Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1417
  Reference Plasmid   NZ_OW967796.1
  Reference Plasmid Size   148717
  Reference Plasmid GC Content   0.48
  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
M0209556 KPCGJMHB_00025 36042 8 Gut 0.26 protein_coding downstream_gene_variant MODIFIER *4819A>C None
M0209557 KPCGJMHB_00037 45790 8 Gut 0.26 protein_coding missense_variant MODERATE 28A>G Thr10Ala
M0209558 KPCGJMHB_00037 46542 3 Gut 0.10 protein_coding synonymous_variant LOW 780A>C Leu260Leu
M0209559 KPCGJMHB_00038 50036 8 Gut 0.26 protein_coding missense_variant MODERATE 511T>C Tyr171His
M0209560 KPCGJMHB_00089 97826 3 Gut 0.10 protein_coding missense_variant MODERATE 410T>C Leu137Pro
M0209561 KPCGJMHB_00095 103886 3 Gut 0.10 protein_coding synonymous_variant LOW 138T>C Ile46Ile
M0209562 KPCGJMHB_00095 103927 3 Gut 0.10 protein_coding missense_variant MODERATE 97G>A Val33Met
M0209563 KPCGJMHB_00096 104662 3 Gut 0.10 protein_coding missense_variant MODERATE 121A>G Ile41Val
M0209564 KPCGJMHB_00100 108284 3 Gut 0.10 protein_coding missense_variant MODERATE 220T>C Ser74Pro
M0209565 KPCGJMHB_00103 109989 3 Gut 0.10 protein_coding synonymous_variant LOW 2151T>C Tyr717Tyr
M0209566 KPCGJMHB_00103 111687 3 Gut 0.10 protein_coding synonymous_variant LOW 453A>G Leu151Leu
M0209567 KPCGJMHB_00001 213 3 Gut 0.10 protein_coding synonymous_variant LOW 213C>T Thr71Thr
M0209568 KPCGJMHB_00001 378 3 Gut 0.10 protein_coding synonymous_variant LOW 378T>C Arg126Arg
M0209569 KPCGJMHB_00001 869 3 Gut 0.10 protein_coding missense_variant MODERATE 869A>C Gln290Pro
M0209570 KPCGJMHB_00001 897 3 Gut 0.10 protein_coding synonymous_variant LOW 897A>G Pro299Pro
M0209571 KPCGJMHB_00004 980 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -2252C>T None
M0209572 KPCGJMHB_00002 1076 3 Gut 0.10 protein_coding missense_variant MODERATE 98A>G Glu33Gly
M0209573 KPCGJMHB_00003 1317 3 Gut 0.10 protein_coding synonymous_variant LOW 687A>C Thr229Thr
M0209574 KPCGJMHB_00003 1353 3 Gut 0.10 protein_coding synonymous_variant LOW 651A>G Ala217Ala
M0209575 KPCGJMHB_00003 1359 3 Gut 0.10 protein_coding synonymous_variant LOW 645G>A Val215Val
M0209576 KPCGJMHB_00003 1401 3 Gut 0.10 protein_coding synonymous_variant LOW 603T>C Val201Val
M0209577 KPCGJMHB_00002 2145 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -972T>C None
M0209578 KPCGJMHB_00002 2177 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -1004T>A None
M0209579 KPCGJMHB_00002 2216 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -1043A>G None
M0209580 KPCGJMHB_00007 5857 4 Gut 0.13 protein_coding synonymous_variant LOW 903T>C Gly301Gly
M0209581 KPCGJMHB_00007 5875 3 Gut 0.10 protein_coding synonymous_variant LOW 921C>T Asp307Asp
M0209582 KPCGJMHB_00007 7276 3 Gut 0.10 protein_coding synonymous_variant LOW 2322C>T Gly774Gly
M0209583 KPCGJMHB_00015 13321 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -94A>T None
M0209584 KPCGJMHB_00015 13702 4 Gut 0.13 protein_coding synonymous_variant LOW 288T>C Ala96Ala
M0209585 KPCGJMHB_00015 14377 4 Gut 0.13 protein_coding synonymous_variant LOW 963A>G Leu321Leu
M0209586 KPCGJMHB_00025 30602 5 Gut 0.16 protein_coding synonymous_variant LOW 567G>A Ala189Ala
M0209587 KPCGJMHB_00028 39762 6 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -2783G>T None
M0209588 KPCGJMHB_00111 115914 3 Gut 0.10 protein_coding stop_lost&splice_region_variant HIGH 436T>C Ter146Glnext*?
M0209589 KPCGJMHB_00109 119678 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -4057A>C None
M0209590 KPCGJMHB_00118 119983 5 Gut 0.16 protein_coding synonymous_variant LOW 288A>T Gly96Gly
M0209591 KPCGJMHB_00109 120214 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -4593C>T None
M0209592 KPCGJMHB_00109 120314 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -4693T>C None
M0209593 KPCGJMHB_00112 121388 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -4486A>G None
M0209594 KPCGJMHB_00112 121422 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -4520T>C None
M0209595 KPCGJMHB_00114 122419 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -4771T>C None
M0209596 KPCGJMHB_00114 122463 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -4815T>C None
M0209597 KPCGJMHB_00121 122811 3 Gut 0.10 protein_coding missense_variant MODERATE 32T>C Leu11Pro
M0209598 KPCGJMHB_00122 122973 3 Gut 0.10 protein_coding synonymous_variant LOW 87G>T Gly29Gly
M0209599 KPCGJMHB_00122 123041 3 Gut 0.10 protein_coding missense_variant MODERATE 19A>G Arg7Gly
M0209600 KPCGJMHB_00123 123167 3 Gut 0.10 protein_coding synonymous_variant LOW 612G>A Pro204Pro
M0209601 KPCGJMHB_00123 123305 3 Gut 0.10 protein_coding synonymous_variant LOW 474G>A Ser158Ser
M0209602 KPCGJMHB_00123 123314 3 Gut 0.10 protein_coding synonymous_variant LOW 465A>G Ala155Ala
M0209603 KPCGJMHB_00123 123461 3 Gut 0.10 protein_coding synonymous_variant LOW 318T>C Phe106Phe
M0209604 KPCGJMHB_00123 123683 3 Gut 0.10 protein_coding synonymous_variant LOW 96T>A Gly32Gly
M0209605 KPCGJMHB_00123 123704 3 Gut 0.10 protein_coding synonymous_variant LOW 75A>G Thr25Thr
M0209606 KPCGJMHB_00123 123771 3 Gut 0.10 protein_coding missense_variant MODERATE 8T>C Val3Ala
M0209607 KPCGJMHB_00124 123882 3 Gut 0.10 protein_coding missense_variant MODERATE 328T>C Ser110Pro
M0209608 KPCGJMHB_00124 124168 3 Gut 0.10 protein_coding synonymous_variant LOW 42T>C Asn14Asn
M0209609 KPCGJMHB_00152 148333 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -4523T>A None
M0209610 KPCGJMHB_00152 148515 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -4705T>A None
M0209611 KPCGJMHB_00152 148585 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -4775G>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
KPCGJMHB_00007 VFG000884 P fimbriae 73.1 0 11 819 0.9878 0.9677 Adherence usher protein PapC experiment
KPCGJMHB_00008 VFG000885 P fimbriae 75.7 7.8e-107 25 267 0.9101 0.9959 Adherence chaperone protein PapD experiment
KPCGJMHB_00036 VFG012513 Salmochelin siderophore 99.5 6.1e-219 1 371 1.0 1 Nutritional/Metabolic factor glucosyltransferase IroB experiment
KPCGJMHB_00037 VFG012509 Salmochelin siderophore 99.6 0 1 1219 1.0 1 Nutritional/Metabolic factor ATP binding cassette transporter experiment
KPCGJMHB_00038 VFG012505 Salmochelin siderophore 99 7.4e-242 1 409 1.0 1 Nutritional/Metabolic factor esterase experiment
KPCGJMHB_00039 VFG012501 Salmochelin siderophore 99.1 3.7e-188 1 318 1.0 1 Nutritional/Metabolic factor esterase experiment
KPCGJMHB_00040 VFG000935 Salmochelin siderophore 97.4 0 1 725 1.0 1 Nutritional/Metabolic factor salmochelin receptor IroN experiment
KPCGJMHB_00152 VFG000885 P fimbriae 73.7 1.2e-104 25 267 0.9101 0.9959 Adherence chaperone protein PapD experiment
KPCGJMHB_00153 VFG000884 P fimbriae 71.9 0 3 836 0.9976 0.9976 Adherence usher protein PapC experiment
KPCGJMHB_00006 VFG042652 Pix pilus 78.3 2.3e-76 1 166 1.0 0.8557 Adherence PixH protein prediction
KPCGJMHB_00007 VFG042585 Sfp fimbriae 91.8 0 1 819 1.0 0.9808 Adherence PapC/FimD family outer membrane usher protein prediction
KPCGJMHB_00008 VFG042586 Sfp fimbriae 89.7 1.9e-125 25 267 0.9101 1 Adherence fimbria/pilus periplasmic chaperone prediction
KPCGJMHB_00036 VFG012515 Salmochelin siderophore 100 9.2e-219 1 371 1.0 1 Nutritional/Metabolic factor glucosyltransferase IroB prediction
KPCGJMHB_00037 VFG012509 Salmochelin siderophore 99.6 0 1 1219 1.0 1 Nutritional/Metabolic factor ATP binding cassette transporter prediction
KPCGJMHB_00038 VFG012508 Salmochelin siderophore 99.5 5e-242 1 409 1.0 1 Nutritional/Metabolic factor esterase prediction
KPCGJMHB_00039 VFG012503 Salmochelin siderophore 99.4 9.4e-188 1 318 1.0 1 Nutritional/Metabolic factor esterase prediction
KPCGJMHB_00040 VFG012499 Salmochelin siderophore 98.1 0 1 725 1.0 1 Nutritional/Metabolic factor salmochelin receptor IroN prediction
KPCGJMHB_00059 VFG042511 Adhesive fimbriae 73.8 9.5e-79 1 187 1.0 0.9791 Adherence FotT prediction
KPCGJMHB_00142 VFG044067 Colicin Ia 99.2 0 1 626 1.0 1 Exotoxin colicin-like pore-forming protein prediction
KPCGJMHB_00152 VFG042586 Sfp fimbriae 95.1 4.4e-130 25 267 0.9101 1 Adherence fimbria/pilus periplasmic chaperone prediction
KPCGJMHB_00153 VFG042585 Sfp fimbriae 91.4 0 3 836 0.9976 0.9988 Adherence PapC/FimD family outer membrane usher protein prediction
KPCGJMHB_00154 VFG042652 Pix pilus 90.3 6.3e-102 1 195 1.0 1.0052 Adherence PixH protein prediction
KPCGJMHB_00155 VFG042583 Sfp fimbriae 73.1 3.9e-66 1 175 1.0 1.0057 Adherence type 1 fimbrial 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
KPCGJMHB_00066 Hydrogen Peroxide (H2O2) [class: Peroxides], Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) [class: Hydrazone], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Sodium Nitrite (NaNo2) [class: Nitrites] 73.4 2.4e-154 8 369 0.9864 0.9973 experiment
KPCGJMHB_00066 Hydrogen Peroxide (H2O2) [class: Peroxides], Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) [class: Hydrazone], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Sodium Nitrite (NaNo2) [class: Nitrites] 81.2 6.7e-174 8 369 0.9810 0.9864 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
KPCGJMHB_00066 ARO:3004114 80.7 3.31e-220 8 369 0.9810 0.9864 monobactam General Bacterial Porin with reduced permeability to beta-lactams reduced permeability to antibiotic






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
KPCGJMHB_00023 PHI:6531 HlyF 80.5 7.5e-176 1 369 1.0000 1.0000 birds colibacillosis hemolysin reduced virulence
KPCGJMHB_00036 PHI:6564 iroB 90.6 1.5e-200 1 371 1.0000 1.0000 rodents pneumonia salmochelin unaffected pathogenicity
KPCGJMHB_00037 PHI:9461 iroC 80.1 0 1 1205 0.9885 0.9926 primates salmonellosis putative ABC transporter protein reduced virulence
KPCGJMHB_00038 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
KPCGJMHB_00039 PHI:4861 IroE 99.1 1.3e-187 1 318 1.0000 1.0000 birds respiratory disease (poultry); systemic disease (poultry) catecholate siderophore esterases unaffected pathogenicity
KPCGJMHB_00040 PHI:9464 iroN 82.1 0 1 725 1.0000 0.9972 primates salmonellosis TonB-dependent outer membrane siderophore receptor protein reduced virulence
KPCGJMHB_00066 PHI:9892 OmpC 79.1 6.2e-170 8 369 0.9810 0.9866 primates shigellosis outer membrane protein C 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
KPCGJMHB_00036 QBC88968.1|GT1 100 1.38e-274 1 371 1 1
KPCGJMHB_00118 AKO58984.1|GH23 100 1.73e-124 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
KPCGJMHB_00007 1.B.11.2.1 73.2 0 11 819 0.9878 0.9689 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family
KPCGJMHB_00018 3.A.1.109.8 70.8 3e-290 4 701 0.9929 0.9873 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
KPCGJMHB_00024 9.B.50.1.1 76.3 1.8e-146 1 316 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
KPCGJMHB_00037 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
KPCGJMHB_00040 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
KPCGJMHB_00043 9.B.50.1.1 90.9 7.4e-172 1 316 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
KPCGJMHB_00066 1.B.1.1.3 78.7 2.2e-167 8 369 0.9810 0.9864 1 Channels/Pores 1.B β-Barrel Porins 1.B.1 The General Bacterial Porin (GBP) Family
KPCGJMHB_00079 1.E.53.1.11 100 1.1e-21 1 49 1.0000 0.7206 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
KPCGJMHB_00142 1.C.1.1.1 99.4 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
KPCGJMHB_00153 1.B.11.2.1 72 0 3 836 0.9976 0.9988 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family