Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1231
  Reference Plasmid   NZ_CP138780.1
  Reference Plasmid Size   307717
  Reference Plasmid GC Content   0.47
  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
M0200512 GBHOFCCG_00110 93865 3 Gut 0.60 protein_coding missense_variant MODERATE 117G>C Met39Ile
M0200513 GBHOFCCG_00107 93989 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -2777A>G None
M0200514 GBHOFCCG_00111 94253 3 Gut 0.60 protein_coding synonymous_variant LOW 213G>A Thr71Thr
M0200515 GBHOFCCG_00107 95102 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -3890C>G None
M0200516 GBHOFCCG_00112 95450 3 Gut 0.60 protein_coding synonymous_variant LOW 276T>C Ser92Ser
M0200517 GBHOFCCG_00113 97317 3 Gut 0.60 protein_coding synonymous_variant LOW 1044G>A Leu348Leu






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







        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
GBHOFCCG_00140 Tellurium (Te) 99.5 6.3e-106 1 191 1.0000 1.0000 experiment
GBHOFCCG_00141 Tellurium (Te) 99 6.3e-106 1 192 1.0000 1.0000 experiment
GBHOFCCG_00142 Tellurium (Te) 99.1 8.8e-191 1 346 1.0000 1.0000 experiment
GBHOFCCG_00143 Tellurium (Te) 100 5.7e-62 1 118 0.7815 0.9672 experiment
GBHOFCCG_00144 Tellurium (Te) 98.8 6.9e-197 45 383 0.8851 1.0000 experiment
GBHOFCCG_00145 Tellurium (Te) 81.9 4.7e-93 1 193 0.9948 1.0000 experiment
GBHOFCCG_00174 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)] 93.6 4.2e-54 1 110 1.0000 1.0000 experiment
GBHOFCCG_00197 Cobalt (Co), Nickel (Ni) 72.4 2.3e-173 14 467 0.9560 0.9520 experiment
GBHOFCCG_00197 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 72.4 2.3e-173 14 467 0.9560 0.9520 experiment
GBHOFCCG_00198 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 76.1 0 1 1032 0.9981 0.9990 experiment
GBHOFCCG_00140 Tellurium (Te) 100 4.9e-104 1 191 1.0000 1.0000 prediction
GBHOFCCG_00141 Tellurium (Te) 100 4.5e-105 1 192 1.0000 1.0000 prediction
GBHOFCCG_00142 Tellurium (Te) 100 1.3e-190 1 346 1.0000 1.0000 prediction
GBHOFCCG_00143 Tellurium (Te) 100 7.4e-79 1 151 1.0000 0.9869 prediction
GBHOFCCG_00144 Tellurium (Te) 100 4.7e-223 1 383 1.0000 1.0000 prediction
GBHOFCCG_00145 Tellurium (Te) 86 5.5e-95 1 193 0.9948 1.0000 prediction
GBHOFCCG_00174 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)] 100 1.7e-53 1 110 1.0000 1.0000 prediction
GBHOFCCG_00197 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 100 5.8e-255 1 477 1.0000 1.0000 prediction
GBHOFCCG_00198 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 98.2 0 1 1044 1.0000 1.0000 prediction
GBHOFCCG_00199 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 97.7 2.9e-204 1 387 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
GBHOFCCG_00173 ARO:3002602 100 5.68e-187 1 259 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
GBHOFCCG_00174 ARO:3005098 93.6 1.69e-70 1 110 1.0000 1.0000 disinfecting agents and antiseptics small multidrug resistance (SMR) antibiotic efflux pump antibiotic efflux
GBHOFCCG_00176 ARO:3000413 100 3.83e-187 1 263 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
GBHOFCCG_00182 ARO:3002539 100 8.8e-195 1 258 1.0000 1.0000 aminoglycoside antibiotic AAC(3) antibiotic inactivation
GBHOFCCG_00184 ARO:3002655 100 1.82e-256 1 341 1.0000 1.0000 aminoglycoside antibiotic APH(4) antibiotic inactivation
GBHOFCCG_00193 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
GBHOFCCG_00194 ARO:3002639 99.3 2.44e-201 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
GBHOFCCG_00197 ARO:3000802 72.8 3.75e-211 19 465 0.9413 0.9374 macrolide antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
GBHOFCCG_00198 ARO:3000801 76 0 1 1032 0.9981 0.9990 macrolide antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
GBHOFCCG_00204 ARO:3002641 100 4.76e-210 1 271 1.0000 1.0000 aminoglycoside antibiotic APH(3') antibiotic inactivation
GBHOFCCG_00209 ARO:3003741 100 1.87e-214 1 294 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
GBHOFCCG_00210 ARO:3003109 100 0 1 491 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
GBHOFCCG_00213 ARO:3000858 100 4.87e-187 1 257 1.0000 1.0000 aminoglycoside antibiotic 16S rRNA methyltransferase (G1405) antibiotic target alteration
GBHOFCCG_00217 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
GBHOFCCG_00220 ARO:3002132 100 3.97e-277 1 379 1.0000 1.0000 cephalosporin DHA beta-lactamase antibiotic inactivation
GBHOFCCG_00227 ARO:3002737 92.6 5.96e-110 1 215 1.0000 1.0000 fluoroquinolone antibiotic quinolone resistance protein (qnr) antibiotic target protection
GBHOFCCG_00234 ARO:3002639 99.3 2.07e-200 63 329 0.8116 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
GBHOFCCG_00235 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation






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
GBHOFCCG_00170 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
GBHOFCCG_00219 PHI:10922 ampR 100 4.9e-170 1 291 1.0000 1.0000 rodents pneumonia regulator of the LysR family reduced virulence
GBHOFCCG_00222 PHI:7660 pspD 84.5 8.3e-29 1 71 0.9342 0.9861 rodents salmonellosis phage-shock protein reduced virulence
GBHOFCCG_00223 PHI:7659 pspC 86.6 7.6e-53 1 119 1.0000 1.0000 rodents salmonellosis phage-shock protein reduced virulence
GBHOFCCG_00224 PHI:7658 pspB 89.2 6e-32 1 74 1.0000 1.0000 rodents salmonellosis phage-shock protein reduced virulence
GBHOFCCG_00225 PHI:7657 pspA 94.6 1e-103 1 222 1.0000 1.0000 rodents salmonellosis phage-shock 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
GBHOFCCG_00086 APD70732.1|GH23 100 7.62e-152 1 204 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
GBHOFCCG_00142 2.A.109.1.1 90.8 1.2e-175 1 346 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.109 The Tellurium Ion Resistance (TerC) Family
GBHOFCCG_00197 2.A.6.2.15 72.4 8.6e-172 14 467 0.9518 1.1692 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
GBHOFCCG_00198 2.A.6.2.15 76.1 0 1 1032 0.9885 2.6462 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
GBHOFCCG_00199 2.A.6.2.15 86.9 3.1e-180 1 387 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
GBHOFCCG_00225 9.B.100.1.1 94.6 2.3e-103 1 222 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.100 The Phage Shock Protein (Psp) Family