Tome (Temperature optima for microorganisms and enzymes) is an open source suite for two fundamental applications:

• predict the optimal growth temperature from proteome sequences
• get homologue enzymes for a given ec number with/without a sequence that have a temperature optima in a specified range.

Li, G., Rabe, K. S., Nielsen, J. & Engqvist, M. K. M. Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima. bioRxiv (2018). doi:10.1101/522342

• macOS
• Linux

cd [directory to tome, where setup.py is]

pip install -e .

There is a folder named 'test' in the package. One can use the instructions in 'Usage' section to test the package.

• ncbi-blast-2.7.1+ (ftp:https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) (This is only mandatory for 'tome predOGT -seq')
• pandas
• Biopython
• numpy
• sklearn
• Pyhton 2.7 or Python 3

tome predOGT --fasta test/proteomes/pyrococcus_horikoshii.fasta

Then you will get following results:

FileName	predOGT (C)
pyrococcus_horikoshii.fasta	94.0

tome predOGT --indir test/proteomes/ -o test/proteomes/predicted_ogt.tsv

Then you will get an tab-seperated output file predicted_ogt.tsv with following contents:

FileName	predOGT (C)
succinivibrio_dextrinosolvens.fasta	38.27
pyrococcus_horikoshii.fasta	94.0
caldanaerobacter_subterraneus.fasta	70.0

In case there would be some warnings due to the versions of sklearn when loading the model, one can use following command to train the model again:

tome predOGT --train

Expected output after training is

A new model has beed successfully trained.
Model performance:
        RMSE: 2.159489340036136
          r2: 0.9552614628185572
  Pearson r:(0.9775886084277753, 0.0)
  Spearman r:SpearmanrResult(correlation=0.93331975456613, pvalue=0.0)

Saving the new model to replace the original one...
Done!

The first time this command is run two files totaling ~2.5 GB will be downloaded from the Zenodo data repository (https://zenodo.org/record/2539114#.XDyAUc_0l0s). These files contain the enzyme annotation data.

For example, we want to get the enzymes with EC 3.2.1.1 with a temperature optima higher 50 °C.

tome getEnzymes --ec 3.2.1.1 --temp_range 50,200 --data_type Topt --outdir test/enzyme_without_seq/

Two output files will be generated: test/enzyme_without_seq/3.2.1.1_all.fasta and test/enzyme_without_seq/3.2.1.1_all.tsv 3.2.1.1_all.fasta contains all sequences for this EC number. This can be used for mutisequence alignment with tools like Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/) enzyme_without_seq/3.2.1.1_all.tsv contains following columns:

• uniprot id
• domain: Domain information of source organism (Archaea/Bacteria/Eukaryote)
• organism: name of source organism
• ogt: optimal growth temperature of source organism
• ogt_source: if the growth temperature is predicted or experimentally determined
• topt: temperature optima of the enzyme
• topt_source: if topt is predicted or experimentally determined
• seqeunce: protein sequence

One can also use following command to find enzymes from organisms with a OGT fall into the temperature range specified with --temp_range. The output files have the same format as above described.

tome getEnzymes --ec 3.2.1.1 --temp_range 50,200 --data_type OGT --outdir test/enzyme_without_seq/

For example, we want to get all homologs of an enzyme with EC 3.2.1.1 from Photobacterium profundum (OGT = 13°C). We want those homologs with a temperature optima higher 50 °C. The sequence for this enzyme is

>Q1Z0D7
MTSLFNTEYASTLSAPSVATNVILHAFDWPYSKVTENAKAIADNGYKAILVSPPLKSFHSKDGTQWWQRYQPQDYRVIDN
QLGNTNDFRTMVEILSLHDIDIYADIVFNHMANESHERSDLNYPNSNIISQYKDKREYFDSIKLFGDLSQPLFSKDDFLS
AFPIKDWKDPWQVQHGRISSGGSDPGLPTLKNNENVVKKQKLYLKALKKIGVKGFRIDAAKHMTLDHIQELCDEDITDGI
HIFGEIITDGGATKEEYELFLQPYLEKTTLGAYDFPLFHTVLDVFNKNASMASLINPYSLGSALENQRAITFAITHDIPN
NDVFLDQVMSEKNEQLAYCYILGRDGGVPLIYTDLDTSGIKNSRGKPRWCEAWNDPIMAKMIHFHNIMHCQPMVIIEQTL
DLLVFSRGHSGIVAINKGKTAVCYKLPAKYSEQDHTEIKEVINMEGVKLSPPSLSTEAGVILQLPAQSCAMLMV

There should be only one sequence in the fasta file. If more than 1 sequence is provided, only the first sequence would be used.

tome getEnzymes --seq test/enzyme_with_seq/test.fasta --ec 3.2.1.1 --temp_range 50,200 --data_type Topt --outdir test/enzyme_with_seq/

Two output files will be created:

• Q1Z0D7_homologs.fasta: a fasta file which contains sequences for all homologs of query enzyme
• Q1Z0D7_homologs.tsv: a tab-seperated file with following columns:
  • uniprot id
  • domain: Domain information of source organism (Archaea/Bacteria/Eukaryote)
  • organism: name of source organism
  • ogt: optimal growth temperature of source organism
  • ogt_source: if the growth temperature is predicted or experimentally determined
  • topt: temperature optima of the enzyme
  • topt_source: if topt is predicted or experimentally determined
  • Identity(%) from blast
  • Coverage(%) from blast
  • seqeunce: protein sequence

In this test case, 44 homologs with a temperature optima higher than 50 °C were found.

One can also use following command to find homologous enzymes from organisms with a OGT fall into the temperature range specified with --temp_range. The output files have the same format as above described.

tome getEnzymes --seq test/enzyme_with_seq/test.fasta --ec 3.2.1.1 --temp_range 50,200 --data_type OGT --outdir test/enzyme_with_seq/

In this case, 13 homologs from organisms with a OGT higher than 50 °C were found

Use following commands you can get detailed information about the arguments of tome.

tome --help/-h
tome predOGT --help/-h
tome getEnzymes --help/-h

Or you can directly contact Martin Engqvist: [email protected] or Gang Li: [email protected]

Gang Li