Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C385
  Reference Plasmid   NZ_AP025748.1
  Reference Plasmid Size   225721
  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
M0163676 GDMIPMLP_00277 221316 10 Gut 0.83 protein_coding synonymous_variant LOW 618T>C Tyr206Tyr
M0163677 GDMIPMLP_00277 221329 10 Gut 0.83 protein_coding stop_gained HIGH 605C>A Ser202*
M0163678 GDMIPMLP_00277 221461 11 Gut 0.92 protein_coding missense_variant MODERATE 473C>A Ala158Asp
M0163679 GDMIPMLP_00277 221729 10 Gut 0.83 protein_coding missense_variant MODERATE 205G>A Ala69Thr
M0163680 GDMIPMLP_00277 221813 10 Gut 0.83 protein_coding missense_variant MODERATE 121G>A Gly41Ser
M0163681 GDMIPMLP_00046 39428 6 Gut 0.50 protein_coding synonymous_variant LOW 39G>A Gln13Gln
M0163682 GDMIPMLP_00046 39434 6 Gut 0.50 protein_coding synonymous_variant LOW 45G>A Ala15Ala
M0163683 GDMIPMLP_00046 39435 6 Gut 0.50 protein_coding missense_variant MODERATE 46A>G Ile16Val
M0163684 GDMIPMLP_00046 39437 6 Gut 0.50 protein_coding synonymous_variant LOW 48T>C Ile16Ile
M0163685 GDMIPMLP_00046 39460 6 Gut 0.50 protein_coding missense_variant MODERATE 71A>G Asp24Gly
M0163686 GDMIPMLP_00046 39461 6 Gut 0.50 protein_coding synonymous_variant LOW 72T>C Asp24Asp
M0163687 GDMIPMLP_00046 39476 6 Gut 0.50 protein_coding synonymous_variant LOW 87G>A Gln29Gln
M0163688 GDMIPMLP_00046 39484 6 Gut 0.50 protein_coding missense_variant MODERATE 95C>T Ala32Val
M0163689 GDMIPMLP_00046 39498 6 Gut 0.50 protein_coding missense_variant MODERATE 109G>A Ala37Thr
M0163690 GDMIPMLP_00046 39500 6 Gut 0.50 protein_coding synonymous_variant LOW 111C>T Ala37Ala
M0163691 GDMIPMLP_00046 39518 6 Gut 0.50 protein_coding synonymous_variant LOW 129G>A Thr43Thr
M0163692 GDMIPMLP_00046 39564 6 Gut 0.50 protein_coding missense_variant MODERATE 175G>A Gly59Arg
M0163693 GDMIPMLP_00046 39578 6 Gut 0.50 protein_coding synonymous_variant LOW 189T>A Gly63Gly
M0163694 GDMIPMLP_00046 39589 6 Gut 0.50 protein_coding missense_variant MODERATE 200G>C Ser67Thr
M0163695 GDMIPMLP_00046 39620 6 Gut 0.50 protein_coding synonymous_variant LOW 231A>G Glu77Glu
M0163696 GDMIPMLP_00046 39626 6 Gut 0.50 protein_coding synonymous_variant LOW 237A>G Glu79Glu
M0163697 GDMIPMLP_00046 39642 6 Gut 0.50 protein_coding missense_variant MODERATE 253C>T Arg85Cys
M0163698 GDMIPMLP_00047 39715 6 Gut 0.50 protein_coding start_lost HIGH 3G>A Met1?
M0163699 GDMIPMLP_00047 39741 6 Gut 0.50 protein_coding missense_variant MODERATE 29A>G Glu10Gly
M0163700 GDMIPMLP_00047 39769 6 Gut 0.50 protein_coding synonymous_variant LOW 57C>T Ser19Ser
M0163701 GDMIPMLP_00047 39802 6 Gut 0.50 protein_coding synonymous_variant LOW 90T>C His30His
M0163702 GDMIPMLP_00047 39826 6 Gut 0.50 protein_coding synonymous_variant LOW 114G>T Pro38Pro
M0163703 GDMIPMLP_00047 39931 6 Gut 0.50 protein_coding synonymous_variant LOW 219T>C Arg73Arg
M0163704 GDMIPMLP_00047 40002 6 Gut 0.50 protein_coding missense_variant MODERATE 290C>T Ala97Val
M0163705 GDMIPMLP_00047 40058 6 Gut 0.50 protein_coding missense_variant MODERATE 346A>G Thr116Ala
M0163706 GDMIPMLP_00047 40165 6 Gut 0.50 protein_coding synonymous_variant LOW 453T>C Phe151Phe
M0163707 GDMIPMLP_00047 40196 6 Gut 0.50 protein_coding missense_variant MODERATE 484G>T Gly162Trp
M0163708 GDMIPMLP_00047 40201 6 Gut 0.50 protein_coding stop_gained HIGH 489G>A Trp163*
M0163709 GDMIPMLP_00047 40204 6 Gut 0.50 protein_coding synonymous_variant LOW 492G>A Arg164Arg
M0163710 GDMIPMLP_00047 40243 6 Gut 0.50 protein_coding synonymous_variant LOW 531G>A Ala177Ala






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
GDMIPMLP_00003 VFG002039 Heat-stable toxin (ST) 76.4 4.5e-25 1 72 1.0 1 Exotoxin heat stable enterotoxin I experiment
GDMIPMLP_00206 VFG002039 Heat-stable toxin (ST) 93.1 1.5e-33 1 72 1.0 1 Exotoxin heat stable enterotoxin I experiment
GDMIPMLP_00211 VFG000842 Hemolysin 94.2 6.1e-97 1 171 1.0 1 Exotoxin Hemolysin C experiment
GDMIPMLP_00212 VFG000840 Hemolysin 95.4 0 1 997 1.0 0.999 Exotoxin Hemolysin A experiment
GDMIPMLP_00213 VFG000841 Hemolysin 97.3 0 1 705 1.0 0.9986 Exotoxin Hemolysin B experiment
GDMIPMLP_00214 VFG000843 Hemolysin 96.2 2.7e-259 1 479 1.0 1 Exotoxin Hemolysin D experiment
GDMIPMLP_00241 VFG038285 Exe T2SS 76.3 5.6e-59 1 139 0.9653 0.972 Effector delivery system general secretion pathway protein G experiment
GDMIPMLP_00246 VFG000846 StcE 78.5 0 1 883 0.9977 0.9833 Exoenzyme metalloprotease experiment
GDMIPMLP_00003 VFG002039 Heat-stable toxin (ST) 76.4 3.3e-24 1 72 1.0 1 Exotoxin heat stable enterotoxin I prediction
GDMIPMLP_00020 VFG035429 AAI/SCI-II T6SS 84.1 0 1 842 0.9988 0.9918 Effector delivery system type VI secretion system ATPase TssH prediction
GDMIPMLP_00021 VFG035424 AAI/SCI-II T6SS 75.2 0 1 1134 1.0 1 Effector delivery system type VI secretion protein prediction
GDMIPMLP_00022 VFG035422 AAI/SCI-II T6SS 71.9 4.2e-77 1 196 1.0 1 Effector delivery system DotU family type IV/VI secretion system protein prediction
GDMIPMLP_00030 VFG035409 AAI/SCI-II T6SS 76.7 2e-212 1 450 1.0 0.9574 Effector delivery system type VI secretion system baseplate subunit TssK prediction
GDMIPMLP_00031 VFG035404 AAI/SCI-II T6SS 80.3 3e-85 1 183 1.0 1 Effector delivery system type VI secretion lipoprotein TssJ prediction
GDMIPMLP_00032 VFG035399 AAI/SCI-II T6SS 84.6 3.2e-176 1 358 1.0 1 Effector delivery system type VI secretion system protein TssA prediction
GDMIPMLP_00033 VFG035394 AAI/SCI-II T6SS 90.9 1.3e-47 1 99 1.0 1 Effector delivery system PAAR domain-containing protein prediction
GDMIPMLP_00034 VFG035389 AAI/SCI-II T6SS 74.5 4.1e-64 1 153 1.0 0.9871 Effector delivery system hypothetical protein prediction
GDMIPMLP_00035 VFG035384 AAI/SCI-II T6SS 78 6.1e-306 7 660 0.9909 0.9909 Effector delivery system type VI secretion system tip protein VgrG prediction
GDMIPMLP_00036 VFG035379 AAI/SCI-II T6SS 83.8 1.6e-158 10 318 0.9656 0.9968 Effector delivery system type VI secretion system baseplate subunit TssG prediction
GDMIPMLP_00037 VFG035374 AAI/SCI-II T6SS 84.7 2.7e-305 1 600 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssF prediction
GDMIPMLP_00038 VFG035369 AAI/SCI-II T6SS 85 1.2e-62 1 140 1.0 1 Effector delivery system hypothetical protein prediction
GDMIPMLP_00040 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
GDMIPMLP_00041 VFG035354 AAI/SCI-II T6SS 89.9 9.8e-77 1 158 1.0 1 Effector delivery system type VI secretion system contractile sheath small subunit prediction
GDMIPMLP_00042 VFG041000 AAI/SCI-II T6SS 71.1 6.3e-72 1 180 1.0 0.9574 Effector delivery system hypothetical protein prediction
GDMIPMLP_00206 VFG002039 Heat-stable toxin (ST) 93.1 1.1e-32 1 72 1.0 1 Exotoxin heat stable enterotoxin I prediction
GDMIPMLP_00211 VFG000842 Hemolysin 94.2 4.6e-96 1 171 1.0 1 Exotoxin Hemolysin C prediction
GDMIPMLP_00212 VFG033890 Hemolysin 95.5 0 1 997 1.0 0.999 Exotoxin Hemolysin A prediction
GDMIPMLP_00213 VFG033882 Hemolysin 97.4 0 1 705 1.0 0.9986 Exotoxin Hemolysin B prediction
GDMIPMLP_00214 VFG000843 Hemolysin 96.2 2e-258 1 479 1.0 1 Exotoxin Hemolysin D prediction
GDMIPMLP_00239 VFG040937 Etp 74.8 8.3e-44 7 121 0.9504 1 Effector delivery system type II secretion system minor pseudopilin GspI prediction
GDMIPMLP_00241 VFG040935 Etp 86.5 4e-69 1 141 0.9792 0.9792 Effector delivery system type II secretion system major pseudopilin GspG prediction
GDMIPMLP_00242 VFG040934 Etp 77.1 4.6e-163 3 409 0.9951 1 Effector delivery system type II secretion system inner membrane protein GspF prediction
GDMIPMLP_00243 VFG040933 Etp 84.1 5.7e-232 1 496 0.998 0.99 Effector delivery system type II secretion system ATPase GspE prediction
GDMIPMLP_00244 VFG040932 Etp 82 4.1e-302 1 654 0.997 0.9985 Effector delivery system variant type II secretion system secretin EtpD prediction
GDMIPMLP_00246 VFG000846 StcE 78.5 0 1 883 0.9977 0.9833 Exoenzyme metalloprotease prediction
GDMIPMLP_00249 VFG034602 Adhesive fimbriae 89.5 5.4e-133 1 257 1.0 1 Adherence fimbrial protein FaeJ prediction
GDMIPMLP_00250 VFG043644 CS31A capsule-like antigen 84.3 2.4e-125 1 254 1.0 1 Adherence CS31A minor subunit prediction
GDMIPMLP_00251 VFG043647 CS31A capsule-like antigen 90.2 2.2e-134 1 265 1.0 0.9962 Adherence fimbrial protein prediction
GDMIPMLP_00252 VFG042560 Adhesive fimbriae 90.6 4.1e-139 1 277 1.0 1 Adherence unknown protein prediction
GDMIPMLP_00253 VFG043645 CS31A capsule-like antigen 90.8 2.1e-74 1 163 1.0 1 Adherence unknown protein prediction
GDMIPMLP_00254 VFG043643 CS31A capsule-like antigen 94.7 6.1e-140 1 263 1.0 1 Adherence unknown protein prediction
GDMIPMLP_00255 VFG042494 Adhesive fimbriae 94.6 0 16 813 0.9815 0.9975 Adherence cshB porin (usher) prediction
GDMIPMLP_00256 VFG042533 CS31A capsule-like antigen 93.7 1.5e-81 28 186 0.8548 0.8833 Adherence ClpC prediction
GDMIPMLP_00280 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
GDMIPMLP_00173 PHI:10997 fdnG 70.3 0 1 1016 1.0000 1.0000 rodents infection formate dehydrogenase, nitrate-inducible, major subunit unaffected pathogenicity
GDMIPMLP_00194 PHI:11267 vrpB (STM2180) 89 3.7e-152 1 299 0.9708 0.9901 rodents infection putative LysR family transcriptional regulator reduced virulence
GDMIPMLP_00216 PHI:6737 L7052 86.1 1.4e-32 1 79 0.9186 0.8404 nematodes urinary tract infection transcriptional regulator 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
GDMIPMLP_00183 ANP05420.1|GT4 100 4.59e-289 1 389 1 1
GDMIPMLP_00184 ANP05419.1|GT4 100 2.33e-300 1 411 1 1
GDMIPMLP_00185 ANP16064.1|GT1 99.7 5.83e-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
GDMIPMLP_00087 2.A.14.1.1 97.8 4.1e-303 1 551 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.14 The Lactate Permease (LctP) Family
GDMIPMLP_00109 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
GDMIPMLP_00173 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
GDMIPMLP_00179 1.B.13.1.6 99.5 2.6e-223 59 439 0.8679 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.13 The Alginate Export Porin (AEP) Family
GDMIPMLP_00212 1.C.11.1.6 95.8 0 1 997 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.11 The Pore-forming RTX Toxin (RTX-toxin) Family
GDMIPMLP_00213 3.A.1.109.1 73 1.6e-299 10 705 0.9872 0.9844 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
GDMIPMLP_00243 3.A.15.1.1 73.2 6.6e-199 10 494 0.9759 2.1272 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.15 The Outer Membrane Protein Secreting Main Terminal Branch (MTB) Family
GDMIPMLP_00244 1.B.22.1.1 73.8 1.3e-263 10 650 0.9771 0.9742 1 Channels/Pores 1.B β-Barrel Porins 1.B.22 The Outer Bacterial Membrane Secretin (Secretin) Family
GDMIPMLP_00255 1.B.11.1.1 94.6 0 15 813 0.9828 0.9840 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family