Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C777
  Reference Plasmid   NZ_CP060942.1
  Reference Plasmid Size   21115
  Reference Plasmid GC Content   0.51
  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
M0177477 ELIPBAAC_00005 3961 4 Gut 0.06 protein_coding missense_variant MODERATE 252C>G Ile84Met
M0177478 ELIPBAAC_00004 4890 5 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -1413G>T None
M0177479 ELIPBAAC_00008 6720 13 Gut 0.21 protein_coding missense_variant MODERATE 934A>G Ser312Gly
M0177480 ELIPBAAC_00009 7780 30 Gut 0.48 protein_coding missense_variant MODERATE 901A>C Ser301Arg
M0177481 ELIPBAAC_00010 8159 30 Gut 0.48 protein_coding missense_variant MODERATE 265A>G Ile89Val
M0177482 ELIPBAAC_00010 8160 13 Gut 0.21 protein_coding missense_variant MODERATE 266T>C Ile89Thr
M0177483 ELIPBAAC_00010 8659 5 Gut 0.08 protein_coding synonymous_variant LOW 765A>C Leu255Leu
M0177484 ELIPBAAC_00010 8718 5 Gut 0.08 protein_coding missense_variant MODERATE 824C>T Thr275Met
M0177485 ELIPBAAC_00012 11482 24 Gut 0.39 protein_coding missense_variant MODERATE 1170G>T Lys390Asn
M0177486 ELIPBAAC_00009 7730 8 Gut 0.13 protein_coding missense_variant MODERATE 851A>G Glu284Gly
M0177487 ELIPBAAC_00014 13494 4 Gut 0.06 protein_coding missense_variant MODERATE 1122A>C Lys374Asn
M0177488 ELIPBAAC_00014 13605 4 Gut 0.06 protein_coding synonymous_variant LOW 1233T>C Thr411Thr
M0177489 ELIPBAAC_00012 10220 3 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -93A>C None
M0177490 ELIPBAAC_00012 11971 3 Gut 0.05 protein_coding synonymous_variant LOW 1659T>C Pro553Pro
M0177491 ELIPBAAC_00011 9918 4 Gut 0.06 protein_coding missense_variant MODERATE 899T>C Phe300Ser
M0177492 ELIPBAAC_00009 6932 4 Gut 0.06 protein_coding missense_variant MODERATE 53T>G Phe18Cys
M0177493 ELIPBAAC_00005 8930 3 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -4718A>G None
M0177494 ELIPBAAC_00011 9868 3 Gut 0.05 protein_coding synonymous_variant LOW 849T>C Asp283Asp
M0177495 ELIPBAAC_00010 8013 3 Gut 0.05 protein_coding missense_variant MODERATE 119C>T Ser40Leu






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
ELIPBAAC_00009 VFG020186 VirK 98.1 1e-186 1 316 1.0 1 Others virulence factor VirK prediction
ELIPBAAC_00010 VFG013087 MsbB2 97.1 1.2e-182 1 314 1.0 1 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase 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
ELIPBAAC_00002 Nickel (Ni), Cobalt (Co) 99.7 4e-174 1 318 1.0000 1.0000 experiment
ELIPBAAC_00003 Nickel (Ni), Cobalt (Co) 100 3.7e-146 1 255 1.0000 1.0000 experiment
ELIPBAAC_00002 Nickel (Ni), Cobalt (Co) 100 2.4e-172 1 318 1.0000 0.9695 prediction
ELIPBAAC_00003 Nickel (Ni), Cobalt (Co) 100 8.5e-144 1 255 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






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
ELIPBAAC_00001 PHI:8008 fecC 99.6 5.9e-149 1 277 1.0000 0.8343 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport system permease protein reduced virulence
ELIPBAAC_00002 PHI:8009 fecD 99.7 6.7e-173 1 318 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport system permease protein reduced virulence
ELIPBAAC_00003 PHI:8010 fecE 100 6.2e-145 1 255 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport ATP-binding protein reduced virulence
ELIPBAAC_00008 PHI:10400 Sfgtr4 (ORF186) 95.6 2.8e-207 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) reduced virulence
ELIPBAAC_00018 PHI:8004 fecI 100 1.3e-93 1 173 1.0000 1.0000 even-toed ungulates bovine mastitis RNA polymerase sigma factor reduced virulence
ELIPBAAC_00019 PHI:8005 fecR 99.7 1.9e-180 1 317 1.0000 1.0000 even-toed ungulates bovine mastitis Fec operon regulator reduced virulence
ELIPBAAC_00020 PHI:8006 fecA 99.5 0 1 774 1.0000 1.0000 even-toed ungulates bovine mastitis ferric citrate outer membrane transporter reduced virulence
ELIPBAAC_00021 PHI:8007 fecB 99 1.6e-163 1 300 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate-binding periplasmic protein 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
ELIPBAAC_00008 ARW86296.1|GT4 100 2.19e-271 1 362 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
ELIPBAAC_00001 3.A.1.14.1 99.6 1.3e-148 1 277 1.0000 1.0863 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
ELIPBAAC_00002 3.A.1.14.1 99.7 1.5e-172 1 318 1.0000 1.2471 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
ELIPBAAC_00003 3.A.1.14.1 100 1.4e-144 1 255 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
ELIPBAAC_00020 1.B.14.1.20 99.5 0 1 774 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
ELIPBAAC_00021 3.A.1.14.1 99 3.5e-163 1 300 1.0000 1.1765 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily