Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C838
  Reference Plasmid   NZ_CP069530.1
  Reference Plasmid Size   96693
  Reference Plasmid GC Content   0.50
  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
M0184483 LBFOJPHB_00090 83487 3 Gut 0.23 protein_coding synonymous_variant LOW 3657G>A Arg1219Arg
M0184484 LBFOJPHB_00090 84087 3 Gut 0.23 protein_coding synonymous_variant LOW 3057A>G Arg1019Arg
M0184485 LBFOJPHB_00090 84756 3 Gut 0.23 protein_coding synonymous_variant LOW 2388G>A Ala796Ala
M0184486 LBFOJPHB_00090 84899 3 Gut 0.23 protein_coding missense_variant MODERATE 2245A>G Met749Val
M0184487 LBFOJPHB_00090 85014 3 Gut 0.23 protein_coding missense_variant MODERATE 2130A>G Ile710Met
M0184488 LBFOJPHB_00090 85575 3 Gut 0.23 protein_coding synonymous_variant LOW 1569T>C Asp523Asp
M0184489 LBFOJPHB_00090 85632 3 Gut 0.23 protein_coding synonymous_variant LOW 1512T>C Thr504Thr
M0184490 LBFOJPHB_00090 85659 3 Gut 0.23 protein_coding synonymous_variant LOW 1485G>A Glu495Glu
M0184491 LBFOJPHB_00090 85663 3 Gut 0.23 protein_coding missense_variant MODERATE 1481A>T Gln494Leu
M0184492 LBFOJPHB_00090 85743 3 Gut 0.23 protein_coding synonymous_variant LOW 1401C>T Ala467Ala
M0184493 LBFOJPHB_00090 85785 3 Gut 0.23 protein_coding synonymous_variant LOW 1359A>C Ala453Ala
M0184494 LBFOJPHB_00090 85786 3 Gut 0.23 protein_coding missense_variant MODERATE 1358C>T Ala453Val
M0184495 LBFOJPHB_00090 86001 3 Gut 0.23 protein_coding synonymous_variant LOW 1143G>A Thr381Thr
M0184496 LBFOJPHB_00090 86247 3 Gut 0.23 protein_coding synonymous_variant LOW 897T>G Ala299Ala
M0184497 LBFOJPHB_00090 86260 3 Gut 0.23 protein_coding missense_variant MODERATE 884T>C Val295Ala
M0184498 LBFOJPHB_00018 20180 3 Gut 0.23 protein_coding missense_variant MODERATE 661A>C Thr221Pro
M0184499 LBFOJPHB_00082 76917 3 Gut 0.23 protein_coding synonymous_variant LOW 843T>C Ala281Ala
M0184500 LBFOJPHB_00082 76983 3 Gut 0.23 protein_coding synonymous_variant LOW 777C>T Arg259Arg
M0184501 LBFOJPHB_00082 76994 3 Gut 0.23 protein_coding missense_variant MODERATE 766A>G Thr256Ala
M0184502 LBFOJPHB_00086 79712 3 Gut 0.23 protein_coding synonymous_variant LOW 192G>A Thr64Thr
M0184503 LBFOJPHB_00086 79899 3 Gut 0.23 protein_coding missense_variant MODERATE 5T>G Met2Arg
M0184504 LBFOJPHB_00079 79953 3 Gut 0.23 protein_coding upstream_gene_variant MODIFIER -4443G>A None
M0184505 LBFOJPHB_00079 79967 3 Gut 0.23 protein_coding upstream_gene_variant MODIFIER -4457T>G None
M0184506 LBFOJPHB_00079 79981 3 Gut 0.23 protein_coding upstream_gene_variant MODIFIER -4471C>T None
M0184507 LBFOJPHB_00079 79993 3 Gut 0.23 protein_coding upstream_gene_variant MODIFIER -4483T>A None
M0184508 LBFOJPHB_00079 80013 3 Gut 0.23 protein_coding upstream_gene_variant MODIFIER -4503A>T None
M0184509 LBFOJPHB_00079 80054 3 Gut 0.23 protein_coding upstream_gene_variant MODIFIER -4544T>G None
M0184510 LBFOJPHB_00088 80810 3 Gut 0.23 protein_coding synonymous_variant LOW 243A>G Lys81Lys
M0184511 LBFOJPHB_00088 80819 3 Gut 0.23 protein_coding synonymous_variant LOW 234T>C Asn78Asn
M0184512 LBFOJPHB_00088 80837 3 Gut 0.23 protein_coding synonymous_variant LOW 216G>A Thr72Thr
M0184513 LBFOJPHB_00089 81242 3 Gut 0.23 protein_coding synonymous_variant LOW 612T>C Ala204Ala
M0184514 LBFOJPHB_00089 81299 3 Gut 0.23 protein_coding synonymous_variant LOW 555T>C Cys185Cys
M0184515 LBFOJPHB_00089 81530 3 Gut 0.23 protein_coding synonymous_variant LOW 324T>C Gly108Gly
M0184516 LBFOJPHB_00089 81533 3 Gut 0.23 protein_coding synonymous_variant LOW 321C>A Ala107Ala
M0184517 LBFOJPHB_00089 81761 3 Gut 0.23 protein_coding synonymous_variant LOW 93G>A Gly31Gly
M0184518 LBFOJPHB_00090 81988 3 Gut 0.23 protein_coding missense_variant MODERATE 5156T>A Val1719Glu
M0184519 LBFOJPHB_00090 82224 3 Gut 0.23 protein_coding synonymous_variant LOW 4920A>T Gly1640Gly
M0184520 LBFOJPHB_00090 82278 3 Gut 0.23 protein_coding synonymous_variant LOW 4866C>T Gly1622Gly
M0184521 LBFOJPHB_00090 82347 3 Gut 0.23 protein_coding synonymous_variant LOW 4797C>T Pro1599Pro
M0184522 LBFOJPHB_00090 82509 3 Gut 0.23 protein_coding synonymous_variant LOW 4635G>A Pro1545Pro
M0184523 LBFOJPHB_00090 82641 3 Gut 0.23 protein_coding synonymous_variant LOW 4503T>C Leu1501Leu
M0184524 LBFOJPHB_00090 82650 3 Gut 0.23 protein_coding synonymous_variant LOW 4494A>T Arg1498Arg
M0184525 LBFOJPHB_00090 82674 3 Gut 0.23 protein_coding synonymous_variant LOW 4470G>A Glu1490Glu
M0184526 LBFOJPHB_00090 82680 3 Gut 0.23 protein_coding synonymous_variant LOW 4464G>A Ala1488Ala






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
LBFOJPHB_00033 VFG001827 ShET2 100 2.7e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
LBFOJPHB_00056 VFG000935 Salmochelin siderophore 98.3 0 1 725 1.0 1 Nutritional/Metabolic factor salmochelin receptor IroN experiment
LBFOJPHB_00057 VFG012501 Salmochelin siderophore 99.7 3.3e-189 1 318 1.0 1 Nutritional/Metabolic factor esterase experiment
LBFOJPHB_00058 VFG012505 Salmochelin siderophore 99 2.2e-241 1 409 1.0 1 Nutritional/Metabolic factor esterase experiment
LBFOJPHB_00059 VFG012509 Salmochelin siderophore 99.5 0 1 1219 1.0 1 Nutritional/Metabolic factor ATP binding cassette transporter experiment
LBFOJPHB_00060 VFG012513 Salmochelin siderophore 98.9 1.5e-217 1 371 1.0 1 Nutritional/Metabolic factor glucosyltransferase IroB experiment
LBFOJPHB_00033 VFG001827 ShET2 100 2e-224 1 391 1.0 1 Exotoxin enterotoxin prediction
LBFOJPHB_00056 VFG012499 Salmochelin siderophore 98.8 0 1 725 1.0 1 Nutritional/Metabolic factor salmochelin receptor IroN prediction
LBFOJPHB_00057 VFG012503 Salmochelin siderophore 99.7 2.5e-188 1 318 1.0 1 Nutritional/Metabolic factor esterase prediction
LBFOJPHB_00058 VFG012505 Salmochelin siderophore 99 1.6e-240 1 409 1.0 1 Nutritional/Metabolic factor esterase prediction
LBFOJPHB_00059 VFG012509 Salmochelin siderophore 99.5 0 1 1219 1.0 1 Nutritional/Metabolic factor ATP binding cassette transporter prediction
LBFOJPHB_00060 VFG012514 Salmochelin siderophore 99.2 5.1e-217 1 371 1.0 1 Nutritional/Metabolic factor glucosyltransferase IroB 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






        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
LBFOJPHB_00075 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
LBFOJPHB_00076 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
LBFOJPHB_00077 ARO:3002660 99.3 4.37e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) 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
LBFOJPHB_00030 PHI:10792 cjrA 97.6 7.5e-163 1 291 1.0000 1.0000 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
LBFOJPHB_00031 PHI:10793 cjrB 98.8 7e-136 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
LBFOJPHB_00032 PHI:10794 cjrC 98.7 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
LBFOJPHB_00033 PHI:10795 senB 99.7 2.1e-224 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
LBFOJPHB_00056 PHI:9464 iroN 81.7 0 1 725 1.0000 0.9972 primates salmonellosis TonB-dependent outer membrane siderophore receptor protein reduced virulence
LBFOJPHB_00057 PHI:4861 IroE 99.4 3.3e-188 1 318 1.0000 1.0000 birds respiratory disease (poultry); systemic disease (poultry) catecholate siderophore esterases unaffected pathogenicity
LBFOJPHB_00058 PHI:4860 IroD 99 2.8e-240 1 409 1.0000 1.0000 birds respiratory disease (poultry); systemic disease (poultry) catecholate siderophore esterases reduced virulence
LBFOJPHB_00059 PHI:9461 iroC 80.1 0 1 1205 0.9885 0.9926 primates salmonellosis putative ABC transporter protein reduced virulence
LBFOJPHB_00060 PHI:6564 iroB 89.5 1.9e-198 1 371 1.0000 1.0000 rodents pneumonia salmochelin 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
LBFOJPHB_00060 QJG65558.1|GT1 99.7 1.14e-273 1 371 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
LBFOJPHB_00016 1.E.53.1.11 95.9 7.1e-21 1 49 1.0000 0.7206 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
LBFOJPHB_00031 2.C.1.1.3 98.8 1.6e-135 1 258 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.C Ion-gradient-driven energizers 2.C.1 The TonB-ExbB-ExbD/TolA-TolQ-TolR Outer Membrane Receptor Energizers and Stabilizers (TonB/TolA) Family
LBFOJPHB_00032 1.B.14.7.1 98.7 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
LBFOJPHB_00056 1.B.14.1.3 81.5 0 1 725 1.0000 0.9972 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
LBFOJPHB_00059 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