kb_DRAM P. normanii annotation with model
Rory Flynn, José Pedro Lopes Faria
Generated October 11, 2022

kb_DRAM P. normanii annotation

Here we are annotating a P. normanii metagenome assembled genome using both DRAM and RAST then using those annotations to build models. The genome is from NCBI genome ID GCA_000398025.1.

Import FASTA File as Assembly from Staging Area
Import a FASTA file from your staging area into your Narrative as an Assembly data object
This app completed without errors in 1m 9s.
Objects
Created Object Name Type Description
Paceibacter_normanii_SCGC_AAA255-P19 Assembly Imported Assembly
Report
Links
  • report.html - HTML summary report for Imported Assembly

Annotate with DRAM

This genome has not had genes called already so we will have DRAM generate the genome object which will then be anntoated with RAST.

Annotate and Distill Assemblies with DRAM
Annotate your assembly with DRAM. Annotations will then be distilled to create an interactive functional summary per assembly.
This app completed without errors in 25m 45s.
Objects
Created Object Name Type Description
Paceibacter_normanii_SCGC_AAA255-P19_DRAM Genome Annotated Genome
NA GenomeSet NA
Report
Summary
Here are the results from your DRAM run.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/128174
  • annotations.tsv - DRAM annotations in a tab separate table format
  • genes.fna - Genes as nucleotides predicted by DRAM with brief annotations
  • genes.faa - Genes as amino acids predicted by DRAM with brief annotations
  • genes.gff - GFF file of all DRAM annotations
  • rrnas.tsv - Tab separated table of rRNAs as detected by barrnap
  • trnas.tsv - Tab separated table of tRNAs as detected by tRNAscan-SE
  • genbank.tar.gz - Compressed folder of output genbank files
  • product.tsv - DRAM product in tabular format
  • metabolism_summary.xlsx - DRAM metabolism summary tables
  • genome_stats.tsv - DRAM genome statistics table

DRAM generates annotations from two separate types: KOs and ECs. The KOs come from annotation with KOfam and the EC's come from KOfam and DBCAN2. To consider all of these annotations at once we must merge them with the "Merge Metaboic Annotations" app.

Merge Metabolic Annotations
Merge multiple metabolic annotations into a single merged annotation based on thresholds
This app completed without errors in 1m 37s.
Objects
Created Object Name Type Description
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_merged Genome Genome with merged annotations
Report
Links
Output from Merge Metabolic Annotations
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/128174

Annotate with RAST

Now that we have our genome full annotated with DRAM we can add on the RAST annotations.

Annotate Microbial Genome with RASTtk - v1.073
Annotate or re-annotate bacterial or archaeal genome using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
This app completed without errors in 4m 27s.
Objects
Created Object Name Type Description
Paceibacter_normanii_SCGC_AAA255-P19_RAST Genome RAST annotation
Summary 
Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of Unknown.
The RAST algorithm was applied to annotating an existing genome: Unknown. 
The sequence for this genome is comprised of 29 contigs containing 553464 nucleotides. 
The input genome has 551 existing coding features and 0 existing non-coding features.
NOTE: Older input genomes did not properly separate coding and non-coding features.
Input genome has the following feature types:
	gene                             551 
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 551 coding features and 0 non-coding features, 0 new features were called, of which 0 are non-coding.
Output genome has the following feature types:
	Coding gene                      551 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
Output from Annotate Microbial Genome with RASTtk - v1.073
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/128174

Merge annotations from DRAM and RAST

Then to combine the DRAM annotations with the RAST annotations we can use "Merge Metabolic Annotations" again.

Merge Metabolic Annotations
Merge multiple metabolic annotations into a single merged annotation based on thresholds
This app completed without errors in 1m 15s.
Objects
Created Object Name Type Description
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST Genome Genome with merged annotations
Report
Links
Output from Merge Metabolic Annotations
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/128174

Compare annotations

Then we can compare the DRAM, RAST and merged DRAM + RAST annotations.

Compare Metabolic Annotations
Conduct a side-by-side comparison of various metabolic annotations mapped into a genome
This app completed without errors in 1m 13s.
Report
Links

Build models

Now we will build a model for the DRAM annotations, RAST annotations and the merged DRAM + RAST annotations. For each set of annotations a model is built, the model is evaluated with MEMOTE and then characterized to determine metabolic characteristics.

DRAM and RAST

Build Metabolic Model
Construct a draft metabolic model based on an annotated genome.
This app completed without errors in 1m 20s.
Objects
Created Object Name Type Description
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model FBAModel FBAModel-14 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model.gf.1 FBA FBA-13 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model.gf.1
Report
Summary
RefGlucoseMinimal media.
Output from Build Metabolic Model
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/128174
Memote - Genome-Scale Model Test Suite
Genome-Scale Model Test Suite
This app completed without errors in 3m 48s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/128174
  • Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model.xml - desc
Run Model Characterization
Runs a variety of algorithms on a model to characterize its quality, pathways, and auxotrophy.
This app completed without errors in 4m 21s.
Objects
Created Object Name Type Description
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model_characterized.auxo_media Media Media-4 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model_characterized.auxo_media
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model_characterized FBAModel FBAModel-14 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model_characterized
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model_characterized.gf.2 FBA FBA-13 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model_characterized.gf.2
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model_characterized.fba FBA FBA-13 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model_characterized.fba
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model_characterized.fba FBA FBA-13 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model_characterized.fba
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model_characterized FBAModel FBAModel-14 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model_characterized
Report
Summary
Carbon-D-Glucose media.Carbon-D-Glucose media.Carbon-D-Glucose media.Paceibacter_normanii_SCGC_AAA255-P19_DRAM_RAST_nontemplate_model_characterized.auxo_media media.Complete media.
Output from Run Model Characterization
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/128174

RAST

Build Metabolic Model
Construct a draft metabolic model based on an annotated genome.
This app completed without errors in 2m 12s.
Objects
Created Object Name Type Description
Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model FBAModel FBAModel-14 Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model
Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model.gf.1 FBA FBA-13 Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model.gf.1
Report
Summary
RefGlucoseMinimal media.
Output from Build Metabolic Model
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/128174
Memote - Genome-Scale Model Test Suite
Genome-Scale Model Test Suite
This app completed without errors in 5m 2s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/128174
  • Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model.xml - desc
Run Model Characterization
Runs a variety of algorithms on a model to characterize its quality, pathways, and auxotrophy.
This app completed without errors in 4m 22s.
Objects
Created Object Name Type Description
Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model_characterized.auxo_media Media Media-4 Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model_characterized.auxo_media
Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model_characterized FBAModel FBAModel-14 Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model_characterized
Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model_characterized.gf.2 FBA FBA-13 Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model_characterized.gf.2
Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model_characterized.fba FBA FBA-13 Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model_characterized.fba
Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model_characterized.fba FBA FBA-13 Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model_characterized.fba
Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model_characterized FBAModel FBAModel-14 Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model_characterized
Report
Summary
Carbon-D-Glucose media.Carbon-D-Glucose media.Carbon-D-Glucose media.Paceibacter_normanii_SCGC_AAA255-P19_RAST_nontemplate_model_characterized.auxo_media media.Complete media.
Output from Run Model Characterization
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/128174

DRAM

Build Metabolic Model
Construct a draft metabolic model based on an annotated genome.
This app completed without errors in 1m 59s.
Objects
Created Object Name Type Description
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model FBAModel FBAModel-14 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model.gf.1 FBA FBA-13 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model.gf.1
Report
Summary
RefGlucoseMinimal media.
Output from Build Metabolic Model
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/128174
Memote - Genome-Scale Model Test Suite
Genome-Scale Model Test Suite
This app completed without errors in 4m 51s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/128174
  • Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model.xml - desc
Run Model Characterization
Runs a variety of algorithms on a model to characterize its quality, pathways, and auxotrophy.
This app completed without errors in 6m 15s.
Objects
Created Object Name Type Description
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model_characterized.auxo_media Media Media-4 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model_characterized.auxo_media
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model_characterized FBAModel FBAModel-14 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model_characterized
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model_characterized.gf.2 FBA FBA-13 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model_characterized.gf.2
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model_characterized.fba FBA FBA-13 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model_characterized.fba
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model_characterized.fba FBA FBA-13 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model_characterized.fba
Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model_characterized FBAModel FBAModel-14 Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model_characterized
Report
Summary
Carbon-D-Glucose media.Carbon-D-Glucose media.Carbon-D-Glucose media.Paceibacter_normanii_SCGC_AAA255-P19_DRAM_nontemplate_model_characterized.auxo_media media.Complete media.
Output from Run Model Characterization
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/128174

Compare models

Finally compare all the built models.

Create Model Set Template
Create a template file for Model Comparison app
This app completed without errors in 1m 11s.
Summary
Found 6 objects from 1 narrative
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/128174
  • model_comparison_template.xlsx - use this file for Model Comparison app
Import TSV/Excel File as FBAModelSet from Staging Area
Import a TSV or Excel file from your staging area into your Narrative as an Attribute Mapping data object
This app completed without errors in 45s.
Objects
Created Object Name Type Description
model_comparison FBAModelSet Imported FBAModelSet
Summary
Import Finished FBAModelSet Name: model_comparison Imported File: model_comparison_template_p_normanii_v1.xlsx
Model Comparison
Retrieve statistical data from models and visualize the comparison via a heatmap
This app completed without errors in 19m 36s.
Report
Links

Released Apps

  1. Build Metabolic Model
    • [1] Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010;28: 977 982. doi:10.1038/nbt.1672
    • [2] Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42: D206 D214. doi:10.1093/nar/gkt1226
    • [3] Latendresse M. Efficiently gap-filling reaction networks. BMC Bioinformatics. 2014;15: 225. doi:10.1186/1471-2105-15-225
    • [4] Dreyfuss JM, Zucker JD, Hood HM, Ocasio LR, Sachs MS, Galagan JE. Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM. PLOS Computational Biology. 2013;9: e1003126. doi:10.1371/journal.pcbi.1003126
    • [5] Mahadevan R, Schilling CH. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng. 2003;5: 264 276.
  2. Compare Metabolic Annotations
    no citations
  3. Import FASTA File as Assembly from Staging Area
    no citations

Apps in Beta

  1. Annotate and Distill Assemblies with DRAM
    • DRAM source code
    • DRAM documentation
    • DRAM publication
  2. Annotate Microbial Genome with RASTtk - v1.073
    • [1] Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics. 2008;9: 75. doi:10.1186/1471-2164-9-75
    • [2] Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42: D206 D214. doi:10.1093/nar/gkt1226
    • [3] Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, et al. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015;5. doi:10.1038/srep08365
    • [4] Kent WJ. BLAT The BLAST-Like Alignment Tool. Genome Res. 2002;12: 656 664. doi:10.1101/gr.229202
    • [5] Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25: 3389-3402. doi:10.1093/nar/25.17.3389
    • [6] Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25: 955 964.
    • [7] Cobucci-Ponzano B, Rossi M, Moracci M. Translational recoding in archaea. Extremophiles. 2012;16: 793 803. doi:10.1007/s00792-012-0482-8
    • [8] Meyer F, Overbeek R, Rodriguez A. FIGfams: yet another set of protein families. Nucleic Acids Res. 2009;37 6643-54. doi:10.1093/nar/gkp698.
    • [9] van Belkum A, Sluijuter M, de Groot R, Verbrugh H, Hermans PW. Novel BOX repeat PCR assay for high-resolution typing of Streptococcus pneumoniae strains. J Clin Microbiol. 1996;34: 1176 1179.
    • [10] Croucher NJ, Vernikos GS, Parkhill J, Bentley SD. Identification, variation and transcription of pneumococcal repeat sequences. BMC Genomics. 2011;12: 120. doi:10.1186/1471-2164-12-120
    • [11] Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11: 119. doi:10.1186/1471-2105-11-119
    • [12] Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23: 673 679. doi:10.1093/bioinformatics/btm009
    • [13] Akhter S, Aziz RK, Edwards RA. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res. 2012;40: e126. doi:10.1093/nar/gks406
  3. Create Model Set Template
    no citations
  4. Import TSV/Excel File as FBAModelSet from Staging Area
    no citations
  5. Memote - Genome-Scale Model Test Suite
    no citations
  6. Merge Metabolic Annotations
    • [1] Griesemer M, Kimbrel JA, Zhou CE, Navid A, D'haeseleer P. Combining multiple functional annotation tools increases coverage of metabolic annotation. BMC Genomics. 2018 Dec 19;19(1):948. doi: 10.1186/s12864-018-5221-9.
    • [2] Hanson AD, Pribat A, Waller JC, de Cr cy-Lagard V. Unknown proteins and orphan enzymes: the missing half of the engineering parts list - and how to find it. Biochem J. 2010;425:1 11. doi: 10.1042/BJ20091328.
    • [3] Ijaq J, Chandrasekharan M, Poddar R, Bethi N, Sundararajan VS. Annotation and curation of uncharacterized proteins- challenges. Front Genet. 2015;6:1750. doi: 10.3389/fgene.2015.00119.
    • [4] Land M, Hauser L, Jun S-R, Nookaew I, Leuze MR, Ahn T-H, et al. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics. 2015;15:141 161. doi: 10.1007/s10142-015-0433-4.
    • [5] Seaver SMD, Liu F, Zhang Q, Jeffryes J, Faria JP, Edirisinghe JN, Mundy M, Chia N, Noor E, Beber ME, Best AA, DeJongh M, Kimbrel JA, D'haeseleer P, McCorkle SR, Bolton JR, Pearson E, Canon S, Wood-Charlson EM, Cottingham RW, Arkin AP, Henry CS. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Res. 2021 Jan 8;49(D1):D1555. doi: 10.1093/nar/gkaa1143.
  7. Model Comparison
    no citations
  8. Run Model Characterization
    • [1] Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010;28: 977 982. doi:10.1038/nbt.1672