Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C73
  Reference Plasmid   CP027641.1
  Reference Plasmid Size   126957
  Reference Plasmid GC Content   0.48
  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
M0143602 BCLLCMAJ_00031 30182 3 Gut 0.43 protein_coding missense_variant MODERATE 370G>A Ala124Thr
M0143603 BCLLCMAJ_00059 55805 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -179G>A None
M0143604 BCLLCMAJ_00059 56431 3 Gut 0.43 protein_coding missense_variant MODERATE 448T>C Tyr150His
M0143605 BCLLCMAJ_00060 56932 3 Gut 0.43 protein_coding synonymous_variant LOW 432A>T Ser144Ser
M0143606 BCLLCMAJ_00060 57158 3 Gut 0.43 protein_coding missense_variant MODERATE 658G>A Asp220Asn
M0143607 BCLLCMAJ_00060 57335 3 Gut 0.43 protein_coding missense_variant MODERATE 835A>G Thr279Ala
M0143608 BCLLCMAJ_00060 57355 3 Gut 0.43 protein_coding synonymous_variant LOW 855G>A Gly285Gly
M0143609 BCLLCMAJ_00060 57883 3 Gut 0.43 protein_coding synonymous_variant LOW 1383A>C Ile461Ile
M0143610 BCLLCMAJ_00060 57904 3 Gut 0.43 protein_coding missense_variant MODERATE 1404T>G Asp468Glu
M0143611 BCLLCMAJ_00060 58099 3 Gut 0.43 protein_coding synonymous_variant LOW 1599G>A Thr533Thr
M0143612 BCLLCMAJ_00060 58227 3 Gut 0.43 protein_coding missense_variant MODERATE 1727C>T Ala576Val
M0143613 BCLLCMAJ_00060 58438 3 Gut 0.43 protein_coding synonymous_variant LOW 1938G>T Pro646Pro
M0143614 BCLLCMAJ_00060 58739 3 Gut 0.43 protein_coding missense_variant MODERATE 2239G>A Gly747Arg
M0143615 BCLLCMAJ_00060 59143 3 Gut 0.43 protein_coding synonymous_variant LOW 2643G>A Val881Val
M0143616 BCLLCMAJ_00060 59344 3 Gut 0.43 protein_coding missense_variant MODERATE 2844T>G Ile948Met
M0143617 BCLLCMAJ_00060 59467 3 Gut 0.43 protein_coding synonymous_variant LOW 2967C>T His989His
M0143618 BCLLCMAJ_00061 59690 3 Gut 0.43 protein_coding synonymous_variant LOW 144T>A Ala48Ala
M0143619 BCLLCMAJ_00061 59699 3 Gut 0.43 protein_coding synonymous_variant LOW 153T>C Ser51Ser
M0143620 BCLLCMAJ_00061 60150 3 Gut 0.43 protein_coding missense_variant MODERATE 604A>C Ile202Leu
M0143621 BCLLCMAJ_00061 60413 3 Gut 0.43 protein_coding synonymous_variant LOW 867C>T Ser289Ser
M0143622 BCLLCMAJ_00062 62655 3 Gut 0.43 protein_coding missense_variant MODERATE 988C>T Leu330Phe
M0143623 BCLLCMAJ_00065 64902 3 Gut 0.43 protein_coding synonymous_variant LOW 696T>G Gly232Gly
M0143624 BCLLCMAJ_00068 65149 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -1850A>C None
M0143625 BCLLCMAJ_00066 65268 3 Gut 0.43 protein_coding synonymous_variant LOW 207A>G Thr69Thr
M0143626 BCLLCMAJ_00066 65283 3 Gut 0.43 protein_coding synonymous_variant LOW 192A>G Glu64Glu
M0143627 BCLLCMAJ_00066 65298 3 Gut 0.43 protein_coding synonymous_variant LOW 177A>G Lys59Lys






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
BCLLCMAJ_00028 VFG001827 ShET2 99.5 3e-224 1 391 1.0 1 Exotoxin enterotoxin experiment
BCLLCMAJ_00059 VFG000842 Hemolysin 97.7 5e-99 1 171 1.0 1 Exotoxin Hemolysin C experiment
BCLLCMAJ_00060 VFG000840 Hemolysin 98.2 0 1 997 1.0 0.999 Exotoxin Hemolysin A experiment
BCLLCMAJ_00061 VFG000841 Hemolysin 99.6 0 1 705 1.0 0.9986 Exotoxin Hemolysin B experiment
BCLLCMAJ_00062 VFG000843 Hemolysin 99 8.6e-266 1 479 1.0 1 Exotoxin Hemolysin D experiment
BCLLCMAJ_00028 VFG001827 ShET2 99.5 2.2e-223 1 391 1.0 1 Exotoxin enterotoxin prediction
BCLLCMAJ_00032 VFG043983 Colicin S4 86.6 9.7e-248 1 498 1.0 0.998 Exotoxin colicin S4 prediction
BCLLCMAJ_00059 VFG000842 Hemolysin 97.7 3.7e-98 1 171 1.0 1 Exotoxin Hemolysin C prediction
BCLLCMAJ_00060 VFG033890 Hemolysin 98.3 0 1 997 1.0 0.999 Exotoxin Hemolysin A prediction
BCLLCMAJ_00061 VFG033882 Hemolysin 99.7 0 1 705 1.0 0.9986 Exotoxin Hemolysin B prediction
BCLLCMAJ_00062 VFG000843 Hemolysin 99 6.5e-265 1 479 1.0 1 Exotoxin Hemolysin D 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
BCLLCMAJ_00025 PHI:10792 cjrA 98.3 4e-164 1 291 1.0000 1.0000 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
BCLLCMAJ_00026 PHI:10793 cjrB 98.4 9.1e-136 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
BCLLCMAJ_00027 PHI:10794 cjrC 98.7 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
BCLLCMAJ_00028 PHI:10795 senB 99.2 2.3e-223 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
BCLLCMAJ_00064 PHI:6737 L7052 80.6 3.9e-36 1 93 0.7623 0.9894 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
BCLLCMAJ_00112 BBF51488.1|GH23 97.6 2.65e-119 1 169 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
BCLLCMAJ_00017 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
BCLLCMAJ_00026 2.C.1.1.3 98.4 2e-135 1 258 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.C Ion-gradient-driven energizers 2.C.1 The TonB-ExbB-ExbD/TolA-TolQ-TolR Outer Membrane Receptor Energizers and Stabilizers (TonB/TolA) Family
BCLLCMAJ_00027 1.B.14.7.1 98.7 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
BCLLCMAJ_00032 1.C.1.3.4 86.6 7.7e-248 1 498 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
BCLLCMAJ_00040 2.A.8.1.9 71.5 4.3e-151 1 418 0.9905 0.9952 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.8 The Gluconate:H+ Symporter (GntP) Family
BCLLCMAJ_00060 1.C.11.1.6 98.4 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
BCLLCMAJ_00061 3.A.1.109.1 73.4 2e-302 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
BCLLCMAJ_00080 2.A.8.1.9 71.5 4.3e-151 1 418 0.9905 0.9952 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.8 The Gluconate:H+ Symporter (GntP) Family