Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C588
  Reference Plasmid   NZ_CP035221.1
  Reference Plasmid Size   239262
  Reference Plasmid GC Content   0.35
  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
M0168968 MCPINKCL_00008 9781 4 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -4770C>T None
M0168969 MCPINKCL_00008 9809 4 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -4798C>T None
M0168970 MCPINKCL_00015 9823 4 Gut 0.33 protein_coding missense_variant MODERATE 953A>G Glu318Gly
M0168971 MCPINKCL_00015 9969 4 Gut 0.33 protein_coding synonymous_variant LOW 807C>T Phe269Phe
M0168972 MCPINKCL_00015 10145 4 Gut 0.33 protein_coding missense_variant MODERATE 631G>A Asp211Asn
M0168973 MCPINKCL_00017 14204 4 Gut 0.33 protein_coding missense_variant MODERATE 1804A>G Thr602Ala
M0168974 MCPINKCL_00015 14370 4 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -3595A>C None
M0168975 MCPINKCL_00020 16749 4 Gut 0.33 protein_coding synonymous_variant LOW 351T>C Asp117Asp
M0168976 MCPINKCL_00019 17254 4 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -1312G>A None
M0168977 MCPINKCL_00019 17312 4 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -1370T>A None
M0168978 MCPINKCL_00163 150134 3 Gut 0.25 protein_coding missense_variant MODERATE 34T>C Phe12Leu
M0168979 MCPINKCL_00164 150415 3 Gut 0.25 protein_coding missense_variant MODERATE 337C>G Pro113Ala






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
MCPINKCL_00024 VFG042998 Bee (biofilm enhancer in enterococci) 98.4 8.2e-207 1 373 1.0 1 Adherence Srt2 prediction
MCPINKCL_00025 VFG042997 Bee (biofilm enhancer in enterococci) 98.7 3.9e-223 1 398 1.0 1 Adherence Srt1 prediction
MCPINKCL_00026 VFG042996 Bee (biofilm enhancer in enterococci) 98 1.4e-275 1 495 1.0 1 Adherence Bee3 prediction
MCPINKCL_00027 VFG042995 Bee (biofilm enhancer in enterococci) 98.8 5.1e-133 1 243 1.0 1 Adherence Bee2 prediction
MCPINKCL_00097 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 98.7 6.7e-124 1 223 1.0 1 Adherence putative housekeeping sortase prediction
MCPINKCL_00098 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 96.6 4.2e-305 1 537 0.9908 0.8161 Adherence PilA 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
MCPINKCL_00004 PHI:5205 HMPREF0351_10118 (WxL locusC) 83.7 6.6e-67 1 141 0.9792 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
MCPINKCL_00021 PHI:5205 HMPREF0351_10118 (WxL locusC) 71.5 2.3e-167 1 389 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
MCPINKCL_00170 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
MCPINKCL_00179 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
MCPINKCL_00191 PHI:5205 HMPREF0351_10118 (WxL locusC) 74.5 3.8e-173 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
MCPINKCL_00208 PHI:5205 HMPREF0351_10118 (WxL locusC) 74.5 2.9e-173 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
MCPINKCL_00241 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






        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
MCPINKCL_00016 ATU29695.1|GH32 100 0 1 479 1 1
MCPINKCL_00083 QAT24339.1|GH36 100 0 1 749 1 1
MCPINKCL_00120 QAT24372.1|GH73 100 2.49e-274 1 401 1 1
MCPINKCL_00198 QAT24442.1|GH70 100 0 1 1746 1 1
MCPINKCL_00226 AOM14759.1|GH13_18 100 0 1 486 1 1
MCPINKCL_00227 QQJ93880.1|GH13_31 100 1.79e-306 1 406 1 1
MCPINKCL_00228 QAA21152.1|GH36 100 0 1 727 1 1
MCPINKCL_00232 AWV59846.1|GH4 100 0 1 436 1 1
MCPINKCL_00251 ATU29695.1|GH32 100 0 1 479 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
MCPINKCL_00153 9.A.59.1.1 72.1 1.3e-15 1 43 1.0000 0.9773 9 Incompletely Characterized Transport Systems 9.A Recognized transporters of unknown biochemical mechanism 9.A.59 The Bacteriocin: Enterocin/Pediocin (BEP) Family
MCPINKCL_00154 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
MCPINKCL_00160 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
MCPINKCL_00161 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
MCPINKCL_00162 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
MCPINKCL_00229 3.A.1.1.28 74.9 1.2e-117 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
MCPINKCL_00230 3.A.1.1.28 74.5 1.3e-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