Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C720
  Reference Plasmid   NZ_CP051689.1
  Reference Plasmid Size   139635
  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
M0173520 IPNNCHHL_00021 31738 5 Gut 0.45 protein_coding missense_variant MODERATE 58A>G Thr20Ala
M0173521 IPNNCHHL_00015 32495 5 Gut 0.45 protein_coding upstream_gene_variant MODIFIER -3721T>C None
M0173522 IPNNCHHL_00023 34343 5 Gut 0.45 protein_coding synonymous_variant LOW 168A>G Ala56Ala
M0173523 IPNNCHHL_00023 34571 6 Gut 0.55 protein_coding synonymous_variant LOW 396A>G Leu132Leu
M0173524 IPNNCHHL_00023 35504 5 Gut 0.45 protein_coding synonymous_variant LOW 1329T>C Gly443Gly
M0173525 IPNNCHHL_00023 37032 3 Gut 0.27 protein_coding missense_variant MODERATE 2857T>G Ser953Ala
M0173526 IPNNCHHL_00023 37391 5 Gut 0.45 protein_coding synonymous_variant LOW 3216A>T Ile1072Ile
M0173527 IPNNCHHL_00024 38171 3 Gut 0.27 protein_coding missense_variant MODERATE 233G>A Arg78His
M0173528 IPNNCHHL_00024 38918 5 Gut 0.45 protein_coding missense_variant MODERATE 980T>G Leu327Arg
M0173529 IPNNCHHL_00026 40476 3 Gut 0.27 protein_coding synonymous_variant LOW 1956C>T His652His
M0173530 IPNNCHHL_00026 40598 4 Gut 0.36 protein_coding missense_variant MODERATE 1834A>G Ser612Gly
M0173531 IPNNCHHL_00026 41204 3 Gut 0.27 protein_coding missense_variant MODERATE 1228A>T Thr410Ser
M0173532 IPNNCHHL_00026 42248 4 Gut 0.36 protein_coding missense_variant MODERATE 184C>A Pro62Thr
M0173533 IPNNCHHL_00026 42590 3 Gut 0.27 protein_coding upstream_gene_variant MODIFIER -159T>A None
M0173534 IPNNCHHL_00013 25083 4 Gut 0.36 protein_coding upstream_gene_variant MODIFIER -38C>T None
M0173535 IPNNCHHL_00015 27154 3 Gut 0.27 protein_coding missense_variant MODERATE 1621C>A Leu541Met
M0173536 IPNNCHHL_00015 27635 5 Gut 0.45 protein_coding synonymous_variant LOW 1140T>C Ser380Ser
M0173537 IPNNCHHL_00016 29029 5 Gut 0.45 protein_coding synonymous_variant LOW 927T>C Leu309Leu
M0173538 IPNNCHHL_00016 29269 5 Gut 0.45 protein_coding synonymous_variant LOW 687G>A Gln229Gln
M0173539 IPNNCHHL_00013 30025 3 Gut 0.27 protein_coding upstream_gene_variant MODIFIER -4980G>A None
M0173540 IPNNCHHL_00014 30074 4 Gut 0.36 protein_coding upstream_gene_variant MODIFIER -3507T>G None
M0173541 IPNNCHHL_00014 30507 4 Gut 0.36 protein_coding upstream_gene_variant MODIFIER -3940C>A None
M0173542 IPNNCHHL_00023 34986 3 Gut 0.27 protein_coding missense_variant MODERATE 811T>G Trp271Gly






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
IPNNCHHL_00022 VFG012513 Salmochelin siderophore 99.2 5.2e-218 1 371 1.0 1 Nutritional/Metabolic factor glucosyltransferase IroB experiment
IPNNCHHL_00023 VFG012509 Salmochelin siderophore 99.5 0 1 1219 1.0 1 Nutritional/Metabolic factor ATP binding cassette transporter experiment
IPNNCHHL_00024 VFG012505 Salmochelin siderophore 99 2.2e-241 1 409 1.0 1 Nutritional/Metabolic factor esterase experiment
IPNNCHHL_00025 VFG012501 Salmochelin siderophore 99.7 3.3e-189 1 318 1.0 1 Nutritional/Metabolic factor esterase experiment
IPNNCHHL_00026 VFG000935 Salmochelin siderophore 98.3 0 1 725 1.0 1 Nutritional/Metabolic factor salmochelin receptor IroN experiment
IPNNCHHL_00051 VFG001827 ShET2 100 2.7e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
IPNNCHHL_00022 VFG012514 Salmochelin siderophore 99.5 1.7e-217 1 371 1.0 1 Nutritional/Metabolic factor glucosyltransferase IroB prediction
IPNNCHHL_00023 VFG012509 Salmochelin siderophore 99.5 0 1 1219 1.0 1 Nutritional/Metabolic factor ATP binding cassette transporter prediction
IPNNCHHL_00024 VFG012505 Salmochelin siderophore 99 1.6e-240 1 409 1.0 1 Nutritional/Metabolic factor esterase prediction
IPNNCHHL_00025 VFG012503 Salmochelin siderophore 99.7 2.5e-188 1 318 1.0 1 Nutritional/Metabolic factor esterase prediction
IPNNCHHL_00026 VFG012499 Salmochelin siderophore 98.8 0 1 725 1.0 1 Nutritional/Metabolic factor salmochelin receptor IroN prediction
IPNNCHHL_00051 VFG001827 ShET2 100 2e-224 1 391 1.0 1 Exotoxin enterotoxin 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






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
IPNNCHHL_00022 PHI:6564 iroB 89.8 6.4e-199 1 371 1.0000 1.0000 rodents pneumonia salmochelin unaffected pathogenicity
IPNNCHHL_00023 PHI:9461 iroC 80.1 0 1 1205 0.9885 0.9926 primates salmonellosis putative ABC transporter protein reduced virulence
IPNNCHHL_00024 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
IPNNCHHL_00025 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
IPNNCHHL_00026 PHI:9464 iroN 81.7 0 1 725 1.0000 0.9972 primates salmonellosis TonB-dependent outer membrane siderophore receptor protein reduced virulence
IPNNCHHL_00051 PHI:10795 senB 99.7 2.1e-224 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
IPNNCHHL_00052 PHI:10794 cjrC 98.7 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
IPNNCHHL_00053 PHI:10793 cjrB 98.8 7e-136 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
IPNNCHHL_00054 PHI:10792 cjrA 97.6 7.5e-163 1 291 1.0000 1.0000 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)






        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
IPNNCHHL_00022 QJG65558.1|GT1 100 2.79e-274 1 371 1 1
IPNNCHHL_00115 AML12690.1|GH23 100 7.04e-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
IPNNCHHL_00023 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
IPNNCHHL_00026 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
IPNNCHHL_00052 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
IPNNCHHL_00053 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
IPNNCHHL_00070 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