Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C970
  Reference Plasmid   NZ_CP086501.1
  Reference Plasmid Size   117620
  Reference Plasmid GC Content   0.51
  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
M0191447 DNNINLGJ_00090 77354 6 Gut 0.67 protein_coding missense_variant MODERATE 829A>G Asn277Asp
M0191448 DNNINLGJ_00090 78012 6 Gut 0.67 protein_coding synonymous_variant LOW 171A>C Thr57Thr
M0191449 DNNINLGJ_00092 79621 6 Gut 0.67 protein_coding synonymous_variant LOW 2187G>T Ala729Ala
M0191450 DNNINLGJ_00092 80029 6 Gut 0.67 protein_coding synonymous_variant LOW 1779G>T Ser593Ser
M0191451 DNNINLGJ_00093 82435 6 Gut 0.67 protein_coding missense_variant MODERATE 263C>T Ala88Val
M0191452 DNNINLGJ_00099 86070 6 Gut 0.67 protein_coding synonymous_variant LOW 825T>C Gly275Gly
M0191453 DNNINLGJ_00099 86240 6 Gut 0.67 protein_coding missense_variant MODERATE 655A>C Ile219Leu
M0191454 DNNINLGJ_00100 87094 6 Gut 0.67 protein_coding synonymous_variant LOW 504A>G Gln168Gln
M0191455 DNNINLGJ_00102 88088 6 Gut 0.67 protein_coding synonymous_variant LOW 3636A>G Lys1212Lys
M0191456 DNNINLGJ_00102 88361 6 Gut 0.67 protein_coding synonymous_variant LOW 3363A>G Glu1121Glu
M0191457 DNNINLGJ_00102 91124 6 Gut 0.67 protein_coding synonymous_variant LOW 600C>A Gly200Gly
M0191458 DNNINLGJ_00102 91420 6 Gut 0.67 protein_coding missense_variant MODERATE 304G>A Ala102Thr
M0191459 DNNINLGJ_00103 91894 6 Gut 0.67 protein_coding synonymous_variant LOW 471T>C Leu157Leu
M0191460 DNNINLGJ_00105 93757 6 Gut 0.67 protein_coding synonymous_variant LOW 58T>C Leu20Leu
M0191461 DNNINLGJ_00106 93834 6 Gut 0.67 protein_coding missense_variant MODERATE 796A>G Ser266Gly
M0191462 DNNINLGJ_00106 94567 6 Gut 0.67 protein_coding synonymous_variant LOW 63C>T Pro21Pro
M0191463 DNNINLGJ_00107 94842 6 Gut 0.67 protein_coding synonymous_variant LOW 243G>A Ala81Ala
M0191464 DNNINLGJ_00107 94962 6 Gut 0.67 protein_coding synonymous_variant LOW 123A>G Arg41Arg
M0191465 DNNINLGJ_00108 95854 6 Gut 0.67 protein_coding synonymous_variant LOW 210G>A Lys70Lys
M0191466 DNNINLGJ_00108 95866 6 Gut 0.67 protein_coding synonymous_variant LOW 198T>C Cys66Cys
M0191467 DNNINLGJ_00108 95869 6 Gut 0.67 protein_coding synonymous_variant LOW 195C>A Pro65Pro
M0191468 DNNINLGJ_00108 95935 6 Gut 0.67 protein_coding missense_variant MODERATE 129G>T Met43Ile
M0191469 DNNINLGJ_00108 95995 6 Gut 0.67 protein_coding synonymous_variant LOW 69T>G Ala23Ala
M0191470 DNNINLGJ_00108 96034 6 Gut 0.67 protein_coding synonymous_variant LOW 30G>A Lys10Lys
M0191471 DNNINLGJ_00102 96074 6 Gut 0.67 protein_coding upstream_gene_variant MODIFIER -4351T>G None
M0191472 DNNINLGJ_00109 97262 6 Gut 0.67 protein_coding missense_variant MODERATE 61A>G Thr21Ala
M0191473 DNNINLGJ_00110 97475 6 Gut 0.67 protein_coding missense_variant MODERATE 761A>G Glu254Gly
M0191474 DNNINLGJ_00110 97526 6 Gut 0.67 protein_coding missense_variant MODERATE 710G>A Arg237Gln
M0191475 DNNINLGJ_00110 97575 6 Gut 0.67 protein_coding missense_variant MODERATE 661C>A Leu221Ile
M0191476 DNNINLGJ_00110 97594 6 Gut 0.67 protein_coding synonymous_variant LOW 642C>A Ala214Ala
M0191477 DNNINLGJ_00110 97612 6 Gut 0.67 protein_coding synonymous_variant LOW 624C>T Gly208Gly
M0191478 DNNINLGJ_00110 97618 6 Gut 0.67 protein_coding synonymous_variant LOW 618C>A Ile206Ile
M0191479 DNNINLGJ_00110 97629 6 Gut 0.67 protein_coding missense_variant MODERATE 607G>A Glu203Lys
M0191480 DNNINLGJ_00110 97649 6 Gut 0.67 protein_coding missense_variant MODERATE 587G>A Cys196Tyr
M0191481 DNNINLGJ_00110 97987 6 Gut 0.67 protein_coding synonymous_variant LOW 249A>G Gly83Gly
M0191482 DNNINLGJ_00110 97992 6 Gut 0.67 protein_coding missense_variant MODERATE 244A>G Thr82Ala
M0191483 DNNINLGJ_00110 98113 6 Gut 0.67 protein_coding synonymous_variant LOW 123A>C Pro41Pro
M0191484 DNNINLGJ_00111 98619 6 Gut 0.67 protein_coding missense_variant MODERATE 922G>A Asp308Asn
M0191485 DNNINLGJ_00111 98695 6 Gut 0.67 protein_coding synonymous_variant LOW 846G>A Lys282Lys
M0191486 DNNINLGJ_00111 99028 6 Gut 0.67 protein_coding synonymous_variant LOW 513T>C His171His
M0191487 DNNINLGJ_00111 99088 6 Gut 0.67 protein_coding synonymous_variant LOW 453A>G Glu151Glu
M0191488 DNNINLGJ_00111 99316 6 Gut 0.67 protein_coding synonymous_variant LOW 225T>C Ala75Ala
M0191489 DNNINLGJ_00111 99318 6 Gut 0.67 protein_coding missense_variant MODERATE 223G>C Ala75Pro
M0191490 DNNINLGJ_00108 100789 5 Gut 0.56 protein_coding upstream_gene_variant MODIFIER -4726A>G None
M0191491 DNNINLGJ_00112 101171 5 Gut 0.56 protein_coding synonymous_variant LOW 342C>T Ser114Ser
M0191492 DNNINLGJ_00113 101645 4 Gut 0.44 protein_coding synonymous_variant LOW 966T>G Arg322Arg
M0191493 DNNINLGJ_00113 101765 4 Gut 0.44 protein_coding synonymous_variant LOW 846C>T Ser282Ser
M0191494 DNNINLGJ_00113 101906 4 Gut 0.44 protein_coding synonymous_variant LOW 705T>A Thr235Thr
M0191495 DNNINLGJ_00114 102825 4 Gut 0.44 protein_coding missense_variant MODERATE 430C>A Arg144Ser






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
DNNINLGJ_00014 VFG043980 Colicin Ib 98.9 0 1 626 1.0 1 Exotoxin colicin-like pore-forming 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
DNNINLGJ_00033 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
DNNINLGJ_00022 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
DNNINLGJ_00026 ARO:3002705 99.3 2.29e-275 1 404 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
DNNINLGJ_00030 ARO:3000900 100 1.03e-207 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
DNNINLGJ_00032 ARO:3000410 100 5.02e-191 1 270 0.8359 0.9677 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
DNNINLGJ_00033 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
DNNINLGJ_00034 ARO:3002601 99.2 2.68e-186 1 259 1.0000 0.9848 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
DNNINLGJ_00035 ARO:3002854 100 9.81e-115 1 157 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr 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
DNNINLGJ_00036 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase 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
DNNINLGJ_00115 AHF22950.1|GH23 100 5.89e-138 1 186 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
DNNINLGJ_00014 1.C.1.1.2 99.8 0 1 626 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
DNNINLGJ_00015 8.B.24.2.1 98.2 2.7e-55 1 110 0.9565 0.8661 8 Accessory Factors Involved in Transport 8.B Ribosomally synthesized protein/peptide toxins/agonists that target channels and carriers 8.B.24 The Colicin Immunity Protein (ColIP) Functional Family
DNNINLGJ_00026 2.A.1.2.110 98 1.3e-213 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)
DNNINLGJ_00078 3.A.7.10.1 99.9 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
DNNINLGJ_00079 3.A.7.10.1 99.4 2.8e-207 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
DNNINLGJ_00080 3.A.7.10.1 100 2.4e-244 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
DNNINLGJ_00081 1.E.53.1.10 86 3e-14 9 51 0.8431 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
DNNINLGJ_00088 9.B.40.1.2 97.8 0 1 722 1.0000 0.9691 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.40 The DotA/TraY (DotA/TraY) Family
DNNINLGJ_00099 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
DNNINLGJ_00100 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
DNNINLGJ_00101 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
DNNINLGJ_00104 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
DNNINLGJ_00105 3.A.7.10.1 100 3.3e-222 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
DNNINLGJ_00106 3.A.7.10.1 99.3 4.8e-159 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
DNNINLGJ_00107 3.A.7.10.1 100 6e-87 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