Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C943
  Reference Plasmid   NZ_CP082800.1
  Reference Plasmid Size   427807
  Reference Plasmid GC Content   0.52
  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
M0189447 NDGHDONL_00161 139290 3 Gut 0.75 protein_coding missense_variant MODERATE 371A>G Gln124Arg






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
NDGHDONL_00159 VFG048348 Type 3 fimbriae 99.2 2e-138 1 238 1.0 1 Biofilm phosphodiesterase experiment
NDGHDONL_00160 VFG043623 Type 3 fimbriae 99.5 2.5e-124 1 211 1.0 1 Biofilm type 3 fimbrial minor pilin subunit MrkF experiment
NDGHDONL_00161 VFG043624 Type 3 fimbriae 99.1 9.7e-184 1 331 1.0 1 Biofilm fimbrial adhesin protein precursor MrkD experiment
NDGHDONL_00162 VFG043625 Type 3 fimbriae 100 0 1 828 1.0 1 Biofilm fimbrial biogenesis outer membrane usher protein mrkC precursor experiment
NDGHDONL_00163 VFG043626 Type 3 fimbriae 100 8.2e-129 1 233 1.0 1 Biofilm fimbrial chaperone protein mrkB precursor experiment
NDGHDONL_00164 VFG043627 Type 3 fimbriae 100 4.1e-108 1 202 1.0 1 Biofilm type 3 fimbrial major pilin subunit MrkA experiment
NDGHDONL_00204 VFG048348 Type 3 fimbriae 100 8.1e-140 1 238 1.0 1 Biofilm phosphodiesterase experiment
NDGHDONL_00205 VFG043623 Type 3 fimbriae 99.5 2.5e-124 1 211 1.0 1 Biofilm type 3 fimbrial minor pilin subunit MrkF experiment
NDGHDONL_00206 VFG043624 Type 3 fimbriae 98.8 1.3e-183 1 331 1.0 1 Biofilm fimbrial adhesin protein precursor MrkD experiment
NDGHDONL_00207 VFG043625 Type 3 fimbriae 100 0 1 828 1.0 1 Biofilm fimbrial biogenesis outer membrane usher protein mrkC precursor experiment
NDGHDONL_00208 VFG043626 Type 3 fimbriae 100 8.2e-129 1 233 1.0 1 Biofilm fimbrial chaperone protein mrkB precursor experiment
NDGHDONL_00209 VFG043627 Type 3 fimbriae 100 4.1e-108 1 202 1.0 1 Biofilm type 3 fimbrial major pilin subunit MrkA experiment
NDGHDONL_00286 VFG000417 Pla 81.7 2.7e-151 1 311 1.0 0.9968 Exoenzyme plasminogen activator protease precursor experiment
NDGHDONL_00159 VFG048344 Type 3 fimbriae 99.6 1.1e-137 1 238 1.0 1 Biofilm phosphodiesterase prediction
NDGHDONL_00160 VFG043623 Type 3 fimbriae 99.5 1.9e-123 1 211 1.0 1 Biofilm type 3 fimbrial minor pilin subunit MrkF prediction
NDGHDONL_00161 VFG043624 Type 3 fimbriae 99.1 7.3e-183 1 331 1.0 1 Biofilm fimbrial adhesin protein precursor MrkD prediction
NDGHDONL_00162 VFG043625 Type 3 fimbriae 100 0 1 828 1.0 1 Biofilm fimbrial biogenesis outer membrane usher protein mrkC precursor prediction
NDGHDONL_00163 VFG048385 Type 3 fimbriae 100 6.2e-128 1 233 1.0 0.9668 Biofilm fimbrial chaperone protein mrkB precursor prediction
NDGHDONL_00164 VFG043627 Type 3 fimbriae 100 3e-107 1 202 1.0 1 Biofilm type 3 fimbrial major pilin subunit MrkA prediction
NDGHDONL_00204 VFG048348 Type 3 fimbriae 100 6.1e-139 1 238 1.0 1 Biofilm phosphodiesterase prediction
NDGHDONL_00205 VFG043623 Type 3 fimbriae 99.5 1.9e-123 1 211 1.0 1 Biofilm type 3 fimbrial minor pilin subunit MrkF prediction
NDGHDONL_00206 VFG043624 Type 3 fimbriae 98.8 9.5e-183 1 331 1.0 1 Biofilm fimbrial adhesin protein precursor MrkD prediction
NDGHDONL_00207 VFG043625 Type 3 fimbriae 100 0 1 828 1.0 1 Biofilm fimbrial biogenesis outer membrane usher protein mrkC precursor prediction
NDGHDONL_00208 VFG048385 Type 3 fimbriae 100 6.2e-128 1 233 1.0 0.9668 Biofilm fimbrial chaperone protein mrkB precursor prediction
NDGHDONL_00209 VFG043627 Type 3 fimbriae 100 3e-107 1 202 1.0 1 Biofilm type 3 fimbrial major pilin subunit MrkA prediction
NDGHDONL_00286 VFG003087 Pla 82.1 5.3e-151 1 311 1.0 0.9968 Exoenzyme plasminogen activator protease precursor 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
NDGHDONL_00043 Arsenic (As), Antimony (Sb), Bismuth (Bi) 100 8.1e-64 1 117 1.0000 1.0000 experiment
NDGHDONL_00044 Arsenic (As), Antimony (Sb) 98.3 1.6e-67 1 120 1.0000 1.0000 experiment
NDGHDONL_00045 Arsenic (As), Antimony (Sb) 99.1 0 1 583 1.0000 1.0000 experiment
NDGHDONL_00046 Arsenic (As), Antimony (Sb) 99.3 1.7e-231 1 429 1.0000 1.0000 experiment
NDGHDONL_00047 Arsenic (As), Antimony (Sb) 99.3 3.5e-77 1 141 1.0000 1.0000 experiment
NDGHDONL_00197 Arsenic (As), Antimony (Sb) 85 1.9e-67 1 140 0.9859 0.9929 experiment
NDGHDONL_00198 Arsenic (As), Antimony (Sb) 87.6 1.1e-206 1 429 1.0000 1.0000 experiment
NDGHDONL_00199 Arsenic (As), Antimony (Sb) 71.5 1.9e-241 12 593 0.9716 0.9983 experiment
NDGHDONL_00321 Tellurium (Te) 81.9 6.2e-93 1 193 0.9948 1.0000 experiment
NDGHDONL_00322 Tellurium (Te) 98.5 1.2e-196 45 383 0.8851 1.0000 experiment
NDGHDONL_00323 Tellurium (Te) 100 5.7e-62 1 118 0.7815 0.9672 experiment
NDGHDONL_00324 Tellurium (Te) 99.1 3.9e-191 1 346 1.0000 1.0000 experiment
NDGHDONL_00325 Tellurium (Te) 98.4 2.4e-105 1 192 1.0000 1.0000 experiment
NDGHDONL_00326 Tellurium (Te) 99 1.1e-105 1 191 1.0000 1.0000 experiment
NDGHDONL_00043 Arsenic (As) 100 1.9e-61 1 117 1.0000 1.0000 prediction
NDGHDONL_00044 Arsenic (As) 100 4.4e-66 1 120 1.0000 1.0000 prediction
NDGHDONL_00045 Arsenic (As), Antimony (Sb) 100 0 1 583 1.0000 1.0000 prediction
NDGHDONL_00046 Arsenic (As), Antimony (Sb) 99.5 4.5e-230 1 428 0.9977 1.0000 prediction
NDGHDONL_00047 Arsenic (As) 100 1.6e-75 1 141 1.0000 1.0000 prediction
NDGHDONL_00197 Arsenic (As) 85.7 1.4e-66 1 140 0.9859 0.9790 prediction
NDGHDONL_00198 Arsenic (As), Antimony (Sb) 88.3 7.7e-206 1 429 1.0000 1.0000 prediction
NDGHDONL_00199 Arsenic (As), Antimony (Sb) 72.5 2.9e-243 12 593 0.9716 0.9983 prediction
NDGHDONL_00202 Arsenic (As) 74.4 3.5e-44 1 117 1.0000 1.0354 prediction
NDGHDONL_00321 Tellurium (Te) 86 7.2e-95 1 193 0.9948 1.0000 prediction
NDGHDONL_00322 Tellurium (Te) 100 4.7e-223 1 383 1.0000 1.0000 prediction
NDGHDONL_00323 Tellurium (Te) 100 7.4e-79 1 151 1.0000 0.9869 prediction
NDGHDONL_00324 Tellurium (Te) 99.4 1.6e-190 1 346 1.0000 1.0000 prediction
NDGHDONL_00325 Tellurium (Te) 100 4.5e-105 1 192 1.0000 1.0000 prediction
NDGHDONL_00326 Tellurium (Te) 100 3.8e-104 1 191 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
NDGHDONL_00023 PHI:6268 lacZ 96.9 0 1 1024 1.0000 1.0000 rodents urinary tract infection beta-galactosidase reduced virulence
NDGHDONL_00027 PHI:10119 STM14_RS07800 (orf319) 79.9 2.9e-155 1 318 0.9969 0.9969 eudicots infection DUF523 and DUF1722 domain-containing protein reduced virulence
NDGHDONL_00164 PHI:6099 MrkA 99.5 5.3e-107 1 202 1.0000 1.0000 rodents pneumonia ferrous iron transporter unaffected pathogenicity
NDGHDONL_00170 PHI:3531 pld1 78.5 2.2e-18 1 56 1.0000 1.0000 rodents urinary tract infection; nosocomial pneumonia; abdominal infection lipid metabolism loss of pathogenicity
NDGHDONL_00209 PHI:6099 MrkA 99.5 5.3e-107 1 202 1.0000 1.0000 rodents pneumonia ferrous iron transporter unaffected pathogenicity
NDGHDONL_00224 PHI:10051 glgA 73.7 8.2e-215 1 476 0.9979 0.9979 rodents salmonellosis glycogen synthase reduced virulence
NDGHDONL_00296 PHI:6268 lacZ 95.9 0 1 1019 1.0000 1.0000 rodents urinary tract infection beta-galactosidase reduced virulence
NDGHDONL_00435 PHI:10119 STM14_RS07800 (orf319) 80.2 9.8e-156 1 318 0.9969 0.9969 eudicots infection DUF523 and DUF1722 domain-containing protein reduced virulence
NDGHDONL_00439 PHI:6268 lacZ 96.9 0 1 1024 1.0000 1.0000 rodents urinary tract infection beta-galactosidase 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
NDGHDONL_00023 APM29325.1|GH2 100 0 1 1024 1 1
NDGHDONL_00096 QPG02256.1|GH23 100 9.39e-116 1 161 1 1
NDGHDONL_00223 ANK24771.1|GT35 100 0 1 815 1 1
NDGHDONL_00224 ATR18460.1|GT5 100 0 1 477 1 1
NDGHDONL_00226 VDZ68364.1|GH13_11 85.5 1.58e-266 4 425 0.9883 0.7226
NDGHDONL_00227 BBS34816.1|CBM48|GH13_9 100 0 1 730 1 1
NDGHDONL_00296 QIV07698.1|GH2 99.5 0 1 1019 1 1
NDGHDONL_00439 APM29325.1|GH2 100 0 1 1024 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
NDGHDONL_00024 2.A.1.5.1 98.8 4.6e-230 1 417 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
NDGHDONL_00045 3.A.4.1.1 85.7 5e-283 1 581 0.9966 1.3543 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
NDGHDONL_00046 3.A.4.1.1 93.7 1.3e-219 1 429 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
NDGHDONL_00162 1.B.11.3.2 87.7 0 1 828 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family
NDGHDONL_00198 3.A.4.1.1 86.2 2.2e-203 1 429 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
NDGHDONL_00199 3.A.4.1.1 71.5 7.1e-240 12 593 0.9716 1.3543 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
NDGHDONL_00207 1.B.11.3.2 87.7 0 1 828 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family
NDGHDONL_00220 2.A.33.1.2 97.1 4e-204 1 382 0.9974 0.9974 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.33 The NhaA Na+:H+ Antiporter (NhaA) Family
NDGHDONL_00286 9.B.50.1.4 82.1 4.2e-151 1 311 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.50 The Outer Membrane Beta-barrel Endoprotease, Omptin (Omptin) Family
NDGHDONL_00297 2.A.1.5.1 98.3 1.9e-228 1 417 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
NDGHDONL_00324 2.A.109.1.1 91.3 3.2e-176 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
NDGHDONL_00438 2.A.1.5.1 98.8 4.6e-230 1 417 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)