Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C906
  Reference Plasmid   NZ_CP076260.1
  Reference Plasmid Size   89049
  Reference Plasmid GC Content   0.49
  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
M0188304 LPFLIAAH_00066 57655 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2331G>A None
M0188305 LPFLIAAH_00066 57877 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2553C>T None
M0188306 LPFLIAAH_00066 57993 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2669T>C None
M0188307 LPFLIAAH_00070 58473 5 Gut 1.00 protein_coding missense_variant MODERATE 244G>A Asp82Asn
M0188308 LPFLIAAH_00070 58554 5 Gut 1.00 protein_coding missense_variant MODERATE 325A>G Ser109Gly
M0188309 LPFLIAAH_00070 58579 5 Gut 1.00 protein_coding missense_variant MODERATE 350A>C His117Pro
M0188310 LPFLIAAH_00066 58861 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3537C>T None
M0188311 LPFLIAAH_00066 59186 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3862G>A None
M0188312 LPFLIAAH_00066 59377 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4053T>C None
M0188313 LPFLIAAH_00066 59531 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4207A>G None
M0188314 LPFLIAAH_00066 59549 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4225A>G None
M0188315 LPFLIAAH_00066 59551 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4227T>G None
M0188316 LPFLIAAH_00066 59556 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4232A>C None
M0188317 LPFLIAAH_00066 59563 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4239C>G None
M0188318 LPFLIAAH_00066 59568 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4244T>A None
M0188319 LPFLIAAH_00066 59591 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4267G>A None
M0188320 LPFLIAAH_00066 59592 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4268A>C None
M0188321 LPFLIAAH_00066 59607 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4283T>C None
M0188322 LPFLIAAH_00066 59611 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4287T>G None
M0188323 LPFLIAAH_00066 59627 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4303T>G None
M0188324 LPFLIAAH_00066 59634 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4310T>C None
M0188325 LPFLIAAH_00066 59644 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4320G>T None
M0188326 LPFLIAAH_00066 59688 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4364G>A None
M0188327 LPFLIAAH_00066 59701 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4377C>T None
M0188328 LPFLIAAH_00066 59708 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4384T>C None
M0188329 LPFLIAAH_00066 59726 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4402T>C None
M0188330 LPFLIAAH_00066 59727 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4403C>T None
M0188331 LPFLIAAH_00066 59741 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4417A>G None
M0188332 LPFLIAAH_00066 59742 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4418G>T None
M0188333 LPFLIAAH_00071 59987 5 Gut 1.00 protein_coding synonymous_variant LOW 159A>G Glu53Glu
M0188334 LPFLIAAH_00071 59993 5 Gut 1.00 protein_coding synonymous_variant LOW 165A>T Thr55Thr
M0188335 LPFLIAAH_00071 60014 5 Gut 1.00 protein_coding synonymous_variant LOW 186A>T Ala62Ala
M0188336 LPFLIAAH_00071 60146 5 Gut 1.00 protein_coding synonymous_variant LOW 318C>T Val106Val
M0188337 LPFLIAAH_00071 60245 5 Gut 1.00 protein_coding synonymous_variant LOW 417T>C Ile139Ile
M0188338 LPFLIAAH_00071 60335 5 Gut 1.00 protein_coding synonymous_variant LOW 507G>T Val169Val
M0188339 LPFLIAAH_00071 60347 5 Gut 1.00 protein_coding synonymous_variant LOW 519C>T Ala173Ala
M0188340 LPFLIAAH_00071 60573 5 Gut 1.00 protein_coding synonymous_variant LOW 745T>C Leu249Leu
M0188341 LPFLIAAH_00069 60830 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3753T>C None
M0188342 LPFLIAAH_00069 60831 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3754G>A None
M0188343 LPFLIAAH_00069 60834 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3757G>A None
M0188344 LPFLIAAH_00069 60860 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3783T>A None
M0188345 LPFLIAAH_00069 60862 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3785G>T None
M0188346 LPFLIAAH_00069 60876 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3799G>C None
M0188347 LPFLIAAH_00072 60889 5 Gut 1.00 protein_coding missense_variant MODERATE 113T>A Leu38Gln
M0188348 LPFLIAAH_00072 60900 5 Gut 1.00 protein_coding synonymous_variant LOW 102A>T Thr34Thr
M0188349 LPFLIAAH_00072 60917 5 Gut 1.00 protein_coding missense_variant MODERATE 85A>G Thr29Ala
M0188350 LPFLIAAH_00072 60922 5 Gut 1.00 protein_coding missense_variant MODERATE 80T>C Leu27Pro
M0188351 LPFLIAAH_00072 60953 5 Gut 1.00 protein_coding missense_variant MODERATE 49T>C Tyr17His
M0188352 LPFLIAAH_00072 60957 5 Gut 1.00 protein_coding missense_variant MODERATE 45C>G Ile15Met
M0188353 LPFLIAAH_00072 60959 5 Gut 1.00 protein_coding missense_variant MODERATE 43A>G Ile15Val
M0188354 LPFLIAAH_00069 61003 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3926T>C None
M0188355 LPFLIAAH_00069 61004 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3927G>A None
M0188356 LPFLIAAH_00069 61023 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3946T>G None
M0188357 LPFLIAAH_00069 61027 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3950T>G None
M0188358 LPFLIAAH_00069 61029 5 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3952T>C None
M0188359 LPFLIAAH_00073 61095 5 Gut 1.00 protein_coding missense_variant MODERATE 737G>A Arg246Lys
M0188360 LPFLIAAH_00073 61136 5 Gut 1.00 protein_coding synonymous_variant LOW 696G>T Gly232Gly
M0188361 LPFLIAAH_00073 61208 5 Gut 1.00 protein_coding synonymous_variant LOW 624T>G Ser208Ser
M0188362 LPFLIAAH_00073 61331 5 Gut 1.00 protein_coding synonymous_variant LOW 501A>G Gly167Gly
M0188363 LPFLIAAH_00073 61469 5 Gut 1.00 protein_coding synonymous_variant LOW 363G>A Thr121Thr
M0188364 LPFLIAAH_00073 61487 5 Gut 1.00 protein_coding synonymous_variant LOW 345C>A Val115Val
M0188365 LPFLIAAH_00073 61559 5 Gut 1.00 protein_coding synonymous_variant LOW 273A>T Gly91Gly
M0188366 LPFLIAAH_00073 61568 5 Gut 1.00 protein_coding synonymous_variant LOW 264C>T Asp88Asp
M0188367 LPFLIAAH_00073 61583 5 Gut 1.00 protein_coding synonymous_variant LOW 249A>G Thr83Thr
M0188368 LPFLIAAH_00073 61628 5 Gut 1.00 protein_coding synonymous_variant LOW 204C>T Thr68Thr






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
LPFLIAAH_00076 PHI:5228 BAHT 84.2 1.1e-212 1 393 0.9680 0.9609 rodents None heptosyltransferase 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
LPFLIAAH_00037 AKO58984.1|GH23 100 1.73e-124 1 169 1 1
LPFLIAAH_00076 QHQ02091.1|GT112 99.3 0 1 406 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
LPFLIAAH_00075 9.B.50.1.2 98.7 1e-184 1 315 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
LPFLIAAH_00083 2.A.7.3.25 83.6 4.2e-135 1 304 0.9651 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily