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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Three Genomes from the Phylum <italic>Acidobacteria</italic> Provide Insight into the Lifestyles of These Microorganisms in Soils<xref ref-type="fn" rid="fn4">▿</xref> <xref ref-type="fn" rid="fn3">†</xref> </title><author><name sortKey="Ward, Naomi L" sort="Ward, Naomi L" uniqKey="Ward N" first="Naomi L." last="Ward">Naomi L. Ward</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Challacombe, Jean F" sort="Challacombe, Jean F" uniqKey="Challacombe J" first="Jean F." last="Challacombe">Jean F. Challacombe</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Janssen, Peter H" sort="Janssen, Peter H" uniqKey="Janssen P" first="Peter H." last="Janssen">Peter H. Janssen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Henrissat, Bernard" sort="Henrissat, Bernard" uniqKey="Henrissat B" first="Bernard" last="Henrissat">Bernard Henrissat</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Coutinho, Pedro M" sort="Coutinho, Pedro M" uniqKey="Coutinho P" first="Pedro M." last="Coutinho">Pedro M. Coutinho</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Wu, Martin" sort="Wu, Martin" uniqKey="Wu M" first="Martin" last="Wu">Martin Wu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Xie, Gary" sort="Xie, Gary" uniqKey="Xie G" first="Gary" last="Xie">Gary Xie</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Haft, Daniel H" sort="Haft, Daniel H" uniqKey="Haft D" first="Daniel H." last="Haft">Daniel H. Haft</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Sait, Michelle" sort="Sait, Michelle" uniqKey="Sait M" first="Michelle" last="Sait">Michelle Sait</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Badger, Jonathan" sort="Badger, Jonathan" uniqKey="Badger J" first="Jonathan" last="Badger">Jonathan Badger</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Barabote, Ravi D" sort="Barabote, Ravi D" uniqKey="Barabote R" first="Ravi D." last="Barabote">Ravi D. Barabote</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Bradley, Brent" sort="Bradley, Brent" uniqKey="Bradley B" first="Brent" last="Bradley">Brent Bradley</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Brettin, Thomas S" sort="Brettin, Thomas S" uniqKey="Brettin T" first="Thomas S." last="Brettin">Thomas S. Brettin</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Brinkac, Lauren M" sort="Brinkac, Lauren M" uniqKey="Brinkac L" first="Lauren M." last="Brinkac">Lauren M. Brinkac</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Bruce, David" sort="Bruce, David" uniqKey="Bruce D" first="David" last="Bruce">David Bruce</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Creasy, Todd" sort="Creasy, Todd" uniqKey="Creasy T" first="Todd" last="Creasy">Todd Creasy</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Daugherty, Sean C" sort="Daugherty, Sean C" uniqKey="Daugherty S" first="Sean C." last="Daugherty">Sean C. Daugherty</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Davidsen, Tanja M" sort="Davidsen, Tanja M" uniqKey="Davidsen T" first="Tanja M." last="Davidsen">Tanja M. Davidsen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Deboy, Robert T" sort="Deboy, Robert T" uniqKey="Deboy R" first="Robert T." last="Deboy">Robert T. Deboy</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Detter, J Chris" sort="Detter, J Chris" uniqKey="Detter J" first="J. Chris" last="Detter">J. Chris Detter</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Dodson, Robert J" sort="Dodson, Robert J" uniqKey="Dodson R" first="Robert J." last="Dodson">Robert J. Dodson</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Durkin, A Scott" sort="Durkin, A Scott" uniqKey="Durkin A" first="A. Scott" last="Durkin">A. Scott Durkin</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Ganapathy, Anuradha" sort="Ganapathy, Anuradha" uniqKey="Ganapathy A" first="Anuradha" last="Ganapathy">Anuradha Ganapathy</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Gwinn Giglio, Michelle" sort="Gwinn Giglio, Michelle" uniqKey="Gwinn Giglio M" first="Michelle" last="Gwinn-Giglio">Michelle Gwinn-Giglio</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Han, Cliff S" sort="Han, Cliff S" uniqKey="Han C" first="Cliff S." last="Han">Cliff S. Han</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Khouri, Hoda" sort="Khouri, Hoda" uniqKey="Khouri H" first="Hoda" last="Khouri">Hoda Khouri</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Kiss, Hajnalka" sort="Kiss, Hajnalka" uniqKey="Kiss H" first="Hajnalka" last="Kiss">Hajnalka Kiss</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Kothari, Sagar P" sort="Kothari, Sagar P" uniqKey="Kothari S" first="Sagar P." last="Kothari">Sagar P. Kothari</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Madupu, Ramana" sort="Madupu, Ramana" uniqKey="Madupu R" first="Ramana" last="Madupu">Ramana Madupu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Nelson, Karen E" sort="Nelson, Karen E" uniqKey="Nelson K" first="Karen E." last="Nelson">Karen E. Nelson</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Nelson, William C" sort="Nelson, William C" uniqKey="Nelson W" first="William C." last="Nelson">William C. Nelson</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Paulsen, Ian" sort="Paulsen, Ian" uniqKey="Paulsen I" first="Ian" last="Paulsen">Ian Paulsen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Penn, Kevin" sort="Penn, Kevin" uniqKey="Penn K" first="Kevin" last="Penn">Kevin Penn</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Ren, Qinghu" sort="Ren, Qinghu" uniqKey="Ren Q" first="Qinghu" last="Ren">Qinghu Ren</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Rosovitz, M J" sort="Rosovitz, M J" uniqKey="Rosovitz M" first="M. J." last="Rosovitz">M. J. Rosovitz</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Selengut, Jeremy D" sort="Selengut, Jeremy D" uniqKey="Selengut J" first="Jeremy D." last="Selengut">Jeremy D. Selengut</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Shrivastava, Susmita" sort="Shrivastava, Susmita" uniqKey="Shrivastava S" first="Susmita" last="Shrivastava">Susmita Shrivastava</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Sullivan, Steven A" sort="Sullivan, Steven A" uniqKey="Sullivan S" first="Steven A." last="Sullivan">Steven A. Sullivan</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Tapia, Roxanne" sort="Tapia, Roxanne" uniqKey="Tapia R" first="Roxanne" last="Tapia">Roxanne Tapia</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Thompson, L Sue" sort="Thompson, L Sue" uniqKey="Thompson L" first="L. Sue" last="Thompson">L. Sue Thompson</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Watkins, Kisha L" sort="Watkins, Kisha L" uniqKey="Watkins K" first="Kisha L." last="Watkins">Kisha L. Watkins</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Yang, Qi" sort="Yang, Qi" uniqKey="Yang Q" first="Qi" last="Yang">Qi Yang</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Yu, Chunhui" sort="Yu, Chunhui" uniqKey="Yu C" first="Chunhui" last="Yu">Chunhui Yu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zafar, Nikhat" sort="Zafar, Nikhat" uniqKey="Zafar N" first="Nikhat" last="Zafar">Nikhat Zafar</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zhou, Liwei" sort="Zhou, Liwei" uniqKey="Zhou L" first="Liwei" last="Zhou">Liwei Zhou</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Kuske, Cheryl R" sort="Kuske, Cheryl R" uniqKey="Kuske C" first="Cheryl R." last="Kuske">Cheryl R. Kuske</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">19201974</idno><idno type="pmc">2663196</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2663196</idno><idno type="RBID">PMC:2663196</idno><idno type="doi">10.1128/AEM.02294-08</idno><date when="2009">2009</date><idno type="wicri:Area/Pmc/Corpus">000F55</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000F55</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Three Genomes from the Phylum <italic>Acidobacteria</italic> Provide Insight into the Lifestyles of These Microorganisms in Soils<xref ref-type="fn" rid="fn4">▿</xref> <xref ref-type="fn" rid="fn3">†</xref> </title><author><name sortKey="Ward, Naomi L" sort="Ward, Naomi L" uniqKey="Ward N" first="Naomi L." last="Ward">Naomi L. Ward</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Challacombe, Jean F" sort="Challacombe, Jean F" uniqKey="Challacombe J" first="Jean F." last="Challacombe">Jean F. Challacombe</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Janssen, Peter H" sort="Janssen, Peter H" uniqKey="Janssen P" first="Peter H." last="Janssen">Peter H. Janssen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Henrissat, Bernard" sort="Henrissat, Bernard" uniqKey="Henrissat B" first="Bernard" last="Henrissat">Bernard Henrissat</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Coutinho, Pedro M" sort="Coutinho, Pedro M" uniqKey="Coutinho P" first="Pedro M." last="Coutinho">Pedro M. Coutinho</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Wu, Martin" sort="Wu, Martin" uniqKey="Wu M" first="Martin" last="Wu">Martin Wu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Xie, Gary" sort="Xie, Gary" uniqKey="Xie G" first="Gary" last="Xie">Gary Xie</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Haft, Daniel H" sort="Haft, Daniel H" uniqKey="Haft D" first="Daniel H." last="Haft">Daniel H. Haft</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Sait, Michelle" sort="Sait, Michelle" uniqKey="Sait M" first="Michelle" last="Sait">Michelle Sait</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Badger, Jonathan" sort="Badger, Jonathan" uniqKey="Badger J" first="Jonathan" last="Badger">Jonathan Badger</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Barabote, Ravi D" sort="Barabote, Ravi D" uniqKey="Barabote R" first="Ravi D." last="Barabote">Ravi D. Barabote</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Bradley, Brent" sort="Bradley, Brent" uniqKey="Bradley B" first="Brent" last="Bradley">Brent Bradley</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Brettin, Thomas S" sort="Brettin, Thomas S" uniqKey="Brettin T" first="Thomas S." last="Brettin">Thomas S. Brettin</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Brinkac, Lauren M" sort="Brinkac, Lauren M" uniqKey="Brinkac L" first="Lauren M." last="Brinkac">Lauren M. Brinkac</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Bruce, David" sort="Bruce, David" uniqKey="Bruce D" first="David" last="Bruce">David Bruce</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Creasy, Todd" sort="Creasy, Todd" uniqKey="Creasy T" first="Todd" last="Creasy">Todd Creasy</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Daugherty, Sean C" sort="Daugherty, Sean C" uniqKey="Daugherty S" first="Sean C." last="Daugherty">Sean C. Daugherty</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Davidsen, Tanja M" sort="Davidsen, Tanja M" uniqKey="Davidsen T" first="Tanja M." last="Davidsen">Tanja M. Davidsen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Deboy, Robert T" sort="Deboy, Robert T" uniqKey="Deboy R" first="Robert T." last="Deboy">Robert T. Deboy</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Detter, J Chris" sort="Detter, J Chris" uniqKey="Detter J" first="J. Chris" last="Detter">J. Chris Detter</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Dodson, Robert J" sort="Dodson, Robert J" uniqKey="Dodson R" first="Robert J." last="Dodson">Robert J. Dodson</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Durkin, A Scott" sort="Durkin, A Scott" uniqKey="Durkin A" first="A. Scott" last="Durkin">A. Scott Durkin</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Ganapathy, Anuradha" sort="Ganapathy, Anuradha" uniqKey="Ganapathy A" first="Anuradha" last="Ganapathy">Anuradha Ganapathy</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Gwinn Giglio, Michelle" sort="Gwinn Giglio, Michelle" uniqKey="Gwinn Giglio M" first="Michelle" last="Gwinn-Giglio">Michelle Gwinn-Giglio</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Han, Cliff S" sort="Han, Cliff S" uniqKey="Han C" first="Cliff S." last="Han">Cliff S. Han</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Khouri, Hoda" sort="Khouri, Hoda" uniqKey="Khouri H" first="Hoda" last="Khouri">Hoda Khouri</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Kiss, Hajnalka" sort="Kiss, Hajnalka" uniqKey="Kiss H" first="Hajnalka" last="Kiss">Hajnalka Kiss</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Kothari, Sagar P" sort="Kothari, Sagar P" uniqKey="Kothari S" first="Sagar P." last="Kothari">Sagar P. Kothari</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Madupu, Ramana" sort="Madupu, Ramana" uniqKey="Madupu R" first="Ramana" last="Madupu">Ramana Madupu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Nelson, Karen E" sort="Nelson, Karen E" uniqKey="Nelson K" first="Karen E." last="Nelson">Karen E. Nelson</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Nelson, William C" sort="Nelson, William C" uniqKey="Nelson W" first="William C." last="Nelson">William C. Nelson</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Paulsen, Ian" sort="Paulsen, Ian" uniqKey="Paulsen I" first="Ian" last="Paulsen">Ian Paulsen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Penn, Kevin" sort="Penn, Kevin" uniqKey="Penn K" first="Kevin" last="Penn">Kevin Penn</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Ren, Qinghu" sort="Ren, Qinghu" uniqKey="Ren Q" first="Qinghu" last="Ren">Qinghu Ren</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Rosovitz, M J" sort="Rosovitz, M J" uniqKey="Rosovitz M" first="M. J." last="Rosovitz">M. J. Rosovitz</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Selengut, Jeremy D" sort="Selengut, Jeremy D" uniqKey="Selengut J" first="Jeremy D." last="Selengut">Jeremy D. Selengut</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Shrivastava, Susmita" sort="Shrivastava, Susmita" uniqKey="Shrivastava S" first="Susmita" last="Shrivastava">Susmita Shrivastava</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Sullivan, Steven A" sort="Sullivan, Steven A" uniqKey="Sullivan S" first="Steven A." last="Sullivan">Steven A. Sullivan</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Tapia, Roxanne" sort="Tapia, Roxanne" uniqKey="Tapia R" first="Roxanne" last="Tapia">Roxanne Tapia</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Thompson, L Sue" sort="Thompson, L Sue" uniqKey="Thompson L" first="L. Sue" last="Thompson">L. Sue Thompson</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Watkins, Kisha L" sort="Watkins, Kisha L" uniqKey="Watkins K" first="Kisha L." last="Watkins">Kisha L. Watkins</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Yang, Qi" sort="Yang, Qi" uniqKey="Yang Q" first="Qi" last="Yang">Qi Yang</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Yu, Chunhui" sort="Yu, Chunhui" uniqKey="Yu C" first="Chunhui" last="Yu">Chunhui Yu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zafar, Nikhat" sort="Zafar, Nikhat" uniqKey="Zafar N" first="Nikhat" last="Zafar">Nikhat Zafar</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zhou, Liwei" sort="Zhou, Liwei" uniqKey="Zhou L" first="Liwei" last="Zhou">Liwei Zhou</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Kuske, Cheryl R" sort="Kuske, Cheryl R" uniqKey="Kuske C" first="Cheryl R." last="Kuske">Cheryl R. Kuske</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">Applied and Environmental Microbiology</title><idno type="ISSN">0099-2240</idno><idno type="eISSN">1098-5336</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The complete genomes of three strains from the phylum <italic>Acidobacteria</italic> were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the <italic>Proteobacteria</italic>, the <italic>Cyanobacteria</italic>, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N<sub>2</sub> fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Appl Environ Microbiol</journal-id><journal-id journal-id-type="publisher-id">aem</journal-id><journal-title>Applied and Environmental Microbiology</journal-title><issn pub-type="ppub">0099-2240</issn><issn pub-type="epub">1098-5336</issn><publisher><publisher-name>American Society for Microbiology (ASM)</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">19201974</article-id><article-id pub-id-type="pmc">2663196</article-id><article-id pub-id-type="publisher-id">2294-08</article-id><article-id pub-id-type="doi">10.1128/AEM.02294-08</article-id><article-categories><subj-group subj-group-type="heading"><subject>Evolutionary and Genomic Microbiology</subject></subj-group></article-categories><title-group><article-title>Three Genomes from the Phylum <italic>Acidobacteria</italic> Provide Insight into the Lifestyles of These Microorganisms in Soils<xref ref-type="fn" rid="fn4">▿</xref> <xref ref-type="fn" rid="fn3">†</xref> </article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Ward</surname><given-names>Naomi L.</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff1">2</xref><xref ref-type="fn" rid="fn1">‡</xref></contrib><contrib contrib-type="author"><name><surname>Challacombe</surname><given-names>Jean F.</given-names></name><xref ref-type="aff" rid="aff1">3</xref><xref ref-type="aff" rid="aff1">4</xref></contrib><contrib contrib-type="author"><name><surname>Janssen</surname><given-names>Peter H.</given-names></name><xref ref-type="aff" rid="aff1">5</xref><xref ref-type="aff" rid="aff1">6</xref></contrib><contrib contrib-type="author"><name><surname>Henrissat</surname><given-names>Bernard</given-names></name><xref ref-type="aff" rid="aff1">7</xref></contrib><contrib contrib-type="author"><name><surname>Coutinho</surname><given-names>Pedro M.</given-names></name><xref ref-type="aff" rid="aff1">7</xref></contrib><contrib contrib-type="author"><name><surname>Wu</surname><given-names>Martin</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="fn2">§</xref></contrib><contrib contrib-type="author"><name><surname>Xie</surname><given-names>Gary</given-names></name><xref ref-type="aff" rid="aff1">3</xref><xref ref-type="aff" rid="aff1">4</xref></contrib><contrib contrib-type="author"><name><surname>Haft</surname><given-names>Daniel H.</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Sait</surname><given-names>Michelle</given-names></name><xref ref-type="aff" rid="aff1">5</xref><xref ref-type="fn" rid="fn2">§</xref></contrib><contrib contrib-type="author"><name><surname>Badger</surname><given-names>Jonathan</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Barabote</surname><given-names>Ravi D.</given-names></name><xref ref-type="aff" rid="aff1">3</xref><xref ref-type="aff" rid="aff1">4</xref></contrib><contrib contrib-type="author"><name><surname>Bradley</surname><given-names>Brent</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Brettin</surname><given-names>Thomas S.</given-names></name><xref ref-type="aff" rid="aff1">3</xref><xref ref-type="aff" rid="aff1">4</xref></contrib><contrib contrib-type="author"><name><surname>Brinkac</surname><given-names>Lauren M.</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Bruce</surname><given-names>David</given-names></name><xref ref-type="aff" rid="aff1">3</xref><xref ref-type="aff" rid="aff1">4</xref></contrib><contrib contrib-type="author"><name><surname>Creasy</surname><given-names>Todd</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Daugherty</surname><given-names>Sean C.</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Davidsen</surname><given-names>Tanja M.</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>DeBoy</surname><given-names>Robert T.</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Detter</surname><given-names>J. Chris</given-names></name><xref ref-type="aff" rid="aff1">3</xref><xref ref-type="aff" rid="aff1">4</xref></contrib><contrib contrib-type="author"><name><surname>Dodson</surname><given-names>Robert J.</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Durkin</surname><given-names>A. Scott</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Ganapathy</surname><given-names>Anuradha</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Gwinn-Giglio</surname><given-names>Michelle</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Han</surname><given-names>Cliff S.</given-names></name><xref ref-type="aff" rid="aff1">3</xref><xref ref-type="aff" rid="aff1">4</xref></contrib><contrib contrib-type="author"><name><surname>Khouri</surname><given-names>Hoda</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Kiss</surname><given-names>Hajnalka</given-names></name><xref ref-type="aff" rid="aff1">3</xref><xref ref-type="aff" rid="aff1">4</xref></contrib><contrib contrib-type="author"><name><surname>Kothari</surname><given-names>Sagar P.</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Madupu</surname><given-names>Ramana</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Nelson</surname><given-names>Karen E.</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Nelson</surname><given-names>William C.</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Paulsen</surname><given-names>Ian</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Penn</surname><given-names>Kevin</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Ren</surname><given-names>Qinghu</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Rosovitz</surname><given-names>M. J.</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Selengut</surname><given-names>Jeremy D.</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Shrivastava</surname><given-names>Susmita</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Sullivan</surname><given-names>Steven A.</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Tapia</surname><given-names>Roxanne</given-names></name><xref ref-type="aff" rid="aff1">3</xref><xref ref-type="aff" rid="aff1">4</xref></contrib><contrib contrib-type="author"><name><surname>Thompson</surname><given-names>L. Sue</given-names></name><xref ref-type="aff" rid="aff1">3</xref><xref ref-type="aff" rid="aff1">4</xref></contrib><contrib contrib-type="author"><name><surname>Watkins</surname><given-names>Kisha L.</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Yang</surname><given-names>Qi</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Yu</surname><given-names>Chunhui</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Zafar</surname><given-names>Nikhat</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Zhou</surname><given-names>Liwei</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Kuske</surname><given-names>Cheryl R.</given-names></name><xref ref-type="aff" rid="aff1">3</xref><xref ref-type="corresp" rid="cor1">*</xref></contrib></contrib-group><aff id="aff1">The Institute for Genomic Research, Rockville, Maryland 20850,<label>1</label> Center of Marine Biotechnology, Baltimore, Maryland 21202,<label>2</label> Bioscience Division, M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545,<label>3</label> Department of Energy Joint Genome Institute, Walnut Creek, California 94598,<label>4</label> Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia,<label>5</label> AgResearch Ltd., Palmerston North 4442, New Zealand,<label>6</label> AFMB—Centre National de la Recherche Scientifique, Universités Aix-Marseille I & II, Marseille, France<label>7</label></aff><author-notes><fn id="cor1"><label>*</label><p>Corresponding author. Mailing address: Bioscience Division, M888, Los Alamos National Laboratory, Los Alamos, NM 87545. Phone: (505) 665-4800. Fax: (505) 665-3024. E-mail: <email>kuske@lanl.gov</email></p></fn><fn id="fn1"><label>‡</label><p>Present address: Department of Molecular Biology, University of Wyoming, Laramie, WY 82071.</p></fn><fn id="fn2"><label>§</label><p>Present address: University of California Davis Genome Center, Davis, CA 95616.</p></fn></author-notes><pub-date pub-type="ppub"><month>4</month><year>2009</year></pub-date><pub-date pub-type="epub"><day>5</day><month>2</month><year>2009</year></pub-date><volume>75</volume><issue>7</issue><fpage>2046</fpage><lpage>2056</lpage><history><date date-type="received"><day>6</day><month>10</month><year>2008</year></date><date date-type="accepted"><day>22</day><month>1</month><year>2009</year></date></history><permissions><copyright-statement>Copyright © 2009, American Society for Microbiology</copyright-statement></permissions><self-uri xlink:title="pdf" xlink:href="zam00709002046.pdf"></self-uri><abstract><p>The complete genomes of three strains from the phylum <italic>Acidobacteria</italic> were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the <italic>Proteobacteria</italic>, the <italic>Cyanobacteria</italic>, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N<sub>2</sub> fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.</p></abstract></article-meta></front><floats-wrap><fig position="float" id="f1"><label>FIG. 1.</label><caption><p>Maximum-likelihood tree reconstructed with the concatenated sequences of 31 proteins, confirming the phylogenetic coherence of the acidobacteria and suggesting a deep relationship to the proteobacteria.</p></caption><graphic xlink:href="zam0070997740001"></graphic></fig><fig position="float" id="f2"><label>FIG. 2.</label><caption><p>Common and unique genes in <italic>A. capsulatum</italic>, Ellin345, and Ellin6076 obtained by bidirectional best-hit analysis of all of the protein sequences in each genome. The values in parentheses are numbers of common genes, including paralogs. Unique genes may include some paralogs within each genome. The numbers of genes in common between any two genomes may also include those that are in common among all three genomes.</p></caption><graphic xlink:href="zam0070997740002"></graphic></fig><fig position="float" id="f3"><label>FIG. 3.</label><caption><p>Neighbor-joining tree of α-glucuronidase genes from fungi and bacteria, showing the close relationship of acidobacterial and fungal genes.</p></caption><graphic xlink:href="zam0070997740003"></graphic></fig><table-wrap position="float" id="t1"><label>TABLE 1.</label><caption><p>General features of the acidobacterial genomes</p></caption><table frame="hsides" rules="groups"><thead><tr><th colspan="1" rowspan="1" align="center" valign="bottom">Strain (subdivision)</th><th colspan="1" rowspan="1" align="center" valign="bottom">Genome size (bp)</th><th colspan="1" rowspan="1" align="center" valign="bottom">% G+C (DNA base composition)</th><th colspan="1" rowspan="1" align="center" valign="bottom">No. of coding sequences</th><th colspan="1" rowspan="1" align="center" valign="bottom">% Coding</th><th colspan="1" rowspan="1" align="center" valign="bottom">No. of rRNA operons</th><th colspan="1" rowspan="1" align="center" valign="bottom">% of proteins similar to proteins of known function in other prokaryotes</th><th colspan="1" rowspan="1" align="center" valign="bottom">% Hypothetical proteins</th><th colspan="1" rowspan="1" align="center" valign="bottom">% Genes in paralogous groups</th><th colspan="1" rowspan="1" align="center" valign="bottom">No. of paralogous groups</th></tr></thead><tbody><tr><td colspan="1" rowspan="1" align="left" valign="top"><italic>A. capsulatum</italic> (1)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">4,127,496</td><td colspan="1" rowspan="1" align="char" char="." valign="top">60.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3,502</td><td colspan="1" rowspan="1" align="char" char="." valign="top">88.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">1</td><td colspan="1" rowspan="1" align="char" char="." valign="top">68</td><td colspan="1" rowspan="1" align="char" char="." valign="top">32</td><td colspan="1" rowspan="1" align="char" char="." valign="top">52.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">652</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Ellin345 (1)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">5,650,368</td><td colspan="1" rowspan="1" align="char" char="." valign="top">58.4</td><td colspan="1" rowspan="1" align="char" char="." valign="top">5,239</td><td colspan="1" rowspan="1" align="char" char="." valign="top">91</td><td colspan="1" rowspan="1" align="char" char="." valign="top">1</td><td colspan="1" rowspan="1" align="char" char="." valign="top">66</td><td colspan="1" rowspan="1" align="char" char="." valign="top">34</td><td colspan="1" rowspan="1" align="char" char="." valign="top">54.6</td><td colspan="1" rowspan="1" align="char" char="." valign="top">670</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Ellin6076 (3)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">9,965,640</td><td colspan="1" rowspan="1" align="char" char="." valign="top">61.9</td><td colspan="1" rowspan="1" align="char" char="." valign="top">8,568</td><td colspan="1" rowspan="1" align="char" char="." valign="top">90.8</td><td colspan="1" rowspan="1" align="char" char="." valign="top">2</td><td colspan="1" rowspan="1" align="char" char="." valign="top">65.2</td><td colspan="1" rowspan="1" align="char" char="." valign="top">34.8</td><td colspan="1" rowspan="1" align="char" char="." valign="top">67.9</td><td colspan="1" rowspan="1" align="char" char="." valign="top">1,128</td></tr></tbody></table></table-wrap><table-wrap position="float" id="t2"><label>TABLE 2.</label><caption><p>Predicted carbon and nitrogen cycling traits of acidobacteria</p></caption><table frame="hsides" rules="groups"><thead><tr><th colspan="1" rowspan="2" align="center" valign="middle">Substrate or property</th><th colspan="1" rowspan="2" align="center" valign="middle">Pathway</th><th colspan="3" rowspan="1" align="center" valign="bottom">Characteristic inferred from genome<xref ref-type="table-fn" rid="t2fn2"><italic>b</italic></xref><hr></hr></th></tr><tr><th colspan="1" rowspan="1" align="center" valign="bottom"><italic>A. capsulatum</italic></th><th colspan="1" rowspan="1" align="center" valign="bottom">Ellin345</th><th colspan="1" rowspan="1" align="center" valign="bottom">Ellin6076</th></tr></thead><tbody><tr><td colspan="1" rowspan="1" align="left" valign="top">Simple sugars<xref ref-type="table-fn" rid="t2fn1"><italic>a</italic></xref></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Arabinose</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> <sc>l</sc>-Arabinose</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Cellobiose</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Fructose</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Galactose</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Galacturonate</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P (1st step)</td><td colspan="1" rowspan="1" align="left" valign="top">P (1st step)<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P (1st step)<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> β-Gentiobiose</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Glucose</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Glucuronate</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P (1st step)</td><td colspan="1" rowspan="1" align="left" valign="top">P (1st step)<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P (1st step)<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Lactose</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Maltose</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">N</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Mannose</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Ribose</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Sucrose</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">P<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Amino acids</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Alanine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Arginine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Arginase<xref ref-type="table-fn" rid="t2fn4"><italic>d</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Arg degradation II</td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Arginine decarboxylase/agmatinase</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P1</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Arginine decarboxylase/agmatine deiminase</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P2</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Arginine deiminase</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Arginase 2</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">P</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Arginase 3</td><td colspan="1" rowspan="1" align="left" valign="top">P1</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P1</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Aspartate</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Asparagine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y (to OAA<xref ref-type="table-fn" rid="t2fn5"><italic>e</italic></xref>)</td><td colspan="1" rowspan="1" align="left" valign="top">Y (to PEP<xref ref-type="table-fn" rid="t2fn6"><italic>f</italic></xref>)</td><td colspan="1" rowspan="1" align="left" valign="top">Y (to OAA)</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Cysteine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">N</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Glutamate</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Glutamate to α-ketoglutarate</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Glutamate to butyrate</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Glutamate to pyruvate</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Glutamate to aspartate to fumarate</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Glutamine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Glutaminase</td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Glutamate synthase</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Glycine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Glycine cleavage system</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Glycine degradation I glycine to CO<sub>2</sub> through formate</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Histidine</td><td colspan="1" rowspan="1" align="left" valign="top">Histidine to glutamate</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Isoleucine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P1</td><td colspan="1" rowspan="1" align="left" valign="top">P1</td><td colspan="1" rowspan="1" align="left" valign="top">P1</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Leucine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P1</td><td colspan="1" rowspan="1" align="left" valign="top">P1<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P1<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Lysine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Methionine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Phenylalanine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Proline</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Serine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Threonine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Tryptophan</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Tyrosine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P2</td><td colspan="1" rowspan="1" align="left" valign="top">P2</td><td colspan="1" rowspan="1" align="left" valign="top">P2</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Valine</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Alcohols</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Butanol</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">N</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Catechol</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Ethanol</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Glycerol</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Mannitol</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Methanol</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Propanol</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P1</td><td colspan="1" rowspan="1" align="left" valign="top">P1<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P1</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Organic acids</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Acetate</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Benzoate</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">P<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Butyrate</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Formate</td><td colspan="1" rowspan="1" align="left" valign="top">Oxidation to CO<sub>2</sub></td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Glycolate</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P1</td><td colspan="1" rowspan="1" align="left" valign="top">P1<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P1</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Lactate</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P2</td><td colspan="1" rowspan="1" align="left" valign="top">Y (<sc>l</sc>-lactate)<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P2</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Tartrate</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">P1<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">P1</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Other</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Chitin</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Pectin</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Starch</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Xylan</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Cellulose</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">P</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Urea</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Nitrogen metabolism</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">N<sub>2</sub> fixation</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Nitrate reduction</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Nitrite reduction</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td><td colspan="1" rowspan="1" align="left" valign="top">Y</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Denitrification</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td><td colspan="1" rowspan="1" align="left" valign="top">N</td></tr></tbody></table><table-wrap-foot><fn id="t2fn1"><label>a</label><p>Unless stated otherwise, the results of testing the use of <sc>d</sc> isomers of sugars and <sc>l</sc> isomers of amino and organic acids are reported.</p></fn><fn id="t2fn2"><label>b</label><p>Y, characteristic found in the genome; N, characteristic not found in the genome; P, partial pathway found; P1, candidate genes for all steps are present, but some enzymes may have different activities even though sequences are similar; P2, gene sequences have not been identified for every step in the pathway, so there were no query sequences available for comparison.</p></fn><fn id="t2fn3"><label>c</label><p>Genomic trait verified by culture on that substrate (<xref ref-type="bibr" rid="r41">41</xref>, <xref ref-type="bibr" rid="r71">71</xref>).</p></fn><fn id="t2fn4"><label>d</label><p>Pathways designated according to Metacyc (<ext-link ext-link-type="uri" xlink:href="http://metacyc.org">http://metacyc.org</ext-link>).</p></fn><fn id="t2fn5"><label>e</label><p>OAA, <italic>O</italic>-acetyl acetate.</p></fn><fn id="t2fn6"><label>f</label><p>PEP, phosphoenolpyruvate.</p></fn></table-wrap-foot></table-wrap><table-wrap position="float" id="t3"><label>TABLE 3.</label><caption><p>Transporters predicted from sequence of three acidobacterial genomes</p></caption><table frame="hsides" rules="groups"><thead><tr><th colspan="1" rowspan="2" align="center" valign="middle">Transporter class</th><th colspan="3" rowspan="1" align="center" valign="bottom">Total no. of predicted transporters<xref ref-type="table-fn" rid="t3fn1"><italic>a</italic></xref><hr></hr></th></tr><tr><th colspan="1" rowspan="1" align="center" valign="bottom"><italic>A. capsulatum</italic></th><th colspan="1" rowspan="1" align="center" valign="bottom">Ellin345</th><th colspan="1" rowspan="1" align="center" valign="bottom">Ellin6076</th></tr></thead><tbody><tr><td colspan="1" rowspan="1" align="left" valign="top">Ion channels</td><td colspan="1" rowspan="1" align="char" char="." valign="top">11 (5)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">13 (7)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">12 (7)</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">ABC transporters</td><td colspan="1" rowspan="1" align="char" char="." valign="top">39 (15)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">70 (15)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">159 (21)</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Secondary porters (total)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">77 (37)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">101 (48)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">152 (57)</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Major facilitators</td><td colspan="1" rowspan="1" align="char" char="." valign="top">22 (9)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">27 (13)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">55 (17)</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Amino acid-polyamine-organocation facilitators</td><td colspan="1" rowspan="1" align="char" char="." valign="top">8 (3)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">17 (6)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">15 (5)</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Resistance-nodulation-cell division transporters</td><td colspan="1" rowspan="1" align="char" char="." valign="top">15 (3)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">12 (3)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">22 (3)</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Drug/metabolite transporters</td><td colspan="1" rowspan="1" align="char" char="." valign="top">5 (2)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">7 (3)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">6 (3)</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Multidrug/oligosaccharidyl- lipid/polysaccharide transporters</td><td colspan="1" rowspan="1" align="char" char="." valign="top">4 (3)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">4 (2)</td><td colspan="1" rowspan="1" align="char" char="." valign="top">6 (3)</td></tr></tbody></table><table-wrap-foot><fn id="t3fn1"><label>a</label><p>The total number of transporter genes in a class is followed in parentheses by the total number of transporter families found in that class for each genome.</p></fn></table-wrap-foot></table-wrap></floats-wrap></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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