Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1913
  Reference Plasmid   1111525849668257_bin.39__k141_314213
  Reference Plasmid Size   93353
  Reference Plasmid GC Content   0.54
  Reference Plasmid Mobility Type   non-mobilizable





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
M0019744 HHJMCKHE_00051 49103 16 Skin 0.11 protein_coding synonymous_variant LOW 816T>C Ala272Ala






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
HHJMCKHE_00007 VFG001443 OmpA 86.6 3.4e-179 1 350 1.0 1.0116 Invasion outer membrane protein A experiment
HHJMCKHE_00065 VFG049899 T6SS 74.4 2.7e-189 1 448 1.0 0.9956 Effector delivery system Type VI secretion system protein TssA experiment
HHJMCKHE_00067 VFG049903 T6SS 71.5 2.1e-192 1 469 1.0 0.9979 Effector delivery system Type VI secretion system protein TssA experiment
HHJMCKHE_00073 VFG049908 T6SS 75.4 1.8e-75 7 177 0.9661 0.9828 Effector delivery system Type VI secretion system protein TssJ experiment
HHJMCKHE_00074 VFG049909 T6SS 79.3 4.2e-195 9 429 0.9814 0.9883 Effector delivery system Type VI secretion system protein Fha experiment
HHJMCKHE_00075 VFG049910 T6SS 79.5 5.7e-169 1 361 0.9972 1.0028 Effector delivery system Type VI secretion system protein TssG experiment
HHJMCKHE_00076 VFG049911 T6SS 82.8 4.19999999999652e-313 1 617 1.0 1.0016 Effector delivery system Type VI secretion system protein TssF experiment
HHJMCKHE_00078 VFG038380 T6SS 71.3 7.6e-217 1 490 1.0 0.9959 Effector delivery system Type VI secretion system contractile sheath large subunit TssC/VipB experiment
HHJMCKHE_00079 VFG049914 T6SS 77.2 7.6e-68 1 167 1.0 1.006 Effector delivery system Type VI secretion system protein TssB experiment
HHJMCKHE_00080 VFG049915 T6SS 96.5 5e-99 1 172 1.0 1 Effector delivery system Type VI secretion system protein, Hcp family experiment
HHJMCKHE_00081 VFG049916 T6SS 71.8 1.6e-257 1 599 0.9076 0.8401 Effector delivery system type VI secretion system effector VgrG experiment
HHJMCKHE_00007 VFG043544 Z1307 87.1 5.2e-179 1 350 1.0 1.0116 Adherence porin OmpA prediction
HHJMCKHE_00064 VFG041158 T6SS 96.2 1.6e-87 1 159 1.0 1 Effector delivery system Hcp family type VI secretion system effector prediction
HHJMCKHE_00065 VFG041159 T6SS 88 3.6e-225 1 446 0.9955 0.955 Effector delivery system type VI secretion system ImpA and VasL domain-containing protein prediction
HHJMCKHE_00067 VFG046084 ACE T6SS 72.1 1.3e-193 1 469 1.0 0.9979 Effector delivery system type VI secretion system protein TssA prediction
HHJMCKHE_00068 VFG041162 T6SS 83.1 3.9e-112 1 249 1.0 1.0163 Effector delivery system type VI secretion system-associated protein TagO prediction
HHJMCKHE_00069 VFG041163 T6SS 85.8 0 1 906 1.0 1.0214 Effector delivery system AAA family ATPase prediction
HHJMCKHE_00072 VFG041165 T6SS 95 1.2e-249 1 443 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssK prediction
HHJMCKHE_00073 VFG041166 T6SS 91 7.1e-84 11 177 0.9435 1 Effector delivery system type VI secretion system lipoprotein TssJ prediction
HHJMCKHE_00074 VFG041167 T6SS 90 4.5e-225 1 429 1.0 1.0023 Effector delivery system type VI secretion system-associated FHA domain protein TagH prediction
HHJMCKHE_00075 VFG041168 T6SS 92 6.1e-199 1 362 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssG prediction
HHJMCKHE_00076 VFG041169 T6SS 90.1 0 1 617 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssF prediction
HHJMCKHE_00078 VFG041170 T6SS 95.7 5.2e-278 1 490 1.0 1 Effector delivery system type VI secretion system contractile sheath large subunit prediction
HHJMCKHE_00079 VFG041171 T6SS 95.8 3.9e-84 1 167 1.0 1 Effector delivery system type VI secretion system contractile sheath small subunit prediction
HHJMCKHE_00080 VFG041172 T6SS 99.4 1.4e-100 1 172 1.0 1 Effector delivery system Hcp family type VI secretion system effector prediction
HHJMCKHE_00081 VFG041173 T6SS 77.3 1e-276 1 599 0.9076 0.8521 Effector delivery system type VI secretion system tip protein VgrG 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
HHJMCKHE_00036 Hydrochloric acid (HCl) [class: Acid] 70.4 5e-41 1 102 1.0385 0.9818 experiment
HHJMCKHE_00036 Hydrochloric acid (HCl) [class: Acid] 100 1.7e-53 1 104 1.0000 1.0000 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
HHJMCKHE_00007 ARO:3005044 84.6 4.32e-215 1 350 1.0171 0.9519 peptide antibiotic General Bacterial Porin with reduced permeability to peptide antibiotics 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
HHJMCKHE_00003 PHI:3676 rmf3 76.4 1.6e-21 1 55 1.0000 1.0000 eudicots fire blight None unaffected pathogenicity
HHJMCKHE_00007 PHI:4160 OmpA2 92.3 8.4e-193 1 350 1.0000 1.0000 moths pneumonia outer membrane proteins reduced virulence
HHJMCKHE_00047 PHI:10387 SEN1538 86.2 5.3e-20 1 57 1.0000 0.9667 rodents salmonellosis conserved hypothetical protein reduced virulence
HHJMCKHE_00054 PHI:10991 efeO 85.9 1.2e-184 1 375 1.0000 1.0000 rodents infection iron uptake system component unaffected pathogenicity
HHJMCKHE_00055 PHI:10992 efeB 83.1 2.2e-211 1 425 0.9953 0.9953 rodents infection deferrochelatase/peroxidase unaffected pathogenicity
HHJMCKHE_00069 PHI:4559 T6SS2 83.2 0 1 906 1.0000 1.0000 birds meningitis type VI secretion systems (T6SSs) effectors effector (plant avirulence determinant)
HHJMCKHE_00070 PHI:12050 impK 86.3 1.3e-48 1 102 0.9808 0.9723 eukaryotes colibacillosis type VI secretion system protein unaffected pathogenicity
HHJMCKHE_00071 PHI:12050 impK 86.1 8.3e-70 1 144 1.0000 0.9723 eukaryotes colibacillosis type VI secretion system protein unaffected pathogenicity
HHJMCKHE_00078 PHI:12051 evpB 86.7 1.8e-257 1 490 1.0000 0.9980 eukaryotes colibacillosis type VI secretion system protein unaffected pathogenicity
HHJMCKHE_00080 PHI:8554 hcp2 97.1 2e-99 1 172 1.0000 1.0000 birds avian colibacillosis hemolysin co-regulation protein reduced virulence
HHJMCKHE_00081 PHI:4560 VgrG 71.8 3.7e-258 1 599 0.9076 0.8275 birds meningitis type VI secretion systems (T6SSs) effectors effector (plant avirulence determinant)






        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





        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
HHJMCKHE_00007 1.B.6.1.1 87.1 4.1e-179 1 350 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.6 The OmpA-OmpF Porin (OOP) Family
HHJMCKHE_00010 2.A.85.1.1 83.6 0 1 706 0.9902 0.9847 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.85 The Aromatic Acid Exporter (ArAE) Family
HHJMCKHE_00011 9.B.55.1.1 85.1 1.6e-68 1 148 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.55 The 4 TMS DUF307/YccF (DUF307) Family
HHJMCKHE_00029 1.A.14.2.1 94.1 1.6e-104 1 219 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.14 The Calcium Transporter A (CaTA) Family (formerly the Testis-Enhanced Gene Transfer (TEGT) Family)
HHJMCKHE_00034 2.A.3.2.5 94.4 1.1e-237 1 444 0.9978 0.9978 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.3 The Amino Acid-Polyamine-Organocation (APC) Family
HHJMCKHE_00052 2.A.21.2.1 95 4.2e-270 1 500 0.9960 0.9960 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.21 The Solute:Sodium Symporter (SSS) Family
HHJMCKHE_00053 2.A.108.2.3 85.5 2.3e-132 1 276 0.9964 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
HHJMCKHE_00054 2.A.108.2.3 85.9 2.6e-184 1 375 1.0000 1.3587 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
HHJMCKHE_00055 2.A.108.2.3 83.1 4.9e-211 1 425 0.9953 1.5254 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family