{"data":{"id":"10.6084/m9.figshare.1092532","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1092532","prefix":"10.6084","suffix":"m9.figshare.1092532","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Zimmermann, Johannes","nameType":"Personal","givenName":"Johannes","familyName":"Zimmermann","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Reconstruction and Analysis of a Genome-wide Metabolic Model of Sulfurospirillum multivorans"}],"publisher":"figshare","container":{},"publicationYear":2014,"subjects":[{"subject":"60114 Systems Biology","subjectScheme":"FOR"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Microbiology"}],"contributors":[],"dates":[{"date":"2014-07-03","dateType":"Created"},{"date":"2014-07-03","dateType":"Updated"},{"date":"2014","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":["3583614 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"\u003cstrong\u003eSupplementary information\u003c/strong\u003e \u003cstrong\u003e\u003cbr\u003e\u003c/strong\u003e \u003cstrong\u003erec_progress.csv - \u003c/strong\u003eManual curation documentation \u003cstrong\u003ecyc_access.py - \u003c/strong\u003elib for cyc2sbml \u003cstrong\u003ecyc2sbml.py - \u003c/strong\u003epython script to export data from pathwaytools to sbml \u003cstrong\u003esm.xml - \u003c/strong\u003esbml model of S. multivorans (bounds are set to a growth with 20mM pyruvate and 5% oxygen) \u003cstrong\u003esmul-26_extended.xml - \u003c/strong\u003eraw sbml model of S. multivorans (has to be complemented and run by test.py) \u003cstrong\u003etest.py - \u003c/strong\u003epython script to read, complement and simulate the sbml model of S. multivorans The recently sequenced and annotated genome of Sulfurospirillum multivorans provides insight into a versatile metabolism. For instance, S. multivorans can mediate organohalide respiration which is a useful bioremediation process to degrade carcinogens like tetra chloroethene. Furthermore, a wide range of of electron donor oxidizing and electron acceptor reducing enzymes was identi?ed in S. multivorans and even oxygen can be used as terminal electron acceptor which is unusual for organohalide respiring organisms. Herein, I want to present a metabolic reconstruction of S. multivorans based on the genome annotation and experimental as well as expert knowledge. In total, it accounts for 761 metabolic genes, 1266 reactions and 995 metabolites. The reconstruction was used to derive a computational model of the metabolism of S. multivorans: Given a certain growth condition, a method called Flux Balance Analysis was applied to predict reaction flows in mmol g^−1 h−1 (gram dry weight) for each reconstructed reaction. Thus, a set of active reactions can be inferred that enables a specific phenotype. Simulations were compared to experimental findings and suggestions for open research topics (carbon unbalance) were made.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"PD94bWwgdmVyc2lvbj0iMS4wIiBlbmNvZGluZz0iVVRGLTgiPz4KPHJlc291cmNlIHhtbG5zPSJodHRwOi8vZGF0YWNpdGUub3JnL3NjaGVtYS9rZXJuZWwtNCIgeG1sbnM6eHNpPSJodHRwOi8vd3d3LnczLm9yZy8yMDAxL1hNTFNjaGVtYS1pbnN0YW5jZSIgeHNpOnNjaGVtYUxvY2F0aW9uPSJodHRwOi8vZGF0YWNpdGUub3JnL3NjaGVtYS9rZXJuZWwtNCBodHRwOi8vc2NoZW1hLmRhdGFjaXRlLm9yZy9tZXRhL2tlcm5lbC00LjEvbWV0YWRhdGEueHNkIj4KICA8aWRlbnRpZmllciBpZGVudGlmaWVyVHlwZT0iRE9JIj4xMC42MDg0L005LkZJR1NIQVJFLjEwOTI1MzI8L2lkZW50aWZpZXI+CiAgPGNyZWF0b3JzPgogICAgPGNyZWF0b3I+CiAgICAgIDxjcmVhdG9yTmFtZT5Kb2hhbm5lcyBaaW1tZXJtYW5uPC9jcmVhdG9yTmFtZT4KICAgIDwvY3JlYXRvcj4KICA8L2NyZWF0b3JzPgogIDx0aXRsZXM+CiAgICA8dGl0bGU+UmVjb25zdHJ1Y3Rpb24gYW5kIEFuYWx5c2lzIG9mIGEgR2Vub21lLXdpZGUgTWV0YWJvbGljIE1vZGVsIG9mIFN1bGZ1cm9zcGlyaWxsdW0gbXVsdGl2b3JhbnM8L3RpdGxlPgogIDwvdGl0bGVzPgogIDxkZXNjcmlwdGlvbnM+CiAgICA8ZGVzY3JpcHRpb24gZGVzY3JpcHRpb25UeXBlPSJBYnN0cmFjdCI+Jmx0O3AmZ3Q7Jmx0O3N0cm9uZyZndDtTdXBwbGVtZW50YXJ5IGluZm9ybWF0aW9uJmx0Oy9zdHJvbmcmZ3Q7Jmx0Oy9wJmd0OwombHQ7cCZndDsmbHQ7c3Ryb25nJmd0OyZsdDticiZndDsmbHQ7L3N0cm9uZyZndDsmbHQ7L3AmZ3Q7CiZsdDtwJmd0OyZsdDtzdHJvbmcmZ3Q7cmVjX3Byb2dyZXNzLmNzdiAtwqAmbHQ7L3N0cm9uZyZndDtNYW51YWwgY3VyYXRpb24gZG9jdW1lbnRhdGlvbiZsdDsvcCZndDsKJmx0O3AmZ3Q7Jmx0O3N0cm9uZyZndDtjeWNfYWNjZXNzLnB5IC3CoCZsdDsvc3Ryb25nJmd0O2xpYiBmb3IgY3ljMnNibWwmbHQ7L3AmZ3Q7CiZsdDtwJmd0OyZsdDtzdHJvbmcmZ3Q7Y3ljMnNibWwucHkgLcKgJmx0Oy9zdHJvbmcmZ3Q7cHl0aG9uIHNjcmlwdCB0byBleHBvcnQgZGF0YSBmcm9tIHBhdGh3YXl0b29scyB0byBzYm1sJmx0Oy9wJmd0OwombHQ7cCZndDsmbHQ7c3Ryb25nJmd0O3NtLnhtbCAtwqAmbHQ7L3N0cm9uZyZndDtzYm1sIG1vZGVsIG9mIFMuIG11bHRpdm9yYW5zIChib3VuZHMgYXJlIHNldCB0byBhIGdyb3d0aCB3aXRoIDIwbU0gcHlydXZhdGUgYW5kIDUlIG94eWdlbikmbHQ7L3AmZ3Q7CiZsdDtwJmd0OyZsdDtzdHJvbmcmZ3Q7c211bC0yNl9leHRlbmRlZC54bWwgLcKgJmx0Oy9zdHJvbmcmZ3Q7cmF3IHNibWwgbW9kZWwgb2YgUy4gbXVsdGl2b3JhbnMgKGhhcyB0byBiZSBjb21wbGVtZW50ZWQgYW5kIHJ1biBieSB0ZXN0LnB5KSZsdDsvcCZndDsKJmx0O3AmZ3Q7Jmx0O3N0cm9uZyZndDt0ZXN0LnB5IC3CoCZsdDsvc3Ryb25nJmd0O3B5dGhvbiBzY3JpcHQgdG8gcmVhZCwgY29tcGxlbWVudCBhbmQgc2ltdWxhdGUgdGhlIHNibWwgbW9kZWwgb2YgUy4gbXVsdGl2b3JhbnMmbHQ7L3AmZ3Q7CiZsdDtwJmd0O8KgJmx0Oy9wJmd0OwombHQ7cCZndDvCoCZsdDsvcCZndDsKJmx0O3AmZ3Q7VGhlIHJlY2VudGx5IHNlcXVlbmNlZCBhbmQgYW5ub3RhdGVkIGdlbm9tZSBvZiBTdWxmdXJvc3BpcmlsbHVtIG11bHRpdm9yYW5zIHByb3ZpZGVzIGluc2lnaHQgaW50byBhIHZlcnNhdGlsZSBtZXRhYm9saXNtLiBGb3IgaW5zdGFuY2UsIFMuIG11bHRpdm9yYW5zIGNhbiBtZWRpYXRlIG9yZ2Fub2hhbGlkZSByZXNwaXJhdGlvbiB3aGljaCBpcyBhIHVzZWZ1bCBiaW9yZW1lZGlhdGlvbiBwcm9jZXNzIHRvIGRlZ3JhZGUgY2FyY2lub2dlbnMgbGlrZSB0ZXRyYSBjaGxvcm9ldGhlbmUuIEZ1cnRoZXJtb3JlLCBhIHdpZGUgcmFuZ2Ugb2Ygb2YgZWxlY3Ryb24gZG9ub3Igb3hpZGl6aW5nIGFuZCBlbGVjdHJvbiBhY2NlcHRvciByZWR1Y2luZyBlbnp5bWVzIHdhcyBpZGVudGk/ZWQgaW4gUy4gbXVsdGl2b3JhbnMgYW5kIGV2ZW4gb3h5Z2VuIGNhbiBiZSB1c2VkIGFzIHRlcm1pbmFsIGVsZWN0cm9uIGFjY2VwdG9yIHdoaWNoIGlzIHVudXN1YWwgZm9yIG9yZ2Fub2hhbGlkZSByZXNwaXJpbmcgb3JnYW5pc21zLiBIZXJlaW4sIEkgd2FudCB0byBwcmVzZW50IGEgbWV0YWJvbGljIHJlY29uc3RydWN0aW9uIG9mIFMuIG11bHRpdm9yYW5zIGJhc2VkIG9uIHRoZSBnZW5vbWUgYW5ub3RhdGlvbiBhbmQgZXhwZXJpbWVudGFsIGFzIHdlbGwgYXMgZXhwZXJ0IGtub3dsZWRnZS4gSW4gdG90YWwsIGl0IGFjY291bnRzIGZvciA3NjEgbWV0YWJvbGljIGdlbmVzLCAxMjY2IHJlYWN0aW9ucyBhbmQgOTk1IG1ldGFib2xpdGVzLiBUaGUgcmVjb25zdHJ1Y3Rpb24gd2FzIHVzZWQgdG8gZGVyaXZlIGEgY29tcHV0YXRpb25hbCBtb2RlbCBvZiB0aGUgbWV0YWJvbGlzbSBvZiBTLiBtdWx0aXZvcmFuczogR2l2ZW4gYSBjZXJ0YWluIGdyb3d0aCBjb25kaXRpb24sIGEgbWV0aG9kIGNhbGxlZCBGbHV4IEJhbGFuY2UgQW5hbHlzaXMgd2FzIGFwcGxpZWQgdG8gcHJlZGljdCByZWFjdGlvbiBmbG93cyBpbiBtbW9sIGde4oiSMSBo4oiSMSAoZ3JhbSBkcnkgd2VpZ2h0KSBmb3IgZWFjaCByZWNvbnN0cnVjdGVkIHJlYWN0aW9uLiBUaHVzLCBhIHNldCBvZiBhY3RpdmUgcmVhY3Rpb25zIGNhbiBiZSBpbmZlcnJlZCB0aGF0IGVuYWJsZXMgYSBzcGVjaWZpYyBwaGVub3R5cGUuIFNpbXVsYXRpb25zIHdlcmUgY29tcGFyZWQgdG8gZXhwZXJpbWVudGFsIGZpbmRpbmdzIGFuZCBzdWdnZXN0aW9ucyBmb3Igb3BlbiByZXNlYXJjaCB0b3BpY3MgKGNhcmJvbiB1bmJhbGFuY2UpIHdlcmUgbWFkZS4mbHQ7L3AmZ3Q7PC9kZXNjcmlwdGlvbj4KICA8L2Rlc2NyaXB0aW9ucz4KICA8c3ViamVjdHM+CiAgICA8c3ViamVjdCBzY2hlbWVVUkk9Imh0dHA6Ly93d3cuYWJzLmdvdi5hdS9hdXNzdGF0cy9hYnNALm5zZi8wLzZCQjQyN0FCOTY5NkMyMjVDQTI1NzQxODAwMDQ0NjNFIiBzdWJqZWN0U2NoZW1lPSJGT1IiPjYwMTE0IFN5c3RlbXMgQmlvbG9neTwvc3ViamVjdD4KICAgIDxzdWJqZWN0Pk1pY3JvYmlvbG9neTwvc3ViamVjdD4KICA8L3N1YmplY3RzPgogIDxwdWJsaXNoZXI+Zmlnc2hhcmU8L3B1Ymxpc2hlcj4KICA8cHVibGljYXRpb25ZZWFyPjIwMTQ8L3B1YmxpY2F0aW9uWWVhcj4KICA8ZGF0ZXM+CiAgICA8ZGF0ZSBkYXRlVHlwZT0iQ3JlYXRlZCI+MjAxNC0wNy0wMzwvZGF0ZT4KICAgIDxkYXRlIGRhdGVUeXBlPSJVcGRhdGVkIj4yMDE0LTA3LTAzPC9kYXRlPgogIDwvZGF0ZXM+CiAgPHJlc291cmNlVHlwZSByZXNvdXJjZVR5cGVHZW5lcmFsPSJEYXRhc2V0Ij5EYXRhc2V0PC9yZXNvdXJjZVR5cGU+CiAgPHNpemVzPgogICAgPHNpemU+MzU4MzYxNCBCeXRlczwvc2l6ZT4KICA8L3NpemVzPgogIDxyaWdodHNMaXN0PgogICAgPHJpZ2h0cyByaWdodHNVUkk9Imh0dHBzOi8vY3JlYXRpdmVjb21tb25zLm9yZy9saWNlbnNlcy9ieS80LjAvIj5DQyBCWSA0LjA8L3JpZ2h0cz4KICA8L3JpZ2h0c0xpc3Q+CjwvcmVzb3VyY2U+","url":"https://figshare.com/articles/dataset/Reconstruction_and_Analysis_of_a_Genome_wide_Metabolic_Model_of_Sulfurospirillum_multivorans/1092532","contentUrl":null,"metadataVersion":1,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds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