Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1065
  Reference Plasmid   NZ_CP103535.1
  Reference Plasmid Size   94558
  Reference Plasmid GC Content   0.53
  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
M0195541 NPHLFAGP_00011 11203 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -2650A>G None
M0195542 NPHLFAGP_00017 12911 3 Gut 0.14 protein_coding synonymous_variant LOW 1269T>C Tyr423Tyr
M0195543 NPHLFAGP_00017 13037 3 Gut 0.14 protein_coding synonymous_variant LOW 1395T>C Arg465Arg
M0195544 NPHLFAGP_00017 13041 3 Gut 0.14 protein_coding synonymous_variant LOW 1399C>A Arg467Arg
M0195545 NPHLFAGP_00017 13196 3 Gut 0.14 protein_coding synonymous_variant LOW 1554G>A Ala518Ala
M0195546 NPHLFAGP_00017 13218 3 Gut 0.14 protein_coding missense_variant MODERATE 1576A>G Lys526Glu
M0195547 NPHLFAGP_00017 13421 3 Gut 0.14 protein_coding synonymous_variant LOW 1779A>G Glu593Glu
M0195548 NPHLFAGP_00017 13424 3 Gut 0.14 protein_coding synonymous_variant LOW 1782C>A Pro594Pro
M0195549 NPHLFAGP_00017 13852 4 Gut 0.18 protein_coding missense_variant MODERATE 2210G>A Arg737Lys
M0195550 NPHLFAGP_00017 14323 3 Gut 0.14 protein_coding missense_variant MODERATE 2681G>A Arg894Gln
M0195551 NPHLFAGP_00015 14448 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -3382A>C None
M0195552 NPHLFAGP_00018 14692 3 Gut 0.14 protein_coding synonymous_variant LOW 2193C>A Pro731Pro
M0195553 NPHLFAGP_00018 14799 3 Gut 0.14 protein_coding missense_variant MODERATE 2086A>T Arg696Trp
M0195554 NPHLFAGP_00018 15043 3 Gut 0.14 protein_coding synonymous_variant LOW 1842G>A Arg614Arg
M0195555 NPHLFAGP_00018 15046 3 Gut 0.14 protein_coding synonymous_variant LOW 1839C>A Pro613Pro
M0195556 NPHLFAGP_00018 15151 3 Gut 0.14 protein_coding synonymous_variant LOW 1734G>A Val578Val
M0195557 NPHLFAGP_00018 16135 3 Gut 0.14 protein_coding synonymous_variant LOW 750T>A Gly250Gly
M0195558 NPHLFAGP_00018 16138 3 Gut 0.14 protein_coding synonymous_variant LOW 747C>G Gly249Gly
M0195559 NPHLFAGP_00018 16146 3 Gut 0.14 protein_coding missense_variant MODERATE 739G>A Val247Ile
M0195560 NPHLFAGP_00018 16156 3 Gut 0.14 protein_coding synonymous_variant LOW 729G>A Leu243Leu
M0195561 NPHLFAGP_00018 16192 3 Gut 0.14 protein_coding synonymous_variant LOW 693C>A Thr231Thr
M0195562 NPHLFAGP_00018 16297 3 Gut 0.14 protein_coding synonymous_variant LOW 588G>A Glu196Glu
M0195563 NPHLFAGP_00018 16470 3 Gut 0.14 protein_coding missense_variant MODERATE 415G>A Val139Ile
M0195564 NPHLFAGP_00018 16519 3 Gut 0.14 protein_coding synonymous_variant LOW 366T>C Asn122Asn
M0195565 NPHLFAGP_00018 16555 3 Gut 0.14 protein_coding synonymous_variant LOW 330A>C Ala110Ala
M0195566 NPHLFAGP_00018 16562 3 Gut 0.14 protein_coding missense_variant MODERATE 323C>T Ser108Phe
M0195567 NPHLFAGP_00018 16573 3 Gut 0.14 protein_coding synonymous_variant LOW 312A>G Ala104Ala
M0195568 NPHLFAGP_00018 16617 3 Gut 0.14 protein_coding synonymous_variant LOW 268C>A Arg90Arg
M0195569 NPHLFAGP_00018 16657 3 Gut 0.14 protein_coding synonymous_variant LOW 228G>A Thr76Thr
M0195570 NPHLFAGP_00018 16697 3 Gut 0.14 protein_coding missense_variant MODERATE 188C>T Thr63Met
M0195571 NPHLFAGP_00018 16732 3 Gut 0.14 protein_coding synonymous_variant LOW 153T>C Cys51Cys
M0195572 NPHLFAGP_00018 16762 3 Gut 0.14 protein_coding synonymous_variant LOW 123C>G Ala41Ala
M0195573 NPHLFAGP_00018 16796 3 Gut 0.14 protein_coding missense_variant MODERATE 89T>C Ile30Thr
M0195574 NPHLFAGP_00018 16827 3 Gut 0.14 protein_coding synonymous_variant LOW 58C>T Leu20Leu
M0195575 NPHLFAGP_00019 17571 3 Gut 0.14 protein_coding missense_variant MODERATE 419A>C Lys140Thr
M0195576 NPHLFAGP_00019 17596 3 Gut 0.14 protein_coding missense_variant MODERATE 394C>T Pro132Ser
M0195577 NPHLFAGP_00019 17686 3 Gut 0.14 protein_coding missense_variant MODERATE 304T>A Tyr102Asn
M0195578 NPHLFAGP_00020 18412 4 Gut 0.18 protein_coding synonymous_variant LOW 891G>C Pro297Pro
M0195579 NPHLFAGP_00020 18415 4 Gut 0.18 protein_coding synonymous_variant LOW 888T>C Pro296Pro
M0195580 NPHLFAGP_00020 18451 4 Gut 0.18 protein_coding synonymous_variant LOW 852G>T Leu284Leu
M0195581 NPHLFAGP_00020 18497 4 Gut 0.18 protein_coding missense_variant MODERATE 806G>A Gly269Asp
M0195582 NPHLFAGP_00020 18508 4 Gut 0.18 protein_coding synonymous_variant LOW 795C>A Ile265Ile
M0195583 NPHLFAGP_00020 18547 4 Gut 0.18 protein_coding synonymous_variant LOW 756G>A Pro252Pro
M0195584 NPHLFAGP_00018 19512 4 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -2628C>T None
M0195585 NPHLFAGP_00023 21422 4 Gut 0.18 protein_coding synonymous_variant LOW 54T>C Ala18Ala
M0195586 NPHLFAGP_00024 21895 4 Gut 0.18 protein_coding synonymous_variant LOW 318T>C Val106Val
M0195587 NPHLFAGP_00024 21999 4 Gut 0.18 protein_coding missense_variant MODERATE 422C>T Ala141Val
M0195588 NPHLFAGP_00027 22753 4 Gut 0.18 protein_coding synonymous_variant LOW 291T>C Cys97Cys
M0195589 NPHLFAGP_00027 22794 4 Gut 0.18 protein_coding missense_variant MODERATE 250G>A Glu84Lys
M0195590 NPHLFAGP_00020 23738 4 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -4436A>T None
M0195591 NPHLFAGP_00029 24032 4 Gut 0.18 protein_coding missense_variant MODERATE 118C>T Leu40Phe
M0195592 NPHLFAGP_00020 24083 4 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -4781A>G None
M0195593 NPHLFAGP_00020 24086 4 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -4784T>C None
M0195594 NPHLFAGP_00020 24087 4 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -4785C>T None
M0195595 NPHLFAGP_00020 24088 4 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -4786T>G None
M0195596 NPHLFAGP_00030 24230 4 Gut 0.18 protein_coding missense_variant MODERATE 1562T>C Leu521Pro
M0195597 NPHLFAGP_00030 24935 4 Gut 0.18 protein_coding missense_variant MODERATE 857G>A Arg286His
M0195598 NPHLFAGP_00030 24971 4 Gut 0.18 protein_coding missense_variant MODERATE 821G>A Arg274Lys
M0195599 NPHLFAGP_00030 25007 4 Gut 0.18 protein_coding missense_variant MODERATE 785G>A Ser262Asn
M0195600 NPHLFAGP_00030 25047 4 Gut 0.18 protein_coding missense_variant MODERATE 745A>G Thr249Ala
M0195601 NPHLFAGP_00030 25054 4 Gut 0.18 protein_coding synonymous_variant LOW 738T>C Ile246Ile
M0195602 NPHLFAGP_00030 25072 4 Gut 0.18 protein_coding missense_variant MODERATE 720C>G Asp240Glu
M0195603 NPHLFAGP_00032 27789 4 Gut 0.18 protein_coding synonymous_variant LOW 1183C>T Leu395Leu
M0195604 NPHLFAGP_00032 28438 4 Gut 0.18 protein_coding synonymous_variant LOW 534T>C Ile178Ile
M0195605 NPHLFAGP_00033 29450 4 Gut 0.18 protein_coding missense_variant MODERATE 166C>G Pro56Ala
M0195606 NPHLFAGP_00033 29519 5 Gut 0.23 protein_coding missense_variant MODERATE 97G>A Ala33Thr
M0195607 NPHLFAGP_00036 31692 5 Gut 0.23 protein_coding synonymous_variant LOW 2748T>C Ser916Ser
M0195608 NPHLFAGP_00044 40457 6 Gut 0.27 protein_coding missense_variant MODERATE 22A>T Thr8Ser
M0195609 NPHLFAGP_00045 40550 4 Gut 0.18 protein_coding synonymous_variant LOW 291G>A Val97Val
M0195610 NPHLFAGP_00046 43385 6 Gut 0.27 protein_coding missense_variant MODERATE 1534G>A Ala512Thr
M0195611 NPHLFAGP_00055 52691 6 Gut 0.27 protein_coding synonymous_variant LOW 210G>A Gly70Gly
M0195612 NPHLFAGP_00055 52694 6 Gut 0.27 protein_coding missense_variant MODERATE 207T>A Ser69Arg
M0195613 NPHLFAGP_00058 55344 4 Gut 0.18 protein_coding synonymous_variant LOW 804C>T Pro268Pro
M0195614 NPHLFAGP_00058 55998 6 Gut 0.27 protein_coding synonymous_variant LOW 150T>C Arg50Arg
M0195615 NPHLFAGP_00058 56106 6 Gut 0.27 protein_coding missense_variant MODERATE 42A>T Glu14Asp
M0195616 NPHLFAGP_00053 56216 4 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -4461C>T 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






        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
NPHLFAGP_00076 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase 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






        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
NPHLFAGP_00055 QGQ17802.1|GH23 100 9.39e-116 1 161 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
NPHLFAGP_00018 3.A.7.10.1 79.7 0 1 723 0.9439 7.5313 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
NPHLFAGP_00020 3.A.7.10.1 75.3 9.3e-189 1 401 0.9155 4.1771 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
NPHLFAGP_00029 1.E.53.1.10 97.7 9.7e-18 8 50 0.8600 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
NPHLFAGP_00043 3.A.7.10.1 74.9 1.5e-138 1 324 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
NPHLFAGP_00045 3.A.7.10.1 73.3 1.9e-40 1 116 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
NPHLFAGP_00048 3.A.7.10.1 77.8 5.1e-175 1 379 0.9921 3.9479 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
NPHLFAGP_00049 3.A.7.10.1 77.9 6.6e-124 1 271 0.9748 2.8021 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