Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1248
  Reference Plasmid   NZ_CP143434.1
  Reference Plasmid Size   233036
  Reference Plasmid GC Content   0.36
  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
M0201032 DFBJMECC_00191 170975 3 Gut 0.15 protein_coding synonymous_variant LOW 672G>A Ala224Ala
M0201033 DFBJMECC_00192 172838 3 Gut 0.15 protein_coding synonymous_variant LOW 912G>A Lys304Lys
M0201034 DFBJMECC_00124 113964 3 Gut 0.15 protein_coding missense_variant MODERATE 30A>C Glu10Asp
M0201035 DFBJMECC_00125 114061 3 Gut 0.15 protein_coding missense_variant MODERATE 1374G>T Lys458Asn
M0201036 DFBJMECC_00125 114184 3 Gut 0.15 protein_coding synonymous_variant LOW 1251T>G Thr417Thr
M0201037 DFBJMECC_00125 114187 3 Gut 0.15 protein_coding synonymous_variant LOW 1248A>T Gly416Gly
M0201038 DFBJMECC_00125 114193 3 Gut 0.15 protein_coding synonymous_variant LOW 1242T>C Asp414Asp
M0201039 DFBJMECC_00125 114196 3 Gut 0.15 protein_coding synonymous_variant LOW 1239C>T Thr413Thr
M0201040 DFBJMECC_00125 114199 3 Gut 0.15 protein_coding synonymous_variant LOW 1236A>C Ala412Ala
M0201041 DFBJMECC_00125 114211 3 Gut 0.15 protein_coding synonymous_variant LOW 1224T>C Gly408Gly
M0201042 DFBJMECC_00126 116449 3 Gut 0.15 protein_coding missense_variant MODERATE 831T>G Phe277Leu






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
DFBJMECC_00007 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 98.2 2e-123 1 223 1.0 1 Adherence putative housekeeping sortase prediction
DFBJMECC_00008 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 99.5 0 1 658 1.0 1 Adherence PilA prediction
DFBJMECC_00009 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 98.8 3.2e-138 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
DFBJMECC_00010 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 100 2.4e-133 1 251 1.0 1 Adherence cell wall-associated LPXTG-like protein prediction
DFBJMECC_00011 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 97.7 1.4e-37 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
DFBJMECC_00012 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.3 0 1 696 1.0 1 Adherence minor pilin subunit 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
DFBJMECC_00029 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 1e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DFBJMECC_00060 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 1e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DFBJMECC_00076 PHI:5205 HMPREF0351_10118 (WxL locusC) 89.6 4.4e-206 1 394 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DFBJMECC_00084 PHI:5205 HMPREF0351_10118 (WxL locusC) 71.3 2.8e-165 1 389 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DFBJMECC_00115 PHI:5205 HMPREF0351_10118 (WxL locusC) 74.2 8.4e-173 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DFBJMECC_00130 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 1e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DFBJMECC_00146 PHI:5205 HMPREF0351_10118 (WxL locusC) 74.2 2.4e-172 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DFBJMECC_00151 PHI:5205 HMPREF0351_10118 (WxL locusC) 74.2 1.1e-172 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DFBJMECC_00187 PHI:5205 HMPREF0351_10118 (WxL locusC) 79.1 3.6e-184 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence






        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
DFBJMECC_00023 QAR74591.1|GH73 99.5 1.44e-273 1 401 1 1
DFBJMECC_00100 AOM14759.1|GH13_18 100 0 1 486 1 1
DFBJMECC_00101 QQJ93880.1|GH13_31 100 1.79e-306 1 406 1 1
DFBJMECC_00102 QAA21152.1|GH36 100 0 1 727 1 1
DFBJMECC_00106 QEN53531.1|GH4 100 0 1 436 1 1
DFBJMECC_00125 QEN53546.1|GH32 100 0 1 479 1 1
DFBJMECC_00192 QAR74517.1|GH65 100 0 1 764 1 1
DFBJMECC_00254 QAT24339.1|GH36 100 0 1 749 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
DFBJMECC_00059 9.A.59.1.1 100 4.9e-21 1 44 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.A Recognized transporters of unknown biochemical mechanism 9.A.59 The Bacteriocin: Enterocin/Pediocin (BEP) Family
DFBJMECC_00066 3.A.1.122.3 75.8 3.6e-163 3 405 0.9951 1.7797 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DFBJMECC_00067 3.A.1.122.3 92.5 3.1e-119 1 227 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DFBJMECC_00068 3.A.1.122.3 89.2 1.6e-192 1 399 1.0000 1.7577 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DFBJMECC_00103 3.A.1.1.28 75.3 5.4e-118 5 276 0.9855 0.7294 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DFBJMECC_00104 3.A.1.1.28 74.1 2.8e-125 1 290 1.0000 0.7692 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DFBJMECC_00135 3.A.7.14.1 98.5 1e-134 1 262 1.0000 1.4317 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
DFBJMECC_00136 3.A.7.14.1 98.3 2.5e-87 1 175 0.9722 0.9563 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
DFBJMECC_00138 1.C.24.1.10 97.2 5.1e-36 1 71 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.24 The Pediocin (Pediocin) Family