Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1386
  Reference Plasmid   NZ_MT151380.1
  Reference Plasmid Size   159889
  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
M0208800 GKCHAHMN_00004 3288 4 Gut 1.00 protein_coding missense_variant MODERATE 418C>T Arg140Cys
M0208801 GKCHAHMN_00022 13447 4 Gut 1.00 protein_coding synonymous_variant LOW 159C>T His53His
M0208802 GKCHAHMN_00113 84667 4 Gut 1.00 protein_coding missense_variant MODERATE 302T>C Phe101Ser
M0208803 GKCHAHMN_00124 102306 4 Gut 1.00 protein_coding missense_variant MODERATE 2747C>T Ala916Val
M0208804 GKCHAHMN_00138 114050 4 Gut 1.00 protein_coding missense_variant MODERATE 52C>T His18Tyr
M0208805 GKCHAHMN_00170 137856 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -143T>G None
M0208806 GKCHAHMN_00172 139724 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -189G>A 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







        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
GKCHAHMN_00054 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Pyronin Y [class: Xanthene], Rhodamine 6G [class: Xanthene], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Acridine Orange [class: Acridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Sodium Deoxycholate (SDC) [class: Acid], Crystal Violet [class: Triarylmethane], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)] 100 1.1e-60 1 115 1.0000 1.0000 experiment






        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
GKCHAHMN_00038 ARO:3004621 99 6.49e-211 1 286 1.0000 1.0000 aminoglycoside antibiotic AAC(3) antibiotic inactivation
GKCHAHMN_00041 ARO:3001396 100 6.06e-199 16 291 0.9485 1.0000 cephalosporin OXA beta-lactamase antibiotic inactivation
GKCHAHMN_00042 ARO:3002581 98 1.4e-140 2 199 0.9950 0.9754 aminoglycoside antibiotic AAC(6') antibiotic inactivation
GKCHAHMN_00046 ARO:3001878 100 1.15e-202 1 291 1.0000 1.0000 cephalosporin CTX-M beta-lactamase antibiotic inactivation
GKCHAHMN_00050 ARO:3002847 100 4.06e-115 1 150 1.0000 1.0000 rifamycin antibiotic rifampin ADP-ribosyltransferase (Arr) antibiotic inactivation
GKCHAHMN_00051 ARO:3002695 100 1.06e-299 1 419 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
GKCHAHMN_00052 ARO:3001405 100 2.23e-192 1 266 1.0000 1.0000 cephalosporin OXA beta-lactamase antibiotic inactivation
GKCHAHMN_00053 ARO:3002601 99.2 4.73e-188 10 272 0.9669 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
GKCHAHMN_00054 ARO:3005010 100 2.01e-78 1 115 1.0000 1.0000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
GKCHAHMN_00055 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
GKCHAHMN_00059 ARO:3003019 100 2.79e-135 1 186 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
GKCHAHMN_00071 ARO:3002705 99.8 2.79e-276 1 404 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
GKCHAHMN_00074 ARO:3000165 99.5 3.48e-285 1 399 1.0000 0.9410 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
GKCHAHMN_00077 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
GKCHAHMN_00078 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
GKCHAHMN_00079 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement






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
GKCHAHMN_00049 PHI:9804 int 100 3.8e-14 1 37 0.1160 1.0000 rodents gastroenteritis integrase reduced virulence
GKCHAHMN_00117 PHI:11406 dsbC 99.6 7e-135 1 235 1.0000 1.0000 rodents pneumonia thiol:disulfide interchange protein reduced virulence
GKCHAHMN_00168 PHI:11588 PPECC33_0249 (Rhs1) 93.4 0 1 1295 0.9120 0.9104 primates infection classic rearrangement hotspot 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
GKCHAHMN_00183 AIO10552.2|GH23 100 6.52e-238 9 346 0.9769 1
GKCHAHMN_00185 AIO10245.2|GH23 100 0 1 1204 1 1
GKCHAHMN_00188 QDC33125.1|GH23 100 5.28e-123 1 177 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
GKCHAHMN_00051 2.A.1.2.3 99.3 1.1e-231 1 419 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
GKCHAHMN_00071 2.A.1.2.110 98.8 5.3e-215 1 404 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
GKCHAHMN_00074 2.A.1.2.4 99.7 1.1e-217 1 390 0.9774 0.9774 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)