Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1169
  Reference Plasmid   NZ_CP127264.1
  Reference Plasmid Size   115098
  Reference Plasmid GC Content   0.50
  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
M0199126 DEDCFCEF_00052 48779 4 Gut 0.17 protein_coding synonymous_variant LOW 300C>A Val100Val
M0199127 DEDCFCEF_00052 48830 4 Gut 0.17 protein_coding synonymous_variant LOW 249C>A Arg83Arg
M0199128 DEDCFCEF_00052 48842 4 Gut 0.17 protein_coding synonymous_variant LOW 237G>A Ser79Ser
M0199129 DEDCFCEF_00052 48851 4 Gut 0.17 protein_coding missense_variant MODERATE 228A>C Gln76His
M0199130 DEDCFCEF_00046 50112 4 Gut 0.17 protein_coding upstream_gene_variant MODIFIER -4948T>C None
M0199131 DEDCFCEF_00047 50429 3 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -4198T>C None
M0199132 DEDCFCEF_00047 50753 5 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -4522A>C None
M0199133 DEDCFCEF_00047 50759 5 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -4528C>T None
M0199134 DEDCFCEF_00047 50822 3 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -4591A>G None
M0199135 DEDCFCEF_00047 50823 3 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -4592T>C None
M0199136 DEDCFCEF_00050 51998 4 Gut 0.17 protein_coding upstream_gene_variant MODIFIER -4562A>G None
M0199137 DEDCFCEF_00045 43367 3 Gut 0.13 protein_coding synonymous_variant LOW 1347G>A Leu449Leu
M0199138 DEDCFCEF_00045 43457 3 Gut 0.13 protein_coding synonymous_variant LOW 1257A>C Val419Val
M0199139 DEDCFCEF_00045 43910 3 Gut 0.13 protein_coding synonymous_variant LOW 804G>A Ala268Ala
M0199140 DEDCFCEF_00045 43927 3 Gut 0.13 protein_coding synonymous_variant LOW 787A>C Arg263Arg
M0199141 DEDCFCEF_00045 43943 3 Gut 0.13 protein_coding synonymous_variant LOW 771C>T Asp257Asp
M0199142 DEDCFCEF_00045 43958 3 Gut 0.13 protein_coding synonymous_variant LOW 756C>T Val252Val
M0199143 DEDCFCEF_00045 43982 3 Gut 0.13 protein_coding synonymous_variant LOW 732T>A Ala244Ala
M0199144 DEDCFCEF_00045 44051 3 Gut 0.13 protein_coding synonymous_variant LOW 663C>T Ser221Ser
M0199145 DEDCFCEF_00045 44369 4 Gut 0.17 protein_coding synonymous_variant LOW 345G>A Val115Val
M0199146 DEDCFCEF_00052 48916 4 Gut 0.17 protein_coding missense_variant MODERATE 163C>T His55Tyr
M0199147 DEDCFCEF_00050 52208 3 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -4772T>C None
M0199148 DEDCFCEF_00051 48281 3 Gut 0.13 protein_coding missense_variant MODERATE 11C>T Thr4Ile
M0199149 DEDCFCEF_00045 48307 3 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -3594A>T None






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
DEDCFCEF_00061 VFG042382 EtpA 99.8 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB experiment
DEDCFCEF_00061 VFG042382 EtpA 99.8 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB prediction
DEDCFCEF_00081 VFG033834 Pic 99.4 0 1 1364 1.0 0.9985 Effector delivery system Pic serine protease precursor, autotransporter prediction
DEDCFCEF_00084 VFG041000 AAI/SCI-II T6SS 92 4.8e-99 1 188 1.0 1 Effector delivery system hypothetical 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






        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
DEDCFCEF_00039 AHF22950.1|GH23 97.3 4.47e-133 1 186 1 1
DEDCFCEF_00070 ATB16983.1|GT41 100 0 1 636 1 0.9984





        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
DEDCFCEF_00001 3.A.7.10.1 99.2 0 1 763 1.0000 7.9479 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
DEDCFCEF_00002 3.A.7.10.1 96.9 1.2e-202 1 356 1.0000 3.7083 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
DEDCFCEF_00003 3.A.7.10.1 98.3 3.3e-241 1 402 1.0000 4.1875 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
DEDCFCEF_00005 1.E.53.1.10 90.7 4.1e-16 8 50 0.8600 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
DEDCFCEF_00011 9.B.40.1.2 97.6 0 1 745 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.40 The DotA/TraY (DotA/TraY) Family
DEDCFCEF_00025 3.A.7.10.1 99.4 8.8e-184 1 327 1.0000 3.4063 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
DEDCFCEF_00026 3.A.7.10.1 99.6 3.3e-129 1 230 1.0000 2.3958 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
DEDCFCEF_00027 3.A.7.10.1 100 1.3e-57 1 115 1.0000 1.1979 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
DEDCFCEF_00030 3.A.7.10.1 99 4.6e-56 1 96 1.0000 1.0000 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
DEDCFCEF_00031 3.A.7.10.1 98.4 2.8e-218 1 382 1.0000 3.9792 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
DEDCFCEF_00032 3.A.7.10.1 100 5.6e-160 1 272 1.0000 2.8333 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
DEDCFCEF_00033 3.A.7.10.1 99.3 2.3e-86 1 152 1.0000 1.5833 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
DEDCFCEF_00061 1.B.20.3.3 99.8 0 1 603 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.20 The Two-Partner Secretion (TPS) Family
DEDCFCEF_00071 9.B.127.1.3 98.8 1.2e-93 1 164 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.127 The DUF2919 (PF11143) Family