DOI: 10.5061/dryad.jdfn2z3kw
title: Data from: Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways

description: Microbial secondary metabolites are a rich source for pharmaceutical
 discoveries and play crucial ecological functions. While tools exist to
 identify secondary metabolite clusters in genomes, precise
 sequence-to-function mapping remains challenging because neither function
 nor substrate specificity of biosynthesis enzymes can accurately be
 predicted. Here we developed a knowledge-guided bioinformatic pipeline to
 solve these issues. We analyzed 1928 genomes of Pseudomonas bacteria and
 focused on iron-scavenging pyoverdines as model metabolites. Our pipeline
 predicted 188 chemically different pyoverdines with nearly 100% structural
 accuracy and the presence of 94 distinct receptor groups required for the
 uptake of iron-loaded pyoverdines. Our pipeline unveils an enormous yet
 overlooked diversity of siderophores (151 new structures) and receptors
 (91 new groups). Our approach, combining feature sequence with
 phylogenetic approaches, is extendable to other metabolites and microbial
 genera, and thus emerges as powerful tool to reconstruct bacterial
 secondary metabolism pathways based on sequence data.
description: All genome data and gene data were collected from the open
 dataset (e.g., MIBiG 3.0 ,<em>Pseudomonas</em> Genome
 Database), please check the corresponding article for details. 
description: # Data from: Feature sequence-based genome mining uncovers the hidden
 diversity of bacterial siderophore pathways
 [https://doi.org/10.5061/dryad.jdfn2z3kw](https://doi.org/10.5061/dryad.jdfn2z3kw) ## Description of the data and file structure # Pyoverdine-genome-mining ### Files and variables #### File: data\_code.tar.gz **Description:** #Programs generating the data and figures for this work are: * The folder "./Phytree/" contains data and programs about the phylogenetic tree that related to Figure1e. Details can be seen in the "readme.txt" file in that folder * The folder "./Section1to4_Pyoverdine/" contains programs that clean and annotate pyoverdine synthetase from fragmented sequences, which is related to Figure 2-4. Details can be seen in the "readme.txt" file in that folder. * The folder "./Figure4_Chord/" contains data and programs that assess the diversity and horizontal gene transfers of the pyoverdine synthetase and receptors across the Psudomonas genus, which is related to Figure 4. Details can be seen in the "readme.txt" file in that folder * The folder "./Section5to6_Receper" contains data and programs that clean and annotate fpvA receptors in Psudomonas genomes, which are related to Figure 5 to 6. Details can be seen in the "readme.mlx" or "readme.html" file in that folder ## Code/software Details can be seen in the "readme.txt" file in every folder. anyio @ file:///tmp/build/80754af9/anyio_1644481698350/work/dist argon2-cffi @ file:///opt/conda/conda-bld/argon2-cffi_1645000214183/work argon2-cffi-bindings @ file:///tmp/build/80754af9/argon2-cffi-bindings_1644569684262/work arrow @ file:///croot/arrow_1676588132104/work asttokens @ file:///opt/conda/conda-bld/asttokens_1646925590279/work attrs @ file:///croot/attrs_1695717823297/work Babel @ file:///croot/babel_1671781930836/work backcall @ file:///home/ktietz/src/ci/backcall_1611930011877/work beautifulsoup4==4.10.0 biopython==1.78 biothings-client==0.2.6 bleach @ file:///opt/conda/conda-bld/bleach_1641577558959/work blinker==1.4 bokeh @ file:///tmp/abs_34854e1f-d7d3-4f22-85d9-1075588e4ecdga64o0qg/croots/recipe/bokeh_1658136654619/work Bottleneck @ file:///home/conda/feedstock_root/build_artifacts/bottleneck_1611195606760/work Brotli @ file:///tmp/abs_ecyw11_7ze/croots/recipe/brotli-split_1659616059936/work certifi==2020.12.5 cffi @ file:///tmp/abs_98z5h56wf8/croots/recipe/cffi_1659598650955/work cftime @ file:///croot/cftime_1678830372931/work charset-normalizer @ file:///tmp/build/80754af9/charset-normalizer_1630003229654/work click @ file:///croot/click_1698129812380/work cloudpickle @ file:///croot/cloudpickle_1683040006038/work comm @ file:///croot/comm_1671231121260/work contourpy @ file:///opt/conda/conda-bld/contourpy_1663827406301/work cryptography @ file:///croot/cryptography_1694444244250/work custom-inherit @ file:///home/conda/feedstock_root/build_artifacts/custom-inherit_1630153266448/work cycler @ file:///tmp/build/80754af9/cycler_1637851556182/work Cython==0.29.23 cytoolz @ file:///croot/cytoolz_1701723583781/work dask @ file:///home/conda/feedstock_root/build_artifacts/dask-core_1624037261016/work debugpy @ file:///croot/debugpy_1690905042057/work decorator==4.4.2 defusedxml @ file:///tmp/build/80754af9/defusedxml_1615228127516/work DendroPy @ git+[https://github.com/jeetsukumaran/DendroPy.git@0b0d8df448d32a8d829b91204b817ce6c98fb6ec](https://github.com/jeetsukumaran/DendroPy.git@0b0d8df448d32a8d829b91204b817ce6c98fb6ec) dill==0.3.4 distributed @ file:///home/conda/feedstock_root/build_artifacts/distributed_1624044619102/work dna-features-viewer==3.1.2 drmaa==0.7.9 entrypoints @ file:///tmp/build/80754af9/entrypoints_1649926445639/work et-xmlfile==1.1.0 ete3==3.1.2 executing @ file:///opt/conda/conda-bld/executing_1646925071911/work fastcluster==1.2.4 fastDamerauLevenshtein==1.0.7 fastjsonschema @ file:///opt/conda/conda-bld/python-fastjsonschema_1661371079312/work Flask==0.12.5 Flask-Mail==0.9.1 fonttools==4.25.0 fsspec @ file:///croot/fsspec_1701286474621/work future @ file:///croot/future_1677599870788/work grandalf==0.7 hdbscan==0.8.27 HeapDict @ file:///Users/ktietz/demo/mc3/conda-bld/heapdict_1630598515714/work idna @ file:///croot/idna_1666125576474/work imageio @ file:///croot/imageio_1695996454134/work importlib-metadata @ file:///croot/importlib_metadata-suite_1704813515092/work importlib-resources @ file:///croot/importlib_resources-suite_1704281845041/work intervaltree==2.1.0 ipykernel @ file:///croot/ipykernel_1691121631942/work ipympl==0.8.0 ipython @ file:///croot/ipython_1691532092695/work ipython-genutils @ file:///tmp/build/80754af9/ipython_genutils_1606773439826/work ipywidgets==7.6.5 itsdangerous==2.0.1 jdcal @ file:///Users/ktietz/demo/mc3/conda-bld/jdcal_1630584345063/work jedi @ file:///tmp/build/80754af9/jedi_1644315233700/work Jinja2 @ file:///croot/jinja2_1706733616596/work joblib==1.0.1 json5 @ file:///tmp/build/80754af9/json5_1624432770122/work jsonschema @ file:///croot/jsonschema_1699041609003/work jsonschema-specifications @ file:///croot/jsonschema-specifications_1699032386549/work jupyter-server @ file:///croot/jupyter_server_1671707632269/work jupyter_client @ file:///croot/jupyter_client_1676329080601/work jupyter_core @ file:///croot/jupyter_core_1698937308754/work jupyterlab @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_1633634490182/work jupyterlab-pygments @ file:///croot/jupyterlab_pygments_1700168593176/work jupyterlab-widgets @ file:///croot/jupyterlab_widgets_1700168618520/work jupyterlab_server @ file:///croot/jupyterlab_server_1699555425460/work kiwisolver @ file:///croot/kiwisolver_1672387140495/work llvmlite==0.36.0 lmdb @ file:///croot/python-lmdb_1682522346377/work locket @ file:///opt/conda/conda-bld/locket_1652903118915/work lxml @ file:///home/conda/feedstock_root/build_artifacts/lxml_1616532290492/work Markdown==2.6.11 MarkupSafe @ file:///croot/markupsafe_1704205993651/work matlabengineforpython===R2021a matplotlib==3.2.2 matplotlib-inline @ file:///opt/conda/conda-bld/matplotlib-inline_1662014470464/work matplotlib-venn @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-venn_1603640976466/work minepy==1.2.5 mistune @ file:///opt/conda/conda-bld/mistune_1661496219659/work msgpack @ file:///opt/conda/conda-bld/msgpack-python_1652362659880/work multipledispatch==0.6.0 multiprocess==0.70.12.2 multitax==1.3.1 munkres==1.1.4 mygene==3.2.2 nbclassic @ file:///croot/nbclassic_1681756170010/work nbclient @ file:///croot/nbclient_1698934205032/work nbconvert @ file:///croot/nbconvert_1699022732553/work nbformat @ file:///croot/nbformat_1694616755618/work nest-asyncio @ file:///croot/nest-asyncio_1672387112409/work netCDF4 @ file:///tmp/build/80754af9/netcdf4_1613684184693/work netgraph==4.9.0 networkx @ file:///croot/networkx_1690561992265/work notebook @ file:///croot/notebook_1690984815942/work notebook_shim @ file:///croot/notebook-shim_1699455894279/work numba==0.53.1 numpy @ file:///croot/numpy_and_numpy_base_1682520569166/work openpyxl==3.1.2 optional-django==0.1.0 p-tqdm==1.3.3 packaging @ file:///croot/packaging_1693575174725/work pandas==1.5.3 pandocfilters @ file:///opt/conda/conda-bld/pandocfilters_1643405455980/work parso @ file:///opt/conda/conda-bld/parso_1641458642106/work partd @ file:///croot/partd_1698702562572/work pathos==0.2.8 pbr==5.6.0 peewee==2.10.2 pexpect @ file:///tmp/build/80754af9/pexpect_1605563209008/work pickleshare @ file:///tmp/build/80754af9/pickleshare_1606932040724/work Pillow @ file:///croot/pillow_1696580024257/work pkgutil_resolve_name @ file:///croot/pkgutil-resolve-name_1704297459416/work platformdirs @ file:///croot/platformdirs_1692205439124/work pooch @ file:///croot/pooch_1695850093751/work pox==0.3.0 ppft==1.6.6.4 prometheus-client @ file:///tmp/abs_d3zeliano1/croots/recipe/prometheus_client_1659455100375/work prompt-toolkit @ file:///croot/prompt-toolkit_1704404351921/work psutil @ file:///opt/conda/conda-bld/psutil_1656431268089/work ptyprocess @ file:///tmp/build/80754af9/ptyprocess_1609355006118/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl pure-eval @ file:///opt/conda/conda-bld/pure_eval_1646925070566/work pycparser @ file:///tmp/build/80754af9/pycparser_1636541352034/work Pygments @ file:///croot/pygments_1684279966437/work pynndescent==0.5.2 pyOpenSSL @ file:///croot/pyopenssl_1690223430423/work pyparsing @ file:///opt/conda/conda-bld/pyparsing_1661452539315/work pypng==0.0.20 PySocks @ file:///tmp/build/80754af9/pysocks_1605305779399/work python-crontab==2.2.8 python-dateutil @ file:///tmp/build/80754af9/python-dateutil_1626374649649/work pytz @ file:///croot/pytz_1695131579487/work PyWavelets @ file:///croot/pywavelets_1670425177960/work PyYAML==5.4.1 pyzmq @ file:///opt/conda/conda-bld/pyzmq_1657724186960/work rectangle-packer==2.0.1 referencing @ file:///croot/referencing_1699012038513/work reportlab @ file:///croot/reportlab_1702055118304/work requests @ file:///croot/requests_1690400202158/work rpds-py @ file:///croot/rpds-py_1698945930462/work scikit-image==0.18.3 scikit-learn==0.24.2 scipy==1.10.1 seaborn==0.11.1 Send2Trash @ file:///croot/send2trash_1699371139552/work sip==4.19.13 six @ file:///tmp/build/80754af9/six_1644875935023/work sniffio @ file:///croot/sniffio_1705431295498/work sortedcontainers @ file:///tmp/build/80754af9/sortedcontainers_1623949099177/work soupsieve==2.2.1 stack-data @ file:///opt/conda/conda-bld/stack_data_1646927590127/work tblib @ file:///Users/ktietz/demo/mc3/conda-bld/tblib_1629402031467/work tendo==0.2.15 terminado @ file:///croot/terminado_1671751832461/work textdistance==4.5.0 threadpoolctl==2.1.0 tifffile==2020.10.1 tinycss2 @ file:///croot/tinycss2_1668168815555/work toolz @ file:///croot/toolz_1667464077321/work tornado @ file:///croot/tornado_1696936946304/work toyplot==0.19.0 toytree @ file:///home/conda/feedstock_root/build_artifacts/toytree_1605293789943/work tqdm==4.64.0 traitlets @ file:///croot/traitlets_1671143879854/work typing_extensions @ file:///croot/typing_extensions_1705599297034/work tzdata==2023.4 umap-learn==0.5.1 UpSetPlot==0.6.1 urllib3 @ file:///croot/urllib3_1698257533958/work wcwidth @ file:///Users/ktietz/demo/mc3/conda-bld/wcwidth_1629357192024/work webencodings==0.5.1 websocket-client @ file:///tmp/build/80754af9/websocket-client_1614804261064/work Werkzeug==0.16.1 widgetsnbextension @ file:///home/conda/feedstock_root/build_artifacts/widgetsnbextension_1605475534911/work xarray @ file:///home/conda/feedstock_root/build_artifacts/xarray_1621474818012/work xlrd==1.2.0 zict @ file:///croot/zict_1695832839030/work zipp @ file:///croot/zipp_1704206909481/work ## Access information Other publicly accessible locations of the data: [https://github.com/ZhiyuanLab/Pyoverdine-genome-mining](https://github.com/ZhiyuanLab/Pyoverdine-genome-mining)