Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C384
  Reference Plasmid   NZ_AP025742.1
  Reference Plasmid Size   224339
  Reference Plasmid GC Content   0.47
  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
M0163648 HBBCPNBM_00262 212523 3 Gut 0.75 protein_coding missense_variant MODERATE 343A>G Thr115Ala
M0163649 HBBCPNBM_00262 212579 3 Gut 0.75 protein_coding missense_variant MODERATE 287C>T Ala96Val
M0163650 HBBCPNBM_00262 212606 3 Gut 0.75 protein_coding missense_variant MODERATE 260T>C Val87Ala
M0163651 HBBCPNBM_00262 212650 3 Gut 0.75 protein_coding synonymous_variant LOW 216T>C Arg72Arg
M0163652 HBBCPNBM_00262 212729 3 Gut 0.75 protein_coding missense_variant MODERATE 137G>A Arg46His
M0163653 HBBCPNBM_00262 212764 3 Gut 0.75 protein_coding synonymous_variant LOW 102G>A Arg34Arg
M0163654 HBBCPNBM_00262 212770 3 Gut 0.75 protein_coding synonymous_variant LOW 96G>A Gln32Gln
M0163655 HBBCPNBM_00262 212773 3 Gut 0.75 protein_coding synonymous_variant LOW 93A>G Gln31Gln
M0163656 HBBCPNBM_00262 212779 3 Gut 0.75 protein_coding synonymous_variant LOW 87T>C His29His
M0163657 HBBCPNBM_00262 212840 3 Gut 0.75 protein_coding missense_variant MODERATE 26A>G Glu9Gly
M0163658 HBBCPNBM_00263 212939 3 Gut 0.75 protein_coding missense_variant MODERATE 253C>T Arg85Cys
M0163659 HBBCPNBM_00263 212955 3 Gut 0.75 protein_coding synonymous_variant LOW 237A>G Glu79Glu
M0163660 HBBCPNBM_00263 212961 3 Gut 0.75 protein_coding synonymous_variant LOW 231A>G Glu77Glu
M0163661 HBBCPNBM_00263 213003 3 Gut 0.75 protein_coding synonymous_variant LOW 189T>A Gly63Gly
M0163662 HBBCPNBM_00263 213017 3 Gut 0.75 protein_coding missense_variant MODERATE 175G>A Gly59Arg
M0163663 HBBCPNBM_00263 213026 3 Gut 0.75 protein_coding synonymous_variant LOW 166A>C Arg56Arg
M0163664 HBBCPNBM_00263 213060 3 Gut 0.75 protein_coding synonymous_variant LOW 132A>G Pro44Pro
M0163665 HBBCPNBM_00263 213063 3 Gut 0.75 protein_coding synonymous_variant LOW 129G>A Thr43Thr
M0163666 HBBCPNBM_00263 213083 3 Gut 0.75 protein_coding missense_variant MODERATE 109G>A Ala37Thr
M0163667 HBBCPNBM_00263 213097 3 Gut 0.75 protein_coding missense_variant MODERATE 95C>T Ala32Val
M0163668 HBBCPNBM_00263 213144 3 Gut 0.75 protein_coding synonymous_variant LOW 48T>C Val16Val
M0163669 HBBCPNBM_00263 213150 3 Gut 0.75 protein_coding synonymous_variant LOW 42C>G Arg14Arg
M0163670 HBBCPNBM_00262 217664 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4799G>T None
M0163671 HBBCPNBM_00262 217827 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4962T>C None
M0163672 HBBCPNBM_00265 217838 4 Gut 1.00 protein_coding stop_lost&splice_region_variant HIGH 193T>G Ter65Gluext*?
M0163673 HBBCPNBM_00265 217840 4 Gut 1.00 protein_coding stop_gained HIGH 191C>A Ser64*
M0163674 HBBCPNBM_00266 218227 4 Gut 1.00 protein_coding missense_variant MODERATE 205G>A Ala69Thr
M0163675 HBBCPNBM_00266 218311 4 Gut 1.00 protein_coding missense_variant MODERATE 121G>A Gly41Ser






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
HBBCPNBM_00151 VFG001445 TraJ 77.9 1.9e-85 1 195 0.8553 0.9701 Invasion unknown protein experiment
HBBCPNBM_00217 VFG000842 Hemolysin 94.2 6.1e-97 1 171 1.0 1 Exotoxin Hemolysin C experiment
HBBCPNBM_00264 VFG000844 EspP 91.5 0 1 1301 1.0 1.0008 Effector delivery system autotransporter, serine protease experiment
HBBCPNBM_00015 VFG035429 AAI/SCI-II T6SS 83.8 0 1 842 0.9988 0.9918 Effector delivery system type VI secretion system ATPase TssH prediction
HBBCPNBM_00016 VFG035424 AAI/SCI-II T6SS 75 0 1 1134 1.0 1 Effector delivery system type VI secretion protein prediction
HBBCPNBM_00017 VFG035422 AAI/SCI-II T6SS 70.9 3e-75 1 196 1.0 1 Effector delivery system DotU family type IV/VI secretion system protein prediction
HBBCPNBM_00021 VFG035409 AAI/SCI-II T6SS 76.7 2.7e-212 1 450 1.0 0.9574 Effector delivery system type VI secretion system baseplate subunit TssK prediction
HBBCPNBM_00022 VFG035404 AAI/SCI-II T6SS 80.3 3e-85 1 183 1.0 1 Effector delivery system type VI secretion lipoprotein TssJ prediction
HBBCPNBM_00023 VFG035399 AAI/SCI-II T6SS 85.2 6.5e-177 1 358 1.0 1 Effector delivery system type VI secretion system protein TssA prediction
HBBCPNBM_00024 VFG035394 AAI/SCI-II T6SS 90.9 1.3e-47 1 99 1.0 1 Effector delivery system PAAR domain-containing protein prediction
HBBCPNBM_00025 VFG035389 AAI/SCI-II T6SS 74.5 4.1e-64 1 153 1.0 0.9871 Effector delivery system hypothetical protein prediction
HBBCPNBM_00026 VFG035384 AAI/SCI-II T6SS 78 3.6e-306 7 660 0.9909 0.9909 Effector delivery system type VI secretion system tip protein VgrG prediction
HBBCPNBM_00027 VFG035379 AAI/SCI-II T6SS 83.5 2.7e-158 10 318 0.9656 0.9968 Effector delivery system type VI secretion system baseplate subunit TssG prediction
HBBCPNBM_00028 VFG035374 AAI/SCI-II T6SS 84.5 4.7e-305 1 600 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssF prediction
HBBCPNBM_00029 VFG035369 AAI/SCI-II T6SS 85 1e-61 1 140 1.0 1 Effector delivery system hypothetical protein prediction
HBBCPNBM_00030 VFG035364 AAI/SCI-II T6SS 73.1 1.8e-65 7 166 0.9639 0.9524 Effector delivery system type VI secretion system protein AaiC/Hcp2 prediction
HBBCPNBM_00031 VFG035359 AAI/SCI-II T6SS 95.9 1.6e-279 1 492 1.0 1 Effector delivery system type VI secretion system contractile sheath large subunit prediction
HBBCPNBM_00032 VFG035354 AAI/SCI-II T6SS 90.5 2.6e-77 1 158 1.0 1 Effector delivery system type VI secretion system contractile sheath small subunit prediction
HBBCPNBM_00033 VFG041000 AAI/SCI-II T6SS 73.2 4.3e-67 1 164 1.0 0.8723 Effector delivery system hypothetical protein prediction
HBBCPNBM_00151 VFG001445 TraJ 77.9 1.4e-84 1 195 0.8553 0.9701 Invasion unknown protein prediction
HBBCPNBM_00217 VFG000842 Hemolysin 94.2 4.6e-96 1 171 1.0 1 Exotoxin Hemolysin C prediction
HBBCPNBM_00249 VFG034602 Adhesive fimbriae 87.9 5.4e-133 1 257 1.0 1 Adherence fimbrial protein FaeJ prediction
HBBCPNBM_00250 VFG043644 CS31A capsule-like antigen 85.8 1.3e-126 1 254 1.0 1 Adherence CS31A minor subunit prediction
HBBCPNBM_00251 VFG043647 CS31A capsule-like antigen 84.8 7e-123 17 272 0.9412 0.9624 Adherence fimbrial protein prediction
HBBCPNBM_00253 VFG042496 Adhesive fimbriae 90.7 6.1e-74 1 162 0.9939 0.9939 Adherence unknown protein prediction
HBBCPNBM_00254 VFG042553 Adhesive fimbriae 92.9 9e-133 1 253 1.0 0.9806 Adherence F4 (K88) fimbrial chaperone FaeE prediction
HBBCPNBM_00255 VFG042494 Adhesive fimbriae 93.1 0 15 814 0.9828 1 Adherence cshB porin (usher) prediction
HBBCPNBM_00256 VFG042533 CS31A capsule-like antigen 93.1 3.3e-81 20 178 0.8933 0.8833 Adherence ClpC prediction
HBBCPNBM_00264 VFG000844 EspP 91.5 0 1 1301 1.0 1.0008 Effector delivery system autotransporter, serine protease prediction
HBBCPNBM_00271 VFG017870 Icm/dot type IVB locus 77.4 1.7e-89 1 208 0.9905 0.9952 Effector delivery system ParA family 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






        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
HBBCPNBM_00030 PHI:123579 Hcp2 73.1 6.4e-66 7 166 0.9639 0.9524 primates avian colibacillosis type VI secretion system protein effector (plant avirulence determinant)
HBBCPNBM_00231 PHI:10997 fdnG 70.3 0 1 1016 1.0000 1.0000 rodents infection formate dehydrogenase, nitrate-inducible, major subunit 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
HBBCPNBM_00153 QIC02838.1|GH23 99.1 1.93e-155 1 215 1 1
HBBCPNBM_00241 ANO92402.1|GT4 100 5.58e-290 1 389 1 1
HBBCPNBM_00242 ANP05419.1|GT4 99.8 9.5e-300 1 411 1 1
HBBCPNBM_00243 ANP16064.1|GT1 100 1.43e-270 1 386 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
HBBCPNBM_00106 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
HBBCPNBM_00231 5.A.3.2.1 70.3 0 1 1016 1.0000 1.0000 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
HBBCPNBM_00237 1.B.13.1.6 100 3.1e-224 59 439 0.8679 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.13 The Alginate Export Porin (AEP) Family
HBBCPNBM_00255 1.B.11.1.1 92 0 5 814 0.9951 0.9975 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family
HBBCPNBM_00264 1.B.12.4.3 91.5 0 1 1301 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family