB_00113 92188 29 Gut 0.71 protein_coding synonymous_variant LOW 1440T>C Asn480Asn
M0173753 AEPONOFB_00113 92332 29 Gut 0.71 protein_coding synonymous_variant LOW 1584G>T Gly528Gly
M0173754 AEPONOFB_00113 92362 29 Gut 0.71 protein_coding synonymous_variant LOW 1614C>T Arg538Arg
M0173755 AEPONOFB_00113 92392 29 Gut 0.71 protein_coding synonymous_variant LOW 1644T>C Ile548Ile
M0173756 AEPONOFB_00113 92416 29 Gut 0.71 protein_coding synonymous_variant LOW 1668C>T Arg556Arg
M0173757 AEPONOFB_00113 92423 29 Gut 0.71 protein_coding synonymous_variant LOW 1675C>T Leu559Leu
M0173758 AEPONOFB_00113 92428 29 Gut 0.71 protein_coding synonymous_variant LOW 1680G>A Ser560Ser
M0173759 AEPONOFB_00113 92497 29 Gut 0.71 protein_coding synonymous_variant LOW 1749A>C Ala583Ala
M0173760 AEPONOFB_00113 92500 29 Gut 0.71 protein_coding synonymous_variant LOW 1752A>C Ser584Ser
M0173761 AEPONOFB_00113 92833 29 Gut 0.71 protein_coding synonymous_variant LOW 2085T>C Val695Val
M0173762 AEPONOFB_00132 112942 29 Gut 0.71 protein_coding synonymous_variant LOW 4395G>T Thr1465Thr
M0173763 AEPONOFB_00132 112960 29 Gut 0.71 protein_coding synonymous_variant LOW 4413A>G Glu1471Glu
M0173764 AEPONOFB_00132 113011 29 Gut 0.71 protein_coding synonymous_variant LOW 4464A>G Ala1488Ala
M0173765 AEPONOFB_00132 113017 29 Gut 0.71 protein_coding synonymous_variant LOW 4470A>G Glu1490Glu
M0173766 AEPONOFB_00132 113119 29 Gut 0.71 protein_coding synonymous_variant LOW 4572G>A Gln1524Gln
M0173767 AEPONOFB_00132 113147 29 Gut 0.71 protein_coding missense_variant MODERATE 4600T>C Cys1534Arg
M0173768 AEPONOFB_00132 113157 29 Gut 0.71 protein_coding missense_variant MODERATE 4610G>A Arg1537Lys
M0173769 AEPONOFB_00132 113182 29 Gut 0.71 protein_coding synonymous_variant LOW 4635A>G Pro1545Pro
M0173770 AEPONOFB_00132 113230 29 Gut 0.71 protein_coding synonymous_variant LOW 4683A>T Gly1561Gly
M0173771 AEPONOFB_00132 113236 29 Gut 0.71 protein_coding synonymous_variant LOW 4689G>A Val1563Val
M0173772 AEPONOFB_00132 113290 29 Gut 0.71 protein_coding synonymous_variant LOW 4743G>A Glu1581Glu
M0173773 AEPONOFB_00132 113320 29 Gut 0.71 protein_coding synonymous_variant LOW 4773T>C Gly1591Gly
M0173774 AEPONOFB_00132 113350 29 Gut 0.71 protein_coding synonymous_variant LOW 4803C>T Ser1601Ser
M0173775 AEPONOFB_00132 113365 29 Gut 0.71 protein_coding missense_variant MODERATE 4818A>C Arg1606Ser
M0173776 AEPONOFB_00132 113380 29 Gut 0.71 protein_coding synonymous_variant LOW 4833T>C Gly1611Gly
M0173777 AEPONOFB_00132 113409 29 Gut 0.71 protein_coding missense_variant MODERATE 4862G>A Gly1621Asp
M0173778 AEPONOFB_00132 113413 29 Gut 0.71 protein_coding synonymous_variant LOW 4866T>C Gly1622Gly
M0173779 AEPONOFB_00132 113439 29 Gut 0.71 protein_coding missense_variant MODERATE 4892G>A Ser1631Asn
M0173780 AEPONOFB_00132 113488 29 Gut 0.71 protein_coding synonymous_variant LOW 4941G>A Val1647Val
M0173781 AEPONOFB_00132 113536 29 Gut 0.71 protein_coding synonymous_variant LOW 4989C>T Arg1663Arg
M0173782 AEPONOFB_00132 113555 29 Gut 0.71 protein_coding synonymous_variant LOW 5008A>C Arg1670Arg
M0173783 AEPONOFB_00132 113557 29 Gut 0.71 protein_coding missense_variant MODERATE 5010A>T Arg1670Ser
M0173784 AEPONOFB_00132 113590 29 Gut 0.71 protein_coding synonymous_variant LOW 5043T>C Asp1681Asp
M0173785 AEPONOFB_00132 113604 29 Gut 0.71 protein_coding missense_variant MODERATE 5057A>T Gln1686Leu
M0173786 AEPONOFB_00132 113646 29 Gut 0.71 protein_coding missense_variant MODERATE 5099A>C Asp1700Ala
M0173787 AEPONOFB_00132 113706 29 Gut 0.71 protein_coding missense_variant MODERATE 5159A>G Gln1720Arg
M0173788 AEPONOFB_00132 113724 29 Gut 0.71 protein_coding missense_variant MODERATE 5177G>T Gly1726Val
M0173789 AEPONOFB_00132 113805 29 Gut 0.71 protein_coding missense_variant MODERATE 5258T>C Leu1753Pro
M0173790 AEPONOFB_00133 113829 29 Gut 0.71 protein_coding upstream_gene_variant MODIFIER -9T>C None
M0173791 AEPONOFB_00133 113834 29 Gut 0.71 protein_coding upstream_gene_variant MODIFIER -4G>A None
M0173792 AEPONOFB_00133 114047 29 Gut 0.71 protein_coding synonymous_variant LOW 210G>T Leu70Leu
M0173793 AEPONOFB_00077 63852 4 Gut 0.10 protein_coding synonymous_variant LOW 6T>C Thr2Thr
M0173794 AEPONOFB_00078 64422 4 Gut 0.10 protein_coding missense_variant MODERATE 383C>A Ala128Glu
M0173795 AEPONOFB_00078 64445 4 Gut 0.10 protein_coding synonymous_variant LOW 360C>T Gly120Gly
M0173796 AEPONOFB_00078 64446 4 Gut 0.10 protein_coding missense_variant MODERATE 359G>A Gly120Asp






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
AEPONOFB_00003 VFG048621 Aerobactin 99.7 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor IutA experiment
AEPONOFB_00004 VFG000937 Aerobactin 97.9 1.3e-252 1 425 1.0 0.9551 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD experiment
AEPONOFB_00005 VFG000938 Aerobactin 97.4 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC experiment
AEPONOFB_00006 VFG000939 Aerobactin 96.2 1.7e-190 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB experiment
AEPONOFB_00007 VFG000940 Aerobactin 94.9 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD experiment
AEPONOFB_00003 VFG033944 Aerobactin 100 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor precusor IutA prediction
AEPONOFB_00004 VFG033958 Aerobactin 100 3.7e-256 1 425 1.0 1 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD prediction
AEPONOFB_00005 VFG012522 Aerobactin 99.8 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC prediction
AEPONOFB_00006 VFG033993 Aerobactin 99.7 3.2e-196 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB prediction
AEPONOFB_00007 VFG012526 Aerobactin 99.7 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD prediction
AEPONOFB_00024 VFG012590 Iron/manganese transport 100 3.8e-148 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitD prediction
AEPONOFB_00025 VFG012585 Iron/manganese transport 100 1.4e-153 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitC prediction
AEPONOFB_00026 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
AEPONOFB_00027 VFG012575 Iron/manganese transport 99.7 2.2e-173 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
AEPONOFB_00025 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87 9e-133 1 277 0.9719 0.9685 experiment
AEPONOFB_00026 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 77.7 3.7e-115 2 266 0.9636 0.9707 experiment
AEPONOFB_00027 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 75.8 1.5e-133 8 304 0.9770 0.9738 experiment
AEPONOFB_00025 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87.8 3.4e-133 1 279 0.9789 0.9789 prediction
AEPONOFB_00026 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 81.1 2.3e-118 2 266 0.9636 0.9707 prediction
AEPONOFB_00027 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 76.4 5.2e-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
AEPONOFB_00003 PHI:6563 iucA 99.7 0 1 732 1.0000 0.9986 rodents pneumonia aerobactin reduced virulence
AEPONOFB_00004 PHI:3610 iucD 100 1.3e-256 1 425 1.0000 1.0000 birds colibacillosis aerobactin reduced virulence
AEPONOFB_00005 PHI:124069 iucC (PAGR_g3925) 83.7 2e-300 1 577 0.9948 0.9983 monocots None aerobactin siderophores unaffected pathogenicity
AEPONOFB_00006 PHI:124068 iucB (PAGR_g3926) 80 1.2e-158 1 315 1.0000 1.0000 monocots None aerobactin siderophores unaffected pathogenicity
AEPONOFB_00007 PHI:124067 iucA (PAGR_g3927) 78.7 1.5e-271 1 573 0.9983 0.9598 monocots None aerobactin siderophores unaffected pathogenicity
AEPONOFB_00025 PHI:10084 STM14_RS15355 87 1.5e-131 1 277 0.9719 0.9685 eudicots infection iron ABC transporter permease unaffected pathogenicity
AEPONOFB_00026 PHI:10083 STM14_RS15350 77.7 6.1e-114 2 266 0.9636 0.9707 eudicots infection iron ABC transporter permease unaffected pathogenicity
AEPONOFB_00027 PHI:10082 STM14_RS15345 75.8 2.5e-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
AEPONOFB_00097 AXI38019.1|GH23 98.8 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
AEPONOFB_00025 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
AEPONOFB_00026 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
AEPONOFB_00027 3.A.1.15.7 75.8 5.5e-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