Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2295
  Reference Plasmid   1111525849760419_bin.3__k141_141309
  Reference Plasmid Size   16264
  Reference Plasmid GC Content   0.56
  Reference Plasmid Mobility Type   non-mobilizable





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
M0034540 NPIKBFKE_00003 2153 3 Skin 0.75 protein_coding synonymous_variant LOW 888G>A Arg296Arg
M0034541 NPIKBFKE_00004 2168 3 Skin 0.75 protein_coding synonymous_variant LOW 669A>G Ala223Ala
M0034542 NPIKBFKE_00004 2174 3 Skin 0.75 protein_coding synonymous_variant LOW 663A>G Val221Val
M0034543 NPIKBFKE_00004 2201 3 Skin 0.75 protein_coding synonymous_variant LOW 636A>G Glu212Glu
M0034544 NPIKBFKE_00004 2222 3 Skin 0.75 protein_coding synonymous_variant LOW 615T>C His205His
M0034545 NPIKBFKE_00004 2234 3 Skin 0.75 protein_coding synonymous_variant LOW 603A>G Ser201Ser
M0034546 NPIKBFKE_00004 2248 3 Skin 0.75 protein_coding synonymous_variant LOW 589T>C Leu197Leu
M0034547 NPIKBFKE_00004 2279 3 Skin 0.75 protein_coding synonymous_variant LOW 558G>T Val186Val
M0034548 NPIKBFKE_00004 2306 3 Skin 0.75 protein_coding synonymous_variant LOW 531T>C Leu177Leu
M0034549 NPIKBFKE_00004 2321 3 Skin 0.75 protein_coding synonymous_variant LOW 516C>A Gly172Gly
M0034550 NPIKBFKE_00004 2441 3 Skin 0.75 protein_coding synonymous_variant LOW 396A>G Leu132Leu
M0034551 NPIKBFKE_00004 2468 3 Skin 0.75 protein_coding synonymous_variant LOW 369G>C Thr123Thr
M0034552 NPIKBFKE_00004 2480 3 Skin 0.75 protein_coding synonymous_variant LOW 357C>T Arg119Arg
M0034553 NPIKBFKE_00004 2510 3 Skin 0.75 protein_coding synonymous_variant LOW 327T>C Leu109Leu
M0034554 NPIKBFKE_00004 2528 3 Skin 0.75 protein_coding synonymous_variant LOW 309G>C Val103Val
M0034555 NPIKBFKE_00004 2561 3 Skin 0.75 protein_coding synonymous_variant LOW 276C>T Phe92Phe
M0034556 NPIKBFKE_00004 2603 3 Skin 0.75 protein_coding synonymous_variant LOW 234A>G Glu78Glu
M0034557 NPIKBFKE_00004 2639 3 Skin 0.75 protein_coding synonymous_variant LOW 198T>C His66His
M0034558 NPIKBFKE_00004 2642 3 Skin 0.75 protein_coding synonymous_variant LOW 195C>T Gly65Gly
M0034559 NPIKBFKE_00005 3055 3 Skin 0.75 protein_coding synonymous_variant LOW 492G>T Leu164Leu
M0034560 NPIKBFKE_00005 3127 3 Skin 0.75 protein_coding synonymous_variant LOW 420C>T Leu140Leu
M0034561 NPIKBFKE_00005 3150 4 Skin 1.00 protein_coding synonymous_variant LOW 397T>C Leu133Leu
M0034562 NPIKBFKE_00005 3205 3 Skin 0.75 protein_coding synonymous_variant LOW 342A>G Leu114Leu
M0034563 NPIKBFKE_00005 3232 3 Skin 0.75 protein_coding synonymous_variant LOW 315T>G Leu105Leu
M0034564 NPIKBFKE_00005 3238 3 Skin 0.75 protein_coding synonymous_variant LOW 309A>G Leu103Leu
M0034565 NPIKBFKE_00005 3244 3 Skin 0.75 protein_coding synonymous_variant LOW 303T>C His101His
M0034566 NPIKBFKE_00005 3298 3 Skin 0.75 protein_coding synonymous_variant LOW 249A>G Glu83Glu
M0034567 NPIKBFKE_00005 3319 3 Skin 0.75 protein_coding synonymous_variant LOW 228A>G Leu76Leu
M0034568 NPIKBFKE_00005 3349 3 Skin 0.75 protein_coding synonymous_variant LOW 198C>T Phe66Phe
M0034569 NPIKBFKE_00005 3397 3 Skin 0.75 protein_coding synonymous_variant LOW 150G>A Leu50Leu
M0034570 NPIKBFKE_00005 3424 3 Skin 0.75 protein_coding missense_variant MODERATE 123T>G His41Gln
M0034571 NPIKBFKE_00005 3493 3 Skin 0.75 protein_coding synonymous_variant LOW 54G>A Leu18Leu
M0034572 NPIKBFKE_00006 3630 3 Skin 0.75 protein_coding synonymous_variant LOW 1449T>C Cys483Cys
M0034573 NPIKBFKE_00006 3708 3 Skin 0.75 protein_coding synonymous_variant LOW 1371A>G Val457Val
M0034574 NPIKBFKE_00006 3750 3 Skin 0.75 protein_coding synonymous_variant LOW 1329T>C Tyr443Tyr
M0034575 NPIKBFKE_00006 3756 3 Skin 0.75 protein_coding synonymous_variant LOW 1323A>G Glu441Glu
M0034576 NPIKBFKE_00006 3831 3 Skin 0.75 protein_coding synonymous_variant LOW 1248A>T Arg416Arg
M0034577 NPIKBFKE_00006 3900 3 Skin 0.75 protein_coding synonymous_variant LOW 1179A>G Leu393Leu
M0034578 NPIKBFKE_00006 3924 3 Skin 0.75 protein_coding synonymous_variant LOW 1155G>A Pro385Pro
M0034579 NPIKBFKE_00006 3930 3 Skin 0.75 protein_coding synonymous_variant LOW 1149A>T Arg383Arg
M0034580 NPIKBFKE_00006 3945 3 Skin 0.75 protein_coding synonymous_variant LOW 1134C>T Asp378Asp
M0034581 NPIKBFKE_00006 3948 3 Skin 0.75 protein_coding synonymous_variant LOW 1131T>G Pro377Pro
M0034582 NPIKBFKE_00006 3963 3 Skin 0.75 protein_coding synonymous_variant LOW 1116T>C Ser372Ser
M0034583 NPIKBFKE_00006 3975 3 Skin 0.75 protein_coding synonymous_variant LOW 1104T>C Gly368Gly
M0034584 NPIKBFKE_00006 4145 3 Skin 0.75 protein_coding synonymous_variant LOW 934C>T Leu312Leu
M0034585 NPIKBFKE_00006 4197 3 Skin 0.75 protein_coding synonymous_variant LOW 882C>T Arg294Arg
M0034586 NPIKBFKE_00006 4245 3 Skin 0.75 protein_coding synonymous_variant LOW 834A>G Ala278Ala
M0034587 NPIKBFKE_00006 4257 3 Skin 0.75 protein_coding synonymous_variant LOW 822T>C Tyr274Tyr
M0034588 NPIKBFKE_00006 4260 3 Skin 0.75 protein_coding synonymous_variant LOW 819G>C Leu273Leu
M0034589 NPIKBFKE_00006 4266 3 Skin 0.75 protein_coding synonymous_variant LOW 813A>C Val271Val
M0034590 NPIKBFKE_00006 4269 3 Skin 0.75 protein_coding synonymous_variant LOW 810C>T Gly270Gly
M0034591 NPIKBFKE_00006 4272 3 Skin 0.75 protein_coding synonymous_variant LOW 807T>C Leu269Leu
M0034592 NPIKBFKE_00006 4275 3 Skin 0.75 protein_coding synonymous_variant LOW 804C>T Tyr268Tyr
M0034593 NPIKBFKE_00006 4281 3 Skin 0.75 protein_coding synonymous_variant LOW 798C>T Ile266Ile
M0034594 NPIKBFKE_00006 4287 3 Skin 0.75 protein_coding synonymous_variant LOW 792C>A Gly264Gly
M0034595 NPIKBFKE_00006 4383 3 Skin 0.75 protein_coding synonymous_variant LOW 696C>T Tyr232Tyr
M0034596 NPIKBFKE_00006 4389 3 Skin 0.75 protein_coding synonymous_variant LOW 690A>G Lys230Lys
M0034597 NPIKBFKE_00006 4413 3 Skin 0.75 protein_coding synonymous_variant LOW 666T>C Cys222Cys
M0034598 NPIKBFKE_00006 4419 3 Skin 0.75 protein_coding synonymous_variant LOW 660G>T Arg220Arg
M0034599 NPIKBFKE_00006 4455 3 Skin 0.75 protein_coding synonymous_variant LOW 624C>T Ile208Ile
M0034600 NPIKBFKE_00006 4464 3 Skin 0.75 protein_coding synonymous_variant LOW 615G>A Glu205Glu
M0034601 NPIKBFKE_00006 4485 3 Skin 0.75 protein_coding synonymous_variant LOW 594C>T Gly198Gly






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






        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
NPIKBFKE_00004 PHI:10515 narI 90.6 1.1e-116 1 224 0.9956 0.9956 rodents urinary tract infection respiratory nitrate reductase 1 gamma chain reduced virulence
NPIKBFKE_00005 PHI:10514 narJ 86 6.9e-114 1 236 1.0000 1.0000 rodents urinary tract infection nitrate reductase molybdenum cofactor assembly chaperone reduced virulence
NPIKBFKE_00006 PHI:10513 narH 92.2 2.6e-291 1 510 0.9980 0.9980 rodents urinary tract infection respiratory nitrate reductase 1 beta chain reduced virulence
NPIKBFKE_00007 PHI:10512 narG 93.7 0 1 1247 1.0000 1.0000 rodents urinary tract infection respiratory nitrate reductase 1 alpha chain reduced virulence
NPIKBFKE_00008 PHI:123379 narK 88.1 4.5e-234 1 462 1.0000 0.9935 rodents salmonellosis nitrate/nitrite transporter reduced virulence
NPIKBFKE_00009 PHI:124166 narX 77.5 8.8e-259 1 590 0.9966 0.9866 rodents neonatal meningitis two-component system reduced virulence
NPIKBFKE_00010 PHI:124167 narL 95.4 2.5e-110 1 216 1.0000 1.0000 rodents neonatal meningitis two-component system 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





        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
NPIKBFKE_00004 5.A.3.1.1 90.6 2.4e-116 1 224 0.9956 0.9956 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
NPIKBFKE_00006 5.A.3.1.1 92.2 5.8e-291 1 510 0.9980 2.2711 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
NPIKBFKE_00007 5.A.3.1.1 93.7 0 1 1247 1.0000 5.5422 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
NPIKBFKE_00008 2.A.1.8.1 87.2 6.5e-233 1 462 1.0000 0.9978 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)