https://ecoliwiki.org/colipedia/api.php?action=feedcontributions&feedformat=atom&user=Bubunenm EcoliWiki - User contributions [en] 2026-11-03T07:46:07Z User contributions MediaWiki 1.43.11 https://ecoliwiki.org/colipedia/index.php?title=Essential_genes&diff=1373902 Essential genes 2012-12-10T18:36:44Z <p>Bubunenm: /* The list (Edit this) */</p> <hr /> <div>== Introduction and caveats ==<br /> A number of studies have attempted to determine the minimum number of essential genes in ''E. coli''&lt;ref name='PMID:13129938'/&gt;&lt;ref name='PMID:16738554'/&gt;&lt;ref name='PMID:17700540'/&gt;. Although some essentiality has been rigorously tested for individual genes, much of the data comes from determining what is not essential. Any genes that were annotated after these studies were done will be missing from the supplemental data tables that list whether genes are essential or nonessential.<br /> <br /> This page displays a list of ''E. coli'' genes that '''may''' be essential. A more accurate description of this list might be &quot;Genes that have not been shown to be nonessential&quot;. The list is generated by a wiki extension that starts with the members of the Gene Lists for [[:Category:Gene List:MG1655|MG1655]] and removes<br /> * all genes where Keio deletions have been isolated, <br /> * all ins genes that are from insertion elements. <br /> === Manually curating nonessential genes ===<br /> The extension is displayed on this page between a pair of tags that allow addition of nonessential genes from manual curation. Placing a gene page name between the tags '''''removes''''' that gene from the list of candidates for essentiality.<br /> &lt;pre&gt;<br /> &lt;nowiki&gt;<br /> &lt;essentialGenes&gt;<br /> nonessential gene 1:Gene<br /> nonessential gene 2:Gene<br /> etc.<br /> &lt;/essentialGenes&gt;<br /> &lt;/nowiki&gt;<br /> &lt;/pre&gt;<br /> Manual curation so far includes:<br /> * Pseudogenes were recognized by the presence of a gene name with an underscore and a number. <br /> * tRNA genes that can be mutated to nonsense suppressors are marked as nonessential. Note that in many cases these are redundant and not all copies of a tRNA isoacceptor can be simultaneously deleted. <br /> * Similarly, although ribosomal RNA genes are not on this list, at least one of each rRNA is needed for viability.<br /> * Genes where Tn insertions were found by Gerdes et al. &lt;ref name='PMID:13129938'/&gt; were added for to the list of nonessentials.<br /> * Checking what [[PEC]] has to say about the genes<br /> * Limited checking of the literature for specific genes<br /> Community curation is still needed to improve the quality of this list.<br /> <br /> === Missing essential genes ===<br /> In some cases, the Keio collection reports a deletion strain for an essential gene. These often reflect trapping of duplications that provide a second complementing copy of the gene. To add back an essential gene, go to its gene page and edit the alleles table to remove any alleles with the PMID:16738554 code (that's how the extension recognizes the presence of the deletion strain on the list. To update the list on this page, you will need to clear the cache by clicking edit and then saving. See [[rpoD:Gene]] for an example.<br /> <br /> == The list (Edit this)==<br /> &lt;essentialGenes&gt;<br /> List nonessential gene pages here<br /> C0067:Gene<br /> C0293:Gene<br /> C0299:Gene<br /> C0343:Gene<br /> C0362:Gene<br /> C0465:Gene<br /> C0664:Gene<br /> C0719:Gene<br /> accD:Gene<br /> acpH:Gene<br /> adrA:Gene<br /> alaT:Gene<br /> alaU:Gene<br /> alaV:Gene<br /> alaW:Gene<br /> alaX:Gene<br /> araA:Gene<br /> araB:Gene<br /> araD:Gene<br /> arpB_2:Gene<br /> argQ:Gene<br /> argV:Gene<br /> argW:Gene<br /> argY:Gene<br /> argZ:Gene<br /> asnT:Gene<br /> asnU:Gene<br /> asnV:Gene<br /> asnW:Gene<br /> aspT:Gene<br /> aspU:Gene<br /> aspV:Gene<br /> bcsB:Gene<br /> csrA:Gene<br /> csrB:Gene<br /> csrC:Gene<br /> csrD:Gene<br /> cydA:Gene<br /> cydC:Gene<br /> degS:Gene<br /> dicA:Gene<br /> dicF:Gene<br /> dinQ:Gene<br /> dpiA:Gene<br /> dpiB:Gene<br /> dsbD:Gene<br /> dsrA:Gene<br /> efeU_2:Gene<br /> entD:Gene<br /> entS:Gene<br /> etk:Gene<br /> eutD:Gene<br /> eutK:Gene<br /> eutM:Gene<br /> eutR:Gene<br /> eutS:Gene<br /> fadJ:Gene<br /> fadK:Gene<br /> feoC:Gene<br /> fldA:Gene<br /> folA:Gene<br /> folD:Gene<br /> fruL:Gene<br /> ftnA:Gene<br /> ftnB:Gene<br /> ftsN:Gene<br /> ftsX:Gene<br /> gadY:Gene<br /> gapC_1:Gene<br /> gatA:Gene<br /> gatR_2:Gene<br /> gcvB:Gene<br /> gfcB:Gene<br /> ghrA:Gene<br /> ghrB:Gene<br /> glcA:Gene<br /> glnU:Gene<br /> glnV:Gene<br /> glnW:Gene<br /> glnX:Gene<br /> gltT:Gene<br /> gltU:Gene<br /> gltV:Gene<br /> gltW:Gene<br /> glyU:Gene<br /> glyV:Gene<br /> glyW:Gene<br /> glyX:Gene<br /> glyY:Gene<br /> gmm:Gene<br /> gpsA:Gene<br /> gsp:Gene<br /> gspB:Gene<br /> gsiA:Gene<br /> gsiB:Gene<br /> gsiD:Gene<br /> hflB:Gene<br /> hofM:Gene<br /> hspQ:Gene<br /> ileT:Gene<br /> ileU:Gene<br /> ileV:Gene<br /> ileX:Gene<br /> ileY:Gene<br /> ilvG_2:Gene<br /> isrA:Gene<br /> isrB:Gene<br /> isrC:Gene<br /> istR-1:Gene<br /> istR-2:Gene<br /> intZ:Gene<br /> kilR:Gene<br /> kup:Gene<br /> lafU:Gene<br /> lacZ:Gene<br /> ldrA:Gene<br /> ldrB:Gene<br /> ldrC:Gene<br /> ldrD:Gene<br /> leuP:Gene<br /> leuQ:Gene<br /> leuT:Gene<br /> leuV:Gene<br /> leuX:Gene<br /> lfhA:Gene<br /> lolA:Gene<br /> lomR_2:Gene<br /> lysT:Gene<br /> lysQ:Gene<br /> lysV:Gene<br /> lysW:Gene<br /> lysY:Gene<br /> lysZ:Gene<br /> lyx:Gene<br /> mazE:Gene<br /> mazF:Gene<br /> mdtQ:Gene<br /> metT:Gene<br /> metU:Gene<br /> metV:Gene<br /> metW:Gene<br /> metY:Gene<br /> metZ:Gene<br /> micA:Gene<br /> micC:Gene<br /> micF:Gene<br /> minD:Gene<br /> minE:Gene<br /> mnmG:Gene<br /> mokB:Gene<br /> mokC:Gene<br /> mraY:Gene<br /> mreD:Gene<br /> molR_3:Gene<br /> mug:Gene<br /> murA:Gene<br /> murB:Gene<br /> murF:Gene<br /> nadD:Gene<br /> nepI:Gene<br /> omrA:Gene<br /> omrB:Gene<br /> oriC:Gene<br /> orn:Gene<br /> oxyS:Gene<br /> pagP:Gene<br /> pgmB:Gene<br /> pheU:Gene<br /> pheV:Gene<br /> pinE:Gene<br /> pptA:Gene<br /> proK:Gene<br /> proL:Gene<br /> psrD:Gene<br /> psrN:Gene<br /> psrO:Gene<br /> ptrA:Gene<br /> purB:Gene<br /> qmcA:Gene<br /> queC:Gene<br /> queF:Gene<br /> racR:Gene<br /> raiA:Gene<br /> ravA:Gene<br /> rcnA:Gene<br /> rdlA:Gene<br /> rdlB:Gene<br /> rdlC:Gene<br /> rdlD:Gene<br /> rhaA:Gene<br /> rhaB:Gene<br /> rhaD:Gene<br /> rhaM:Gene<br /> rimN:Gene<br /> rlmG:Gene<br /> rlmL:Gene<br /> rluE:Gene<br /> rluF:Gene<br /> rnc:Gene<br /> rnlA:Gene<br /> rpoE:Gene<br /> rplP:Gene<br /> rplV:Gene<br /> rprA:Gene<br /> rpsF:Gene<br /> rpsG:Gene<br /> rpsI:Gene<br /> rpsM:Gene<br /> rpsO:Gene<br /> rpsQ:Gene<br /> rpsT:Gene<br /> rrfA:Gene<br /> rrfB:Gene<br /> rrfC:Gene<br /> rrfD:Gene<br /> rrfE:Gene<br /> rrfF:Gene<br /> rrfG:Gene<br /> rrfH:Gene<br /> rrsA:Gene<br /> rrsB:Gene<br /> rrsC:Gene<br /> rrsD:Gene<br /> rrsE:Gene<br /> rrsF:Gene<br /> rrsG:Gene<br /> rrsH:Gene<br /> rrlA:Gene<br /> rrlB:Gene<br /> rrlC:Gene<br /> rrlD:Gene<br /> rrlE:Gene<br /> rrlF:Gene<br /> rrlG:Gene<br /> rrlH:Gene<br /> rseX:Gene<br /> rsmE:Gene<br /> rsmF:Gene<br /> rttR:Gene<br /> rutA:Gene<br /> rutD:Gene<br /> rutF:Gene<br /> rutR:Gene<br /> rybA:Gene<br /> rydB:Gene<br /> rydC:Gene<br /> ryeA:Gene<br /> ryeB:Gene<br /> ryeE:Gene<br /> rybB:Gene<br /> ryeC:Gene<br /> ryeD:Gene<br /> ryfA:Gene<br /> ryfB:Gene<br /> ryfC:Gene<br /> ryfD:Gene<br /> rygC:Gene<br /> rygD:Gene<br /> rygE:Gene<br /> ryhA:Gene<br /> ryhB:Gene<br /> ryiA:Gene<br /> glmZ:Gene<br /> ryjA:Gene<br /> ryjB:Gene<br /> ryjC:Gene<br /> selC:Gene<br /> serU:Gene<br /> serV:Gene<br /> serW:Gene<br /> serX:Gene<br /> sgrS:Gene<br /> skp:Gene<br /> sokA:Gene<br /> sokB:Gene<br /> sokC:Gene<br /> spf:Gene<br /> sraA:Gene<br /> sroA:Gene<br /> sroB:Gene<br /> sroC:Gene<br /> sroD:Gene<br /> sroF:Gene<br /> sroG:Gene<br /> sroH:Gene<br /> ssrA:Gene<br /> ssrS:Gene<br /> suhB:Gene<br /> tadA:Gene<br /> tdcF:Gene<br /> tff:Gene<br /> thrT:Gene<br /> thrV:Gene<br /> thrW:Gene<br /> tisA:Gene<br /> tisB:Gene<br /> tp2:Gene<br /> tpke70:Gene<br /> trpH:Gene<br /> tusB:Gene<br /> tusC:Gene<br /> tusD:Gene<br /> tusE:Gene<br /> tyrT:Gene<br /> tyrU:Gene<br /> tyrV:Gene<br /> ubiB:Gene<br /> ubiD:Gene<br /> uof:Gene<br /> uspB:Gene<br /> valT:Gene<br /> valU:Gene<br /> valV:Gene<br /> valW:Gene<br /> valX:Gene<br /> valY:Gene<br /> valZ:Gene<br /> ves:Gene<br /> waaU:Gene<br /> wbbL_1:Gene<br /> wzyE:Gene<br /> xni:Gene<br /> yabQ:Gene<br /> yadR:Gene<br /> yafF:Gene<br /> yagG:Gene<br /> ybhU:Gene<br /> ybfK:Gene<br /> yccB:Gene<br /> yceM:Gene<br /> ycgH_2:Gene<br /> ychE_2:Gene<br /> ychG_1:Gene<br /> ychO:Gene<br /> ychS:Gene<br /> yciY:Gene<br /> yciZ:Gene<br /> ydbA_2:Gene<br /> ydfB:Gene<br /> ydfN:Gene<br /> ydgU:Gene<br /> ydiL:Gene<br /> yedN_1:Gene<br /> yedS_3:Gene<br /> yeeL_1:Gene<br /> yefM:Gene<br /> yegZ:Gene<br /> yejM:Gene<br /> yfaS_1:Gene<br /> yfdT:Gene<br /> yffL:Gene<br /> yffN:Gene<br /> yffP:Gene<br /> yffQ:Gene<br /> yffM:Gene<br /> yffO:Gene<br /> yffR:Gene<br /> yffS:Gene<br /> ygdT:Gene<br /> ygiA:Gene<br /> ygiD:Gene<br /> ygiT:Gene<br /> yhbV:Gene<br /> yhhQ:Gene<br /> yi82_1:Gene<br /> ylbE_2:Gene<br /> yibJ:Gene<br /> yibV:Gene<br /> yigP:Gene<br /> yjgX_1:Gene<br /> yjbS:Gene<br /> yjbT:Gene<br /> yjdP:Gene<br /> yjhW:Gene<br /> yjjL:Gene<br /> ykfM:Gene<br /> ykgO:Gene<br /> ylbG:Gene<br /> ylcH:Gene<br /> ylcI:Gene<br /> yliL:Gene<br /> ymfK:Gene<br /> ymgI:Gene<br /> ymgJ:Gene<br /> yncK_2:Gene<br /> yncL:Gene<br /> yneM:Gene<br /> ynhF:Gene<br /> yoaI:Gene<br /> yojO:Gene<br /> ypaB:Gene<br /> ypfM:Gene<br /> ypjK:Gene<br /> yqgD:Gene<br /> yraL:Gene<br /> yrbB:Gene<br /> yrfF:Gene<br /> yrhD:Gene<br /> ytcA:Gene<br /> ytjA:Gene<br /> ysaA:Gene<br /> &lt;/essentialGenes&gt;<br /> <br /> == Evidence ==<br /> Add evidence for nonessentiality here:<br /> &lt;protect&gt;&lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| id=&quot;M48ae3191b3b22&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Gene!!Reference(s)!!Comments<br /> |- <br /> |<br /> [[folA]]<br /> |<br /> PMID:8423162<br /> |<br /> <br /> |- <br /> |<br /> micF<br /> |<br /> PMID:15466019<br /> |<br /> <br /> |- <br /> |<br /> rpsF, rpsI, rpsM, rpsO, rpsQ, and rpsT<br /> |<br /> PMID:17277072<br /> |<br /> precise gene knockout by recombineering <br /> |- <br /> |<br /> accD, degS, dpiA, dpiB, entD, etk,eutD, eutK, eutM, eutR, eutS, fldA, folD, ftnA, ftnB, ftsN, ftsX, gatA, glcA, gpsA, gsp, hflB, intZ, kup, lolA, lyx, mraY, mreD, mug, murA, murB, murF, nadD, pgmB, pptA, ptrA, purB, qmcA, queC, queF, raiA, ravA, rimN, rlmG, rluE, rluF, rplP, rplV, rpsG, rsmE, rsmF, rutA, trpH, ubiD, uspB, xni, yabQ, yadR, ybfK, ychO, ydiL, yejM, yffL yffN, yffP, yffQ, ygiA, ygiD, yhbV, yibJ, yigP, yjjL, ypjK, yraL, yrbB, yrfF, ysaA<br /> |<br /> PMID:13129938<br /> |<br /> accD listed as N* <br /> |- <br /> |<br /> ryeC, ryeD, rygC, rygD<br /> |<br /> PMID:18710431<br /> |<br /> <br /> |- <br /> |<br /> dsrA<br /> |<br /> PMID:8670904<br /> |<br /> <br /> |- <br /> |<br /> csrA<br /> |<br /> PMID:8366066<br /> |<br /> <br /> |- <br /> |<br /> csrB<br /> |<br /> PMID:11567002<br /> |<br /> <br /> |- <br /> |<br /> csrC<br /> |<br /> PMID:12694612<br /> |<br /> <br /> |- <br /> |<br /> csrD<br /> |<br /> PMID:16980588<br /> |<br /> <br /> |- <br /> |<br /> C0067, C0293, C0299, C0343, C0362, C0465, C0664, C0719, alaT, alaU, alaV, alaW, alaX, argQ, argV, argW, argY, argZ, asnT, asnU, asnV, asnW, aspT, aspU, aspV, bcsB, cydA, cydC, dicA, dicF, entS, fadJ, fadK, feoC,fruL, gadY,gcvB,ghrA, ghrB, glnW, gltT, gltU, gltV, gltW, glyU, glyV, glyW, glyX, glyY, gmm, gsiA, gsiB, gsiD,gspB, hofM, hspQ, isrA, isrB, isrC, kilR, ldrA, ldrB, ldrC, ldrD, leuP, leuQ, leuT, lysQ, lysV, lysW, lysY, lysZ, mdtQ, metT, metU, metV, metW, metY, metZ, micA, micC, minD, minE, mnmG, mokB, mokC, nepI, omrA, omrB, pagP, pheU, pheV, proK, proL, psrD, psrN, psrO, racR, rdlA, rdlB, rdlC, rdlD, rhaA, rhaB, rhaD, rhaM, rnc, rpoE, rprA, rseX, rutD,rutF, rutR, rybA, rydB, rydC, ryeA, ryeB, ryeE, ryfA, ryfB, ryfC, ryfD, ryhA, ryhB, ryiA, ryjA, ryjB, ryjC, selC, serW, serX, sgrS, skp, sokA, sokB, sokC, spf, sraA, sroA, sroB, sroC, sroD, sroF, sroG, sroH, ssrS, tadA, tdcF, tff, thrT, thrV, thrW, tisA, tisB, rttR, tpke70, tp2, tyrU, tyrV, ubiB<br /> valT, valU, valV, valW, valX, valY, valZ, waaU, wzyE, yafF, yagG, ybhU, yccB, ydfB, ydfN, ydgU, yffM, yffO, yffR, yffS, ygiD, ygiT, yhhQ, yibV, yjbS, yjbT, yjdP, yjhW, ykfM, ykgO, ylbG, ylcH, ylcI, yliL, ymfK, ymgI, ymgJ, yncL, yneM, ynhF, yoaI, yojO, ypaB, ypfM, yqgD, yrhD, ytcA, ytjA<br /> <br /> |<br /> <br /> |<br /> Covered by deletions (see PEC) <br /> |- <br /> |<br /> suhB<br /> |<br /> PMID:17652087<br /> |<br /> precise gene knockout by recombineering <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22&amp;page=136300&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || ||<br /> |}<br /> &lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22--&gt;&lt;/protect&gt;<br /> Add evidence for essentiality here:<br /> &lt;protect&gt;&lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| id=&quot;Y48ae47a0bea4a&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Gene!!Reference(s)!!Comments<br /> |- <br /> |<br /> nusA<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> rpoD<br /> |<br /> <br /> |<br /> Ts mutants and depletion studies <br /> |- <br /> |<br /> nusE<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> nusG<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> ffh<br /> |<br /> PMID:7559342<br /> |<br /> <br /> |- <br /> |<br /> rpsU<br /> |<br /> PMID:17277072<br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a&amp;page=136300&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || ||<br /> |}<br /> &lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a--&gt;&lt;/protect&gt;<br /> <br /> == See also ==<br /> [[Image:PEC search essentials.jpg|thumb]]<br /> * Baba et al [http://www.nature.com/msb/journal/v2/n1/suppinfo/msb4100050_S1.html supplemental data]<br /> * Gerdes et al [http://www.integratedgenomics.com/online_material/gerdes/supplementary_table.html supplemental data]<br /> * [http://www.shigen.nig.ac.jp/ecoli/pec/ PEC] ([[PEC|EcoliWiki page]]). PEC is a curated database that focuses on phenotypes of ''E. coli'' genes. To display essential genes, go to the [http://www.shigen.nig.ac.jp/ecoli/pec/genes.jsp PEC gene search] and uncheck nonessential, unknown, and Kohara phage (See figure).<br /> * Kato (2007)&lt;ref name='PMID:17700540'/&gt; identified 303 essential genes<br /> <br /> == References ==<br /> {{RefHelp}}<br /> &lt;references/&gt;</div> Bubunenm https://ecoliwiki.org/colipedia/index.php?title=Essential_genes&diff=1373901 Essential genes 2012-12-10T18:35:15Z <p>Bubunenm: /* The list (Edit this) */</p> <hr /> <div>== Introduction and caveats ==<br /> A number of studies have attempted to determine the minimum number of essential genes in ''E. coli''&lt;ref name='PMID:13129938'/&gt;&lt;ref name='PMID:16738554'/&gt;&lt;ref name='PMID:17700540'/&gt;. Although some essentiality has been rigorously tested for individual genes, much of the data comes from determining what is not essential. Any genes that were annotated after these studies were done will be missing from the supplemental data tables that list whether genes are essential or nonessential.<br /> <br /> This page displays a list of ''E. coli'' genes that '''may''' be essential. A more accurate description of this list might be &quot;Genes that have not been shown to be nonessential&quot;. The list is generated by a wiki extension that starts with the members of the Gene Lists for [[:Category:Gene List:MG1655|MG1655]] and removes<br /> * all genes where Keio deletions have been isolated, <br /> * all ins genes that are from insertion elements. <br /> === Manually curating nonessential genes ===<br /> The extension is displayed on this page between a pair of tags that allow addition of nonessential genes from manual curation. Placing a gene page name between the tags '''''removes''''' that gene from the list of candidates for essentiality.<br /> &lt;pre&gt;<br /> &lt;nowiki&gt;<br /> &lt;essentialGenes&gt;<br /> nonessential gene 1:Gene<br /> nonessential gene 2:Gene<br /> etc.<br /> &lt;/essentialGenes&gt;<br /> &lt;/nowiki&gt;<br /> &lt;/pre&gt;<br /> Manual curation so far includes:<br /> * Pseudogenes were recognized by the presence of a gene name with an underscore and a number. <br /> * tRNA genes that can be mutated to nonsense suppressors are marked as nonessential. Note that in many cases these are redundant and not all copies of a tRNA isoacceptor can be simultaneously deleted. <br /> * Similarly, although ribosomal RNA genes are not on this list, at least one of each rRNA is needed for viability.<br /> * Genes where Tn insertions were found by Gerdes et al. &lt;ref name='PMID:13129938'/&gt; were added for to the list of nonessentials.<br /> * Checking what [[PEC]] has to say about the genes<br /> * Limited checking of the literature for specific genes<br /> Community curation is still needed to improve the quality of this list.<br /> <br /> === Missing essential genes ===<br /> In some cases, the Keio collection reports a deletion strain for an essential gene. These often reflect trapping of duplications that provide a second complementing copy of the gene. To add back an essential gene, go to its gene page and edit the alleles table to remove any alleles with the PMID:16738554 code (that's how the extension recognizes the presence of the deletion strain on the list. To update the list on this page, you will need to clear the cache by clicking edit and then saving. See [[rpoD:Gene]] for an example.<br /> <br /> == The list (Edit this)==<br /> &lt;essentialGenes&gt;<br /> List nonessential gene pages here<br /> C0067:Gene<br /> C0293:Gene<br /> C0299:Gene<br /> C0343:Gene<br /> C0362:Gene<br /> C0465:Gene<br /> C0664:Gene<br /> C0719:Gene<br /> accD:Gene<br /> acpH:Gene<br /> adrA:Gene<br /> alaT:Gene<br /> alaU:Gene<br /> alaV:Gene<br /> alaW:Gene<br /> alaX:Gene<br /> araA:Gene<br /> araB:Gene<br /> araD:Gene<br /> arpB_2:Gene<br /> argQ:Gene<br /> argV:Gene<br /> argW:Gene<br /> argY:Gene<br /> argZ:Gene<br /> asnT:Gene<br /> asnU:Gene<br /> asnV:Gene<br /> asnW:Gene<br /> aspT:Gene<br /> aspU:Gene<br /> aspV:Gene<br /> bcsB:Gene<br /> csrA:Gene<br /> csrB:Gene<br /> csrC:Gene<br /> csrD:Gene<br /> cydA:Gene<br /> cydC:Gene<br /> degS:Gene<br /> dicA:Gene<br /> dicF:Gene<br /> dinQ:Gene<br /> dpiA:Gene<br /> dpiB:Gene<br /> dsbD:Gene<br /> dsrA:Gene<br /> efeU_2:Gene<br /> entD:Gene<br /> entS:Gene<br /> etk:Gene<br /> eutD:Gene<br /> eutK:Gene<br /> eutM:Gene<br /> eutR:Gene<br /> eutS:Gene<br /> fadJ:Gene<br /> fadK:Gene<br /> feoC:Gene<br /> fldA:Gene<br /> folA:Gene<br /> folD:Gene<br /> fruL:Gene<br /> ftnA:Gene<br /> ftnB:Gene<br /> ftsN:Gene<br /> ftsX:Gene<br /> gadY:Gene<br /> gapC_1:Gene<br /> gatA:Gene<br /> gatR_2:Gene<br /> gcvB:Gene<br /> gfcB:Gene<br /> ghrA:Gene<br /> ghrB:Gene<br /> glcA:Gene<br /> glnU:Gene<br /> glnV:Gene<br /> glnW:Gene<br /> glnX:Gene<br /> gltT:Gene<br /> gltU:Gene<br /> gltV:Gene<br /> gltW:Gene<br /> glyU:Gene<br /> glyV:Gene<br /> glyW:Gene<br /> glyX:Gene<br /> glyY:Gene<br /> gmm:Gene<br /> gpsA:Gene<br /> gsp:Gene<br /> gspB:Gene<br /> gsiA:Gene<br /> gsiB:Gene<br /> gsiD:Gene<br /> hflB:Gene<br /> hofM:Gene<br /> hspQ:Gene<br /> ileT:Gene<br /> ileU:Gene<br /> ileV:Gene<br /> ileX:Gene<br /> ileY:Gene<br /> ilvG_2:Gene<br /> isrA:Gene<br /> isrB:Gene<br /> isrC:Gene<br /> istR-1:Gene<br /> istR-2:Gene<br /> intZ:Gene<br /> kilR:Gene<br /> kup:Gene<br /> lafU:Gene<br /> lacZ:Gene<br /> ldrA:Gene<br /> ldrB:Gene<br /> ldrC:Gene<br /> ldrD:Gene<br /> leuP:Gene<br /> leuQ:Gene<br /> leuT:Gene<br /> leuV:Gene<br /> leuX:Gene<br /> lfhA:Gene<br /> lolA:Gene<br /> lomR_2:Gene<br /> lysT:Gene<br /> lysQ:Gene<br /> lysV:Gene<br /> lysW:Gene<br /> lysY:Gene<br /> lysZ:Gene<br /> lyx:Gene<br /> mazE:Gene<br /> mazF:Gene<br /> mdtQ:Gene<br /> metT:Gene<br /> metU:Gene<br /> metV:Gene<br /> metW:Gene<br /> metY:Gene<br /> metZ:Gene<br /> micA:Gene<br /> micC:Gene<br /> micF:Gene<br /> minD:Gene<br /> minE:Gene<br /> mnmG:Gene<br /> mokB:Gene<br /> mokC:Gene<br /> mraY:Gene<br /> mreD:Gene<br /> molR_3:Gene<br /> mug:Gene<br /> murA:Gene<br /> murB:Gene<br /> murF:Gene<br /> nadD:Gene<br /> nepI:Gene<br /> omrA:Gene<br /> omrB:Gene<br /> oriC:Gene<br /> orn:Gene<br /> oxyS:Gene<br /> pagP:Gene<br /> pgmB:Gene<br /> pheU:Gene<br /> pheV:Gene<br /> pinE:Gene<br /> pptA:Gene<br /> proK:Gene<br /> proL:Gene<br /> psrD:Gene<br /> psrN:Gene<br /> psrO:Gene<br /> ptrA:Gene<br /> purB:Gene<br /> qmcA:Gene<br /> queC:Gene<br /> queF:Gene<br /> racR:Gene<br /> raiA:Gene<br /> ravA:Gene<br /> rcnA:Gene<br /> rdlA:Gene<br /> rdlB:Gene<br /> rdlC:Gene<br /> rdlD:Gene<br /> rhaA:Gene<br /> rhaB:Gene<br /> rhaD:Gene<br /> rhaM:Gene<br /> rimN:Gene<br /> rlmG:Gene<br /> rlmL:Gene<br /> rluE:Gene<br /> rluF:Gene<br /> rnc:Gene<br /> rnlA:Gene<br /> rpoE:Gene<br /> rplP:Gene<br /> rplV:Gene<br /> rprA:Gene<br /> rpsF:Gene<br /> rpsG:Gene<br /> rpsI:Gene<br /> rpsM:Gene<br /> rpsO:Gene<br /> rpsQ:Gene<br /> rpsT:Gene<br /> rpsU: Gene<br /> rrfA:Gene<br /> rrfB:Gene<br /> rrfC:Gene<br /> rrfD:Gene<br /> rrfE:Gene<br /> rrfF:Gene<br /> rrfG:Gene<br /> rrfH:Gene<br /> rrsA:Gene<br /> rrsB:Gene<br /> rrsC:Gene<br /> rrsD:Gene<br /> rrsE:Gene<br /> rrsF:Gene<br /> rrsG:Gene<br /> rrsH:Gene<br /> rrlA:Gene<br /> rrlB:Gene<br /> rrlC:Gene<br /> rrlD:Gene<br /> rrlE:Gene<br /> rrlF:Gene<br /> rrlG:Gene<br /> rrlH:Gene<br /> rseX:Gene<br /> rsmE:Gene<br /> rsmF:Gene<br /> rttR:Gene<br /> rutA:Gene<br /> rutD:Gene<br /> rutF:Gene<br /> rutR:Gene<br /> rybA:Gene<br /> rydB:Gene<br /> rydC:Gene<br /> ryeA:Gene<br /> ryeB:Gene<br /> ryeE:Gene<br /> rybB:Gene<br /> ryeC:Gene<br /> ryeD:Gene<br /> ryfA:Gene<br /> ryfB:Gene<br /> ryfC:Gene<br /> ryfD:Gene<br /> rygC:Gene<br /> rygD:Gene<br /> rygE:Gene<br /> ryhA:Gene<br /> ryhB:Gene<br /> ryiA:Gene<br /> glmZ:Gene<br /> ryjA:Gene<br /> ryjB:Gene<br /> ryjC:Gene<br /> selC:Gene<br /> serU:Gene<br /> serV:Gene<br /> serW:Gene<br /> serX:Gene<br /> sgrS:Gene<br /> skp:Gene<br /> sokA:Gene<br /> sokB:Gene<br /> sokC:Gene<br /> spf:Gene<br /> sraA:Gene<br /> sroA:Gene<br /> sroB:Gene<br /> sroC:Gene<br /> sroD:Gene<br /> sroF:Gene<br /> sroG:Gene<br /> sroH:Gene<br /> ssrA:Gene<br /> ssrS:Gene<br /> suhB:Gene<br /> tadA:Gene<br /> tdcF:Gene<br /> tff:Gene<br /> thrT:Gene<br /> thrV:Gene<br /> thrW:Gene<br /> tisA:Gene<br /> tisB:Gene<br /> tp2:Gene<br /> tpke70:Gene<br /> trpH:Gene<br /> tusB:Gene<br /> tusC:Gene<br /> tusD:Gene<br /> tusE:Gene<br /> tyrT:Gene<br /> tyrU:Gene<br /> tyrV:Gene<br /> ubiB:Gene<br /> ubiD:Gene<br /> uof:Gene<br /> uspB:Gene<br /> valT:Gene<br /> valU:Gene<br /> valV:Gene<br /> valW:Gene<br /> valX:Gene<br /> valY:Gene<br /> valZ:Gene<br /> ves:Gene<br /> waaU:Gene<br /> wbbL_1:Gene<br /> wzyE:Gene<br /> xni:Gene<br /> yabQ:Gene<br /> yadR:Gene<br /> yafF:Gene<br /> yagG:Gene<br /> ybhU:Gene<br /> ybfK:Gene<br /> yccB:Gene<br /> yceM:Gene<br /> ycgH_2:Gene<br /> ychE_2:Gene<br /> ychG_1:Gene<br /> ychO:Gene<br /> ychS:Gene<br /> yciY:Gene<br /> yciZ:Gene<br /> ydbA_2:Gene<br /> ydfB:Gene<br /> ydfN:Gene<br /> ydgU:Gene<br /> ydiL:Gene<br /> yedN_1:Gene<br /> yedS_3:Gene<br /> yeeL_1:Gene<br /> yefM:Gene<br /> yegZ:Gene<br /> yejM:Gene<br /> yfaS_1:Gene<br /> yfdT:Gene<br /> yffL:Gene<br /> yffN:Gene<br /> yffP:Gene<br /> yffQ:Gene<br /> yffM:Gene<br /> yffO:Gene<br /> yffR:Gene<br /> yffS:Gene<br /> ygdT:Gene<br /> ygiA:Gene<br /> ygiD:Gene<br /> ygiT:Gene<br /> yhbV:Gene<br /> yhhQ:Gene<br /> yi82_1:Gene<br /> ylbE_2:Gene<br /> yibJ:Gene<br /> yibV:Gene<br /> yigP:Gene<br /> yjgX_1:Gene<br /> yjbS:Gene<br /> yjbT:Gene<br /> yjdP:Gene<br /> yjhW:Gene<br /> yjjL:Gene<br /> ykfM:Gene<br /> ykgO:Gene<br /> ylbG:Gene<br /> ylcH:Gene<br /> ylcI:Gene<br /> yliL:Gene<br /> ymfK:Gene<br /> ymgI:Gene<br /> ymgJ:Gene<br /> yncK_2:Gene<br /> yncL:Gene<br /> yneM:Gene<br /> ynhF:Gene<br /> yoaI:Gene<br /> yojO:Gene<br /> ypaB:Gene<br /> ypfM:Gene<br /> ypjK:Gene<br /> yqgD:Gene<br /> yraL:Gene<br /> yrbB:Gene<br /> yrfF:Gene<br /> yrhD:Gene<br /> ytcA:Gene<br /> ytjA:Gene<br /> ysaA:Gene<br /> &lt;/essentialGenes&gt;<br /> <br /> == Evidence ==<br /> Add evidence for nonessentiality here:<br /> &lt;protect&gt;&lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| id=&quot;M48ae3191b3b22&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Gene!!Reference(s)!!Comments<br /> |- <br /> |<br /> [[folA]]<br /> |<br /> PMID:8423162<br /> |<br /> <br /> |- <br /> |<br /> micF<br /> |<br /> PMID:15466019<br /> |<br /> <br /> |- <br /> |<br /> rpsF, rpsI, rpsM, rpsO, rpsQ, and rpsT<br /> |<br /> PMID:17277072<br /> |<br /> precise gene knockout by recombineering <br /> |- <br /> |<br /> accD, degS, dpiA, dpiB, entD, etk,eutD, eutK, eutM, eutR, eutS, fldA, folD, ftnA, ftnB, ftsN, ftsX, gatA, glcA, gpsA, gsp, hflB, intZ, kup, lolA, lyx, mraY, mreD, mug, murA, murB, murF, nadD, pgmB, pptA, ptrA, purB, qmcA, queC, queF, raiA, ravA, rimN, rlmG, rluE, rluF, rplP, rplV, rpsG, rsmE, rsmF, rutA, trpH, ubiD, uspB, xni, yabQ, yadR, ybfK, ychO, ydiL, yejM, yffL yffN, yffP, yffQ, ygiA, ygiD, yhbV, yibJ, yigP, yjjL, ypjK, yraL, yrbB, yrfF, ysaA<br /> |<br /> PMID:13129938<br /> |<br /> accD listed as N* <br /> |- <br /> |<br /> ryeC, ryeD, rygC, rygD<br /> |<br /> PMID:18710431<br /> |<br /> <br /> |- <br /> |<br /> dsrA<br /> |<br /> PMID:8670904<br /> |<br /> <br /> |- <br /> |<br /> csrA<br /> |<br /> PMID:8366066<br /> |<br /> <br /> |- <br /> |<br /> csrB<br /> |<br /> PMID:11567002<br /> |<br /> <br /> |- <br /> |<br /> csrC<br /> |<br /> PMID:12694612<br /> |<br /> <br /> |- <br /> |<br /> csrD<br /> |<br /> PMID:16980588<br /> |<br /> <br /> |- <br /> |<br /> C0067, C0293, C0299, C0343, C0362, C0465, C0664, C0719, alaT, alaU, alaV, alaW, alaX, argQ, argV, argW, argY, argZ, asnT, asnU, asnV, asnW, aspT, aspU, aspV, bcsB, cydA, cydC, dicA, dicF, entS, fadJ, fadK, feoC,fruL, gadY,gcvB,ghrA, ghrB, glnW, gltT, gltU, gltV, gltW, glyU, glyV, glyW, glyX, glyY, gmm, gsiA, gsiB, gsiD,gspB, hofM, hspQ, isrA, isrB, isrC, kilR, ldrA, ldrB, ldrC, ldrD, leuP, leuQ, leuT, lysQ, lysV, lysW, lysY, lysZ, mdtQ, metT, metU, metV, metW, metY, metZ, micA, micC, minD, minE, mnmG, mokB, mokC, nepI, omrA, omrB, pagP, pheU, pheV, proK, proL, psrD, psrN, psrO, racR, rdlA, rdlB, rdlC, rdlD, rhaA, rhaB, rhaD, rhaM, rnc, rpoE, rprA, rseX, rutD,rutF, rutR, rybA, rydB, rydC, ryeA, ryeB, ryeE, ryfA, ryfB, ryfC, ryfD, ryhA, ryhB, ryiA, ryjA, ryjB, ryjC, selC, serW, serX, sgrS, skp, sokA, sokB, sokC, spf, sraA, sroA, sroB, sroC, sroD, sroF, sroG, sroH, ssrS, tadA, tdcF, tff, thrT, thrV, thrW, tisA, tisB, rttR, tpke70, tp2, tyrU, tyrV, ubiB<br /> valT, valU, valV, valW, valX, valY, valZ, waaU, wzyE, yafF, yagG, ybhU, yccB, ydfB, ydfN, ydgU, yffM, yffO, yffR, yffS, ygiD, ygiT, yhhQ, yibV, yjbS, yjbT, yjdP, yjhW, ykfM, ykgO, ylbG, ylcH, ylcI, yliL, ymfK, ymgI, ymgJ, yncL, yneM, ynhF, yoaI, yojO, ypaB, ypfM, yqgD, yrhD, ytcA, ytjA<br /> <br /> |<br /> <br /> |<br /> Covered by deletions (see PEC) <br /> |- <br /> |<br /> suhB<br /> |<br /> PMID:17652087<br /> |<br /> precise gene knockout by recombineering <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22&amp;page=136300&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || ||<br /> |}<br /> &lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22--&gt;&lt;/protect&gt;<br /> Add evidence for essentiality here:<br /> &lt;protect&gt;&lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| id=&quot;Y48ae47a0bea4a&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Gene!!Reference(s)!!Comments<br /> |- <br /> |<br /> nusA<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> rpoD<br /> |<br /> <br /> |<br /> Ts mutants and depletion studies <br /> |- <br /> |<br /> nusE<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> nusG<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> ffh<br /> |<br /> PMID:7559342<br /> |<br /> <br /> |- <br /> |<br /> rpsU<br /> |<br /> PMID:17277072<br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a&amp;page=136300&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || ||<br /> |}<br /> &lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a--&gt;&lt;/protect&gt;<br /> <br /> == See also ==<br /> [[Image:PEC search essentials.jpg|thumb]]<br /> * Baba et al [http://www.nature.com/msb/journal/v2/n1/suppinfo/msb4100050_S1.html supplemental data]<br /> * Gerdes et al [http://www.integratedgenomics.com/online_material/gerdes/supplementary_table.html supplemental data]<br /> * [http://www.shigen.nig.ac.jp/ecoli/pec/ PEC] ([[PEC|EcoliWiki page]]). PEC is a curated database that focuses on phenotypes of ''E. coli'' genes. To display essential genes, go to the [http://www.shigen.nig.ac.jp/ecoli/pec/genes.jsp PEC gene search] and uncheck nonessential, unknown, and Kohara phage (See figure).<br /> * Kato (2007)&lt;ref name='PMID:17700540'/&gt; identified 303 essential genes<br /> <br /> == References ==<br /> {{RefHelp}}<br /> &lt;references/&gt;</div> Bubunenm https://ecoliwiki.org/colipedia/index.php?title=Essential_genes&diff=1373900 Essential genes 2012-12-10T18:26:06Z <p>Bubunenm: /* The list (Edit this) */</p> <hr /> <div>== Introduction and caveats ==<br /> A number of studies have attempted to determine the minimum number of essential genes in ''E. coli''&lt;ref name='PMID:13129938'/&gt;&lt;ref name='PMID:16738554'/&gt;&lt;ref name='PMID:17700540'/&gt;. Although some essentiality has been rigorously tested for individual genes, much of the data comes from determining what is not essential. Any genes that were annotated after these studies were done will be missing from the supplemental data tables that list whether genes are essential or nonessential.<br /> <br /> This page displays a list of ''E. coli'' genes that '''may''' be essential. A more accurate description of this list might be &quot;Genes that have not been shown to be nonessential&quot;. The list is generated by a wiki extension that starts with the members of the Gene Lists for [[:Category:Gene List:MG1655|MG1655]] and removes<br /> * all genes where Keio deletions have been isolated, <br /> * all ins genes that are from insertion elements. <br /> === Manually curating nonessential genes ===<br /> The extension is displayed on this page between a pair of tags that allow addition of nonessential genes from manual curation. Placing a gene page name between the tags '''''removes''''' that gene from the list of candidates for essentiality.<br /> &lt;pre&gt;<br /> &lt;nowiki&gt;<br /> &lt;essentialGenes&gt;<br /> nonessential gene 1:Gene<br /> nonessential gene 2:Gene<br /> etc.<br /> &lt;/essentialGenes&gt;<br /> &lt;/nowiki&gt;<br /> &lt;/pre&gt;<br /> Manual curation so far includes:<br /> * Pseudogenes were recognized by the presence of a gene name with an underscore and a number. <br /> * tRNA genes that can be mutated to nonsense suppressors are marked as nonessential. Note that in many cases these are redundant and not all copies of a tRNA isoacceptor can be simultaneously deleted. <br /> * Similarly, although ribosomal RNA genes are not on this list, at least one of each rRNA is needed for viability.<br /> * Genes where Tn insertions were found by Gerdes et al. &lt;ref name='PMID:13129938'/&gt; were added for to the list of nonessentials.<br /> * Checking what [[PEC]] has to say about the genes<br /> * Limited checking of the literature for specific genes<br /> Community curation is still needed to improve the quality of this list.<br /> <br /> === Missing essential genes ===<br /> In some cases, the Keio collection reports a deletion strain for an essential gene. These often reflect trapping of duplications that provide a second complementing copy of the gene. To add back an essential gene, go to its gene page and edit the alleles table to remove any alleles with the PMID:16738554 code (that's how the extension recognizes the presence of the deletion strain on the list. To update the list on this page, you will need to clear the cache by clicking edit and then saving. See [[rpoD:Gene]] for an example.<br /> <br /> == The list (Edit this)==<br /> &lt;essentialGenes&gt;<br /> List nonessential gene pages here<br /> C0067:Gene<br /> C0293:Gene<br /> C0299:Gene<br /> C0343:Gene<br /> C0362:Gene<br /> C0465:Gene<br /> C0664:Gene<br /> C0719:Gene<br /> accD:Gene<br /> acpH:Gene<br /> adrA:Gene<br /> alaT:Gene<br /> alaU:Gene<br /> alaV:Gene<br /> alaW:Gene<br /> alaX:Gene<br /> araA:Gene<br /> araB:Gene<br /> araD:Gene<br /> arpB_2:Gene<br /> argQ:Gene<br /> argV:Gene<br /> argW:Gene<br /> argY:Gene<br /> argZ:Gene<br /> asnT:Gene<br /> asnU:Gene<br /> asnV:Gene<br /> asnW:Gene<br /> aspT:Gene<br /> aspU:Gene<br /> aspV:Gene<br /> bcsB:Gene<br /> csrA:Gene<br /> csrB:Gene<br /> csrC:Gene<br /> csrD:Gene<br /> cydA:Gene<br /> cydC:Gene<br /> degS:Gene<br /> dicA:Gene<br /> dicF:Gene<br /> dinQ:Gene<br /> dpiA:Gene<br /> dpiB:Gene<br /> dsbD:Gene<br /> dsrA:Gene<br /> efeU_2:Gene<br /> entD:Gene<br /> entS:Gene<br /> etk:Gene<br /> eutD:Gene<br /> eutK:Gene<br /> eutM:Gene<br /> eutR:Gene<br /> eutS:Gene<br /> fadJ:Gene<br /> fadK:Gene<br /> feoC:Gene<br /> fldA:Gene<br /> folA:Gene<br /> folD:Gene<br /> fruL:Gene<br /> ftnA:Gene<br /> ftnB:Gene<br /> ftsN:Gene<br /> ftsX:Gene<br /> gadY:Gene<br /> gapC_1:Gene<br /> gatA:Gene<br /> gatR_2:Gene<br /> gcvB:Gene<br /> gfcB:Gene<br /> ghrA:Gene<br /> ghrB:Gene<br /> glcA:Gene<br /> glnU:Gene<br /> glnV:Gene<br /> glnW:Gene<br /> glnX:Gene<br /> gltT:Gene<br /> gltU:Gene<br /> gltV:Gene<br /> gltW:Gene<br /> glyU:Gene<br /> glyV:Gene<br /> glyW:Gene<br /> glyX:Gene<br /> glyY:Gene<br /> gmm:Gene<br /> gpsA:Gene<br /> gsp:Gene<br /> gspB:Gene<br /> gsiA:Gene<br /> gsiB:Gene<br /> gsiD:Gene<br /> hflB:Gene<br /> hofM:Gene<br /> hspQ:Gene<br /> ileT:Gene<br /> ileU:Gene<br /> ileV:Gene<br /> ileX:Gene<br /> ileY:Gene<br /> ilvG_2:Gene<br /> isrA:Gene<br /> isrB:Gene<br /> isrC:Gene<br /> istR-1:Gene<br /> istR-2:Gene<br /> intZ:Gene<br /> kilR:Gene<br /> kup:Gene<br /> lafU:Gene<br /> lacZ:Gene<br /> ldrA:Gene<br /> ldrB:Gene<br /> ldrC:Gene<br /> ldrD:Gene<br /> leuP:Gene<br /> leuQ:Gene<br /> leuT:Gene<br /> leuV:Gene<br /> leuX:Gene<br /> lfhA:Gene<br /> lolA:Gene<br /> lomR_2:Gene<br /> lysT:Gene<br /> lysQ:Gene<br /> lysV:Gene<br /> lysW:Gene<br /> lysY:Gene<br /> lysZ:Gene<br /> lyx:Gene<br /> mazE:Gene<br /> mazF:Gene<br /> mdtQ:Gene<br /> metT:Gene<br /> metU:Gene<br /> metV:Gene<br /> metW:Gene<br /> metY:Gene<br /> metZ:Gene<br /> micA:Gene<br /> micC:Gene<br /> micF:Gene<br /> minD:Gene<br /> minE:Gene<br /> mnmG:Gene<br /> mokB:Gene<br /> mokC:Gene<br /> mraY:Gene<br /> mreD:Gene<br /> molR_3:Gene<br /> mug:Gene<br /> murA:Gene<br /> murB:Gene<br /> murF:Gene<br /> nadD:Gene<br /> nepI:Gene<br /> omrA:Gene<br /> omrB:Gene<br /> oriC:Gene<br /> orn:Gene<br /> oxyS:Gene<br /> pagP:Gene<br /> pgmB:Gene<br /> pheU:Gene<br /> pheV:Gene<br /> pinE:Gene<br /> pptA:Gene<br /> proK:Gene<br /> proL:Gene<br /> psrD:Gene<br /> psrN:Gene<br /> psrO:Gene<br /> ptrA:Gene<br /> purB:Gene<br /> qmcA:Gene<br /> queC:Gene<br /> queF:Gene<br /> racR:Gene<br /> raiA:Gene<br /> ravA:Gene<br /> rcnA:Gene<br /> rdlA:Gene<br /> rdlB:Gene<br /> rdlC:Gene<br /> rdlD:Gene<br /> rhaA:Gene<br /> rhaB:Gene<br /> rhaD:Gene<br /> rhaM:Gene<br /> rimN:Gene<br /> rlmG:Gene<br /> rlmL:Gene<br /> rluE:Gene<br /> rluF:Gene<br /> rnc:Gene<br /> rnlA:Gene<br /> rpoE:Gene<br /> rplP:Gene<br /> rplV:Gene<br /> rprA:Gene<br /> rpsF:Gene<br /> rpsG:Gene<br /> rpsI:Gene<br /> rpsM:Gene<br /> rpsO:Gene<br /> rpsQ:Gene<br /> rpsT:Gene<br /> rrfA:Gene<br /> rrfB:Gene<br /> rrfC:Gene<br /> rrfD:Gene<br /> rrfE:Gene<br /> rrfF:Gene<br /> rrfG:Gene<br /> rrfH:Gene<br /> rrsA:Gene<br /> rrsB:Gene<br /> rrsC:Gene<br /> rrsD:Gene<br /> rrsE:Gene<br /> rrsF:Gene<br /> rrsG:Gene<br /> rrsH:Gene<br /> rrlA:Gene<br /> rrlB:Gene<br /> rrlC:Gene<br /> rrlD:Gene<br /> rrlE:Gene<br /> rrlF:Gene<br /> rrlG:Gene<br /> rrlH:Gene<br /> rseX:Gene<br /> rsmE:Gene<br /> rsmF:Gene<br /> rttR:Gene<br /> rutA:Gene<br /> rutD:Gene<br /> rutF:Gene<br /> rutR:Gene<br /> rybA:Gene<br /> rydB:Gene<br /> rydC:Gene<br /> ryeA:Gene<br /> ryeB:Gene<br /> ryeE:Gene<br /> rybB:Gene<br /> ryeC:Gene<br /> ryeD:Gene<br /> ryfA:Gene<br /> ryfB:Gene<br /> ryfC:Gene<br /> ryfD:Gene<br /> rygC:Gene<br /> rygD:Gene<br /> rygE:Gene<br /> ryhA:Gene<br /> ryhB:Gene<br /> ryiA:Gene<br /> glmZ:Gene<br /> ryjA:Gene<br /> ryjB:Gene<br /> ryjC:Gene<br /> selC:Gene<br /> serU:Gene<br /> serV:Gene<br /> serW:Gene<br /> serX:Gene<br /> sgrS:Gene<br /> skp:Gene<br /> sokA:Gene<br /> sokB:Gene<br /> sokC:Gene<br /> spf:Gene<br /> sraA:Gene<br /> sroA:Gene<br /> sroB:Gene<br /> sroC:Gene<br /> sroD:Gene<br /> sroF:Gene<br /> sroG:Gene<br /> sroH:Gene<br /> ssrA:Gene<br /> ssrS:Gene<br /> suhB:Gene<br /> tadA:Gene<br /> tdcF:Gene<br /> tff:Gene<br /> thrT:Gene<br /> thrV:Gene<br /> thrW:Gene<br /> tisA:Gene<br /> tisB:Gene<br /> tp2:Gene<br /> tpke70:Gene<br /> trpH:Gene<br /> tusB:Gene<br /> tusC:Gene<br /> tusD:Gene<br /> tusE:Gene<br /> tyrT:Gene<br /> tyrU:Gene<br /> tyrV:Gene<br /> ubiB:Gene<br /> ubiD:Gene<br /> uof:Gene<br /> uspB:Gene<br /> valT:Gene<br /> valU:Gene<br /> valV:Gene<br /> valW:Gene<br /> valX:Gene<br /> valY:Gene<br /> valZ:Gene<br /> ves:Gene<br /> waaU:Gene<br /> wbbL_1:Gene<br /> wzyE:Gene<br /> xni:Gene<br /> yabQ:Gene<br /> yadR:Gene<br /> yafF:Gene<br /> yagG:Gene<br /> ybhU:Gene<br /> ybfK:Gene<br /> yccB:Gene<br /> yceM:Gene<br /> ycgH_2:Gene<br /> ychE_2:Gene<br /> ychG_1:Gene<br /> ychO:Gene<br /> ychS:Gene<br /> yciY:Gene<br /> yciZ:Gene<br /> ydbA_2:Gene<br /> ydfB:Gene<br /> ydfN:Gene<br /> ydgU:Gene<br /> ydiL:Gene<br /> yedN_1:Gene<br /> yedS_3:Gene<br /> yeeL_1:Gene<br /> yefM:Gene<br /> yegZ:Gene<br /> yejM:Gene<br /> yfaS_1:Gene<br /> yfdT:Gene<br /> yffL:Gene<br /> yffN:Gene<br /> yffP:Gene<br /> yffQ:Gene<br /> yffM:Gene<br /> yffO:Gene<br /> yffR:Gene<br /> yffS:Gene<br /> ygdT:Gene<br /> ygiA:Gene<br /> ygiD:Gene<br /> ygiT:Gene<br /> yhbV:Gene<br /> yhhQ:Gene<br /> yi82_1:Gene<br /> ylbE_2:Gene<br /> yibJ:Gene<br /> yibV:Gene<br /> yigP:Gene<br /> yjgX_1:Gene<br /> yjbS:Gene<br /> yjbT:Gene<br /> yjdP:Gene<br /> yjhW:Gene<br /> yjjL:Gene<br /> ykfM:Gene<br /> ykgO:Gene<br /> ylbG:Gene<br /> ylcH:Gene<br /> ylcI:Gene<br /> yliL:Gene<br /> ymfK:Gene<br /> ymgI:Gene<br /> ymgJ:Gene<br /> yncK_2:Gene<br /> yncL:Gene<br /> yneM:Gene<br /> ynhF:Gene<br /> yoaI:Gene<br /> yojO:Gene<br /> ypaB:Gene<br /> ypfM:Gene<br /> ypjK:Gene<br /> yqgD:Gene<br /> yraL:Gene<br /> yrbB:Gene<br /> yrfF:Gene<br /> yrhD:Gene<br /> ytcA:Gene<br /> ytjA:Gene<br /> ysaA:Gene<br /> &lt;/essentialGenes&gt;<br /> <br /> == Evidence ==<br /> Add evidence for nonessentiality here:<br /> &lt;protect&gt;&lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| id=&quot;M48ae3191b3b22&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Gene!!Reference(s)!!Comments<br /> |- <br /> |<br /> [[folA]]<br /> |<br /> PMID:8423162<br /> |<br /> <br /> |- <br /> |<br /> micF<br /> |<br /> PMID:15466019<br /> |<br /> <br /> |- <br /> |<br /> rpsF, rpsI, rpsM, rpsO, rpsQ, and rpsT<br /> |<br /> PMID:17277072<br /> |<br /> precise gene knockout by recombineering <br /> |- <br /> |<br /> accD, degS, dpiA, dpiB, entD, etk,eutD, eutK, eutM, eutR, eutS, fldA, folD, ftnA, ftnB, ftsN, ftsX, gatA, glcA, gpsA, gsp, hflB, intZ, kup, lolA, lyx, mraY, mreD, mug, murA, murB, murF, nadD, pgmB, pptA, ptrA, purB, qmcA, queC, queF, raiA, ravA, rimN, rlmG, rluE, rluF, rplP, rplV, rpsG, rsmE, rsmF, rutA, trpH, ubiD, uspB, xni, yabQ, yadR, ybfK, ychO, ydiL, yejM, yffL yffN, yffP, yffQ, ygiA, ygiD, yhbV, yibJ, yigP, yjjL, ypjK, yraL, yrbB, yrfF, ysaA<br /> |<br /> PMID:13129938<br /> |<br /> accD listed as N* <br /> |- <br /> |<br /> ryeC, ryeD, rygC, rygD<br /> |<br /> PMID:18710431<br /> |<br /> <br /> |- <br /> |<br /> dsrA<br /> |<br /> PMID:8670904<br /> |<br /> <br /> |- <br /> |<br /> csrA<br /> |<br /> PMID:8366066<br /> |<br /> <br /> |- <br /> |<br /> csrB<br /> |<br /> PMID:11567002<br /> |<br /> <br /> |- <br /> |<br /> csrC<br /> |<br /> PMID:12694612<br /> |<br /> <br /> |- <br /> |<br /> csrD<br /> |<br /> PMID:16980588<br /> |<br /> <br /> |- <br /> |<br /> C0067, C0293, C0299, C0343, C0362, C0465, C0664, C0719, alaT, alaU, alaV, alaW, alaX, argQ, argV, argW, argY, argZ, asnT, asnU, asnV, asnW, aspT, aspU, aspV, bcsB, cydA, cydC, dicA, dicF, entS, fadJ, fadK, feoC,fruL, gadY,gcvB,ghrA, ghrB, glnW, gltT, gltU, gltV, gltW, glyU, glyV, glyW, glyX, glyY, gmm, gsiA, gsiB, gsiD,gspB, hofM, hspQ, isrA, isrB, isrC, kilR, ldrA, ldrB, ldrC, ldrD, leuP, leuQ, leuT, lysQ, lysV, lysW, lysY, lysZ, mdtQ, metT, metU, metV, metW, metY, metZ, micA, micC, minD, minE, mnmG, mokB, mokC, nepI, omrA, omrB, pagP, pheU, pheV, proK, proL, psrD, psrN, psrO, racR, rdlA, rdlB, rdlC, rdlD, rhaA, rhaB, rhaD, rhaM, rnc, rpoE, rprA, rseX, rutD,rutF, rutR, rybA, rydB, rydC, ryeA, ryeB, ryeE, ryfA, ryfB, ryfC, ryfD, ryhA, ryhB, ryiA, ryjA, ryjB, ryjC, selC, serW, serX, sgrS, skp, sokA, sokB, sokC, spf, sraA, sroA, sroB, sroC, sroD, sroF, sroG, sroH, ssrS, tadA, tdcF, tff, thrT, thrV, thrW, tisA, tisB, rttR, tpke70, tp2, tyrU, tyrV, ubiB<br /> valT, valU, valV, valW, valX, valY, valZ, waaU, wzyE, yafF, yagG, ybhU, yccB, ydfB, ydfN, ydgU, yffM, yffO, yffR, yffS, ygiD, ygiT, yhhQ, yibV, yjbS, yjbT, yjdP, yjhW, ykfM, ykgO, ylbG, ylcH, ylcI, yliL, ymfK, ymgI, ymgJ, yncL, yneM, ynhF, yoaI, yojO, ypaB, ypfM, yqgD, yrhD, ytcA, ytjA<br /> <br /> |<br /> <br /> |<br /> Covered by deletions (see PEC) <br /> |- <br /> |<br /> suhB<br /> |<br /> PMID:17652087<br /> |<br /> precise gene knockout by recombineering <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22&amp;page=136300&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || ||<br /> |}<br /> &lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22--&gt;&lt;/protect&gt;<br /> Add evidence for essentiality here:<br /> &lt;protect&gt;&lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| id=&quot;Y48ae47a0bea4a&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Gene!!Reference(s)!!Comments<br /> |- <br /> |<br /> nusA<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> rpoD<br /> |<br /> <br /> |<br /> Ts mutants and depletion studies <br /> |- <br /> |<br /> nusE<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> nusG<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> ffh<br /> |<br /> PMID:7559342<br /> |<br /> <br /> |- <br /> |<br /> rpsU<br /> |<br /> PMID:17277072<br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a&amp;page=136300&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || ||<br /> |}<br /> &lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a--&gt;&lt;/protect&gt;<br /> <br /> == See also ==<br /> [[Image:PEC search essentials.jpg|thumb]]<br /> * Baba et al [http://www.nature.com/msb/journal/v2/n1/suppinfo/msb4100050_S1.html supplemental data]<br /> * Gerdes et al [http://www.integratedgenomics.com/online_material/gerdes/supplementary_table.html supplemental data]<br /> * [http://www.shigen.nig.ac.jp/ecoli/pec/ PEC] ([[PEC|EcoliWiki page]]). PEC is a curated database that focuses on phenotypes of ''E. coli'' genes. To display essential genes, go to the [http://www.shigen.nig.ac.jp/ecoli/pec/genes.jsp PEC gene search] and uncheck nonessential, unknown, and Kohara phage (See figure).<br /> * Kato (2007)&lt;ref name='PMID:17700540'/&gt; identified 303 essential genes<br /> <br /> == References ==<br /> {{RefHelp}}<br /> &lt;references/&gt;</div> Bubunenm https://ecoliwiki.org/colipedia/index.php?title=Essential_genes&diff=1373899 Essential genes 2012-12-10T18:13:30Z <p>Bubunenm: Table edited by Bubunenm via TableEdit</p> <hr /> <div>== Introduction and caveats ==<br /> A number of studies have attempted to determine the minimum number of essential genes in ''E. coli''&lt;ref name='PMID:13129938'/&gt;&lt;ref name='PMID:16738554'/&gt;&lt;ref name='PMID:17700540'/&gt;. Although some essentiality has been rigorously tested for individual genes, much of the data comes from determining what is not essential. Any genes that were annotated after these studies were done will be missing from the supplemental data tables that list whether genes are essential or nonessential.<br /> <br /> This page displays a list of ''E. coli'' genes that '''may''' be essential. A more accurate description of this list might be &quot;Genes that have not been shown to be nonessential&quot;. The list is generated by a wiki extension that starts with the members of the Gene Lists for [[:Category:Gene List:MG1655|MG1655]] and removes<br /> * all genes where Keio deletions have been isolated, <br /> * all ins genes that are from insertion elements. <br /> === Manually curating nonessential genes ===<br /> The extension is displayed on this page between a pair of tags that allow addition of nonessential genes from manual curation. Placing a gene page name between the tags '''''removes''''' that gene from the list of candidates for essentiality.<br /> &lt;pre&gt;<br /> &lt;nowiki&gt;<br /> &lt;essentialGenes&gt;<br /> nonessential gene 1:Gene<br /> nonessential gene 2:Gene<br /> etc.<br /> &lt;/essentialGenes&gt;<br /> &lt;/nowiki&gt;<br /> &lt;/pre&gt;<br /> Manual curation so far includes:<br /> * Pseudogenes were recognized by the presence of a gene name with an underscore and a number. <br /> * tRNA genes that can be mutated to nonsense suppressors are marked as nonessential. Note that in many cases these are redundant and not all copies of a tRNA isoacceptor can be simultaneously deleted. <br /> * Similarly, although ribosomal RNA genes are not on this list, at least one of each rRNA is needed for viability.<br /> * Genes where Tn insertions were found by Gerdes et al. &lt;ref name='PMID:13129938'/&gt; were added for to the list of nonessentials.<br /> * Checking what [[PEC]] has to say about the genes<br /> * Limited checking of the literature for specific genes<br /> Community curation is still needed to improve the quality of this list.<br /> <br /> === Missing essential genes ===<br /> In some cases, the Keio collection reports a deletion strain for an essential gene. These often reflect trapping of duplications that provide a second complementing copy of the gene. To add back an essential gene, go to its gene page and edit the alleles table to remove any alleles with the PMID:16738554 code (that's how the extension recognizes the presence of the deletion strain on the list. To update the list on this page, you will need to clear the cache by clicking edit and then saving. See [[rpoD:Gene]] for an example.<br /> <br /> == The list (Edit this)==<br /> &lt;essentialGenes&gt;<br /> List nonessential gene pages here<br /> C0067:Gene<br /> C0293:Gene<br /> C0299:Gene<br /> C0343:Gene<br /> C0362:Gene<br /> C0465:Gene<br /> C0664:Gene<br /> C0719:Gene<br /> accD:Gene<br /> acpH:Gene<br /> adrA:Gene<br /> alaT:Gene<br /> alaU:Gene<br /> alaV:Gene<br /> alaW:Gene<br /> alaX:Gene<br /> araA:Gene<br /> araB:Gene<br /> araD:Gene<br /> arpB_2:Gene<br /> argQ:Gene<br /> argV:Gene<br /> argW:Gene<br /> argY:Gene<br /> argZ:Gene<br /> asnT:Gene<br /> asnU:Gene<br /> asnV:Gene<br /> asnW:Gene<br /> aspT:Gene<br /> aspU:Gene<br /> aspV:Gene<br /> bcsB:Gene<br /> csrA:Gene<br /> csrB:Gene<br /> csrC:Gene<br /> csrD:Gene<br /> cydA:Gene<br /> cydC:Gene<br /> degS:Gene<br /> dicA:Gene<br /> dicF:Gene<br /> dinQ:Gene<br /> dpiA:Gene<br /> dpiB:Gene<br /> dsbD:Gene<br /> dsrA:Gene<br /> efeU_2:Gene<br /> entD:Gene<br /> entS:Gene<br /> etk:Gene<br /> eutD:Gene<br /> eutK:Gene<br /> eutM:Gene<br /> eutR:Gene<br /> eutS:Gene<br /> fadJ:Gene<br /> fadK:Gene<br /> feoC:Gene<br /> fldA:Gene<br /> folA:Gene<br /> folD:Gene<br /> fruL:Gene<br /> ftnA:Gene<br /> ftnB:Gene<br /> ftsN:Gene<br /> ftsX:Gene<br /> gadY:Gene<br /> gapC_1:Gene<br /> gatA:Gene<br /> gatR_2:Gene<br /> gcvB:Gene<br /> gfcB:Gene<br /> ghrA:Gene<br /> ghrB:Gene<br /> glcA:Gene<br /> glnU:Gene<br /> glnV:Gene<br /> glnW:Gene<br /> glnX:Gene<br /> gltT:Gene<br /> gltU:Gene<br /> gltV:Gene<br /> gltW:Gene<br /> glyU:Gene<br /> glyV:Gene<br /> glyW:Gene<br /> glyX:Gene<br /> glyY:Gene<br /> gmm:Gene<br /> gpsA:Gene<br /> gsp:Gene<br /> gspB:Gene<br /> gsiA:Gene<br /> gsiB:Gene<br /> gsiD:Gene<br /> hflB:Gene<br /> hofM:Gene<br /> hspQ:Gene<br /> ileT:Gene<br /> ileU:Gene<br /> ileV:Gene<br /> ileX:Gene<br /> ileY:Gene<br /> ilvG_2:Gene<br /> isrA:Gene<br /> isrB:Gene<br /> isrC:Gene<br /> istR-1:Gene<br /> istR-2:Gene<br /> intZ:Gene<br /> kilR:Gene<br /> kup:Gene<br /> lafU:Gene<br /> lacZ:Gene<br /> ldrA:Gene<br /> ldrB:Gene<br /> ldrC:Gene<br /> ldrD:Gene<br /> leuP:Gene<br /> leuQ:Gene<br /> leuT:Gene<br /> leuV:Gene<br /> leuX:Gene<br /> lfhA:Gene<br /> lolA:Gene<br /> lomR_2:Gene<br /> lysT:Gene<br /> lysQ:Gene<br /> lysV:Gene<br /> lysW:Gene<br /> lysY:Gene<br /> lysZ:Gene<br /> lyx:Gene<br /> mazE:Gene<br /> mazF:Gene<br /> mdtQ:Gene<br /> metT:Gene<br /> metU:Gene<br /> metV:Gene<br /> metW:Gene<br /> metY:Gene<br /> metZ:Gene<br /> micA:Gene<br /> micC:Gene<br /> micF:Gene<br /> minD:Gene<br /> minE:Gene<br /> mnmG:Gene<br /> mokB:Gene<br /> mokC:Gene<br /> mraY:Gene<br /> mreD:Gene<br /> molR_3:Gene<br /> mug:Gene<br /> murA:Gene<br /> murB:Gene<br /> murF:Gene<br /> nadD:Gene<br /> nepI:Gene<br /> omrA:Gene<br /> omrB:Gene<br /> oriC:Gene<br /> orn:Gene<br /> oxyS:Gene<br /> pagP:Gene<br /> pgmB:Gene<br /> pheU:Gene<br /> pheV:Gene<br /> pinE:Gene<br /> pptA:Gene<br /> proK:Gene<br /> proL:Gene<br /> psrD:Gene<br /> psrN:Gene<br /> psrO:Gene<br /> ptrA:Gene<br /> purB:Gene<br /> qmcA:Gene<br /> queC:Gene<br /> queF:Gene<br /> racR:Gene<br /> raiA:Gene<br /> ravA:Gene<br /> rcnA:Gene<br /> rdlA:Gene<br /> rdlB:Gene<br /> rdlC:Gene<br /> rdlD:Gene<br /> rhaA:Gene<br /> rhaB:Gene<br /> rhaD:Gene<br /> rhaM:Gene<br /> rimN:Gene<br /> rlmG:Gene<br /> rlmL:Gene<br /> rluE:Gene<br /> rluF:Gene<br /> rnc:Gene<br /> rnlA:Gene<br /> rpoE:Gene<br /> rplP:Gene<br /> rplV:Gene<br /> rprA:Gene<br /> rpsF:Gene<br /> rpsG:Gene<br /> rpsI:Gene<br /> rpsM:Gene<br /> rpsO:Gene<br /> rpsQ:Gene<br /> rpsT:Gene<br /> rrfA:Gene<br /> rrfB:Gene<br /> rrfC:Gene<br /> rrfD:Gene<br /> rrfE:Gene<br /> rrfF:Gene<br /> rrfG:Gene<br /> rrfH:Gene<br /> rrsA:Gene<br /> rrsB:Gene<br /> rrsC:Gene<br /> rrsD:Gene<br /> rrsE:Gene<br /> rrsF:Gene<br /> rrsG:Gene<br /> rrsH:Gene<br /> rrlA:Gene<br /> rrlB:Gene<br /> rrlC:Gene<br /> rrlD:Gene<br /> rrlE:Gene<br /> rrlF:Gene<br /> rrlG:Gene<br /> rrlH:Gene<br /> rseX:Gene<br /> rsmE:Gene<br /> rsmF:Gene<br /> rttR:Gene<br /> rutA:Gene<br /> rutD:Gene<br /> rutF:Gene<br /> rutR:Gene<br /> rybA:Gene<br /> rydB:Gene<br /> rydC:Gene<br /> ryeA:Gene<br /> ryeB:Gene<br /> ryeE:Gene<br /> rybB:Gene<br /> ryeC:Gene<br /> ryeD:Gene<br /> ryfA:Gene<br /> ryfB:Gene<br /> ryfC:Gene<br /> ryfD:Gene<br /> rygC:Gene<br /> rygD:Gene<br /> rygE:Gene<br /> ryhA:Gene<br /> ryhB:Gene<br /> ryiA:Gene<br /> glmZ:Gene<br /> ryjA:Gene<br /> ryjB:Gene<br /> ryjC:Gene<br /> selC:Gene<br /> serU:Gene<br /> serV:Gene<br /> serW:Gene<br /> serX:Gene<br /> sgrS:Gene<br /> skp:Gene<br /> sokA:Gene<br /> sokB:Gene<br /> sokC:Gene<br /> spf:Gene<br /> sraA:Gene<br /> sroA:Gene<br /> sroB:Gene<br /> sroC:Gene<br /> sroD:Gene<br /> sroF:Gene<br /> sroG:Gene<br /> sroH:Gene<br /> ssrA:Gene<br /> ssrS:Gene<br /> tadA:Gene<br /> tdcF:Gene<br /> tff:Gene<br /> thrT:Gene<br /> thrV:Gene<br /> thrW:Gene<br /> tisA:Gene<br /> tisB:Gene<br /> tp2:Gene<br /> tpke70:Gene<br /> trpH:Gene<br /> tusB:Gene<br /> tusC:Gene<br /> tusD:Gene<br /> tusE:Gene<br /> tyrT:Gene<br /> tyrU:Gene<br /> tyrV:Gene<br /> ubiB:Gene<br /> ubiD:Gene<br /> uof:Gene<br /> uspB:Gene<br /> valT:Gene<br /> valU:Gene<br /> valV:Gene<br /> valW:Gene<br /> valX:Gene<br /> valY:Gene<br /> valZ:Gene<br /> ves:Gene<br /> waaU:Gene<br /> wbbL_1:Gene<br /> wzyE:Gene<br /> xni:Gene<br /> yabQ:Gene<br /> yadR:Gene<br /> yafF:Gene<br /> yagG:Gene<br /> ybhU:Gene<br /> ybfK:Gene<br /> yccB:Gene<br /> yceM:Gene<br /> ycgH_2:Gene<br /> ychE_2:Gene<br /> ychG_1:Gene<br /> ychO:Gene<br /> ychS:Gene<br /> yciY:Gene<br /> yciZ:Gene<br /> ydbA_2:Gene<br /> ydfB:Gene<br /> ydfN:Gene<br /> ydgU:Gene<br /> ydiL:Gene<br /> yedN_1:Gene<br /> yedS_3:Gene<br /> yeeL_1:Gene<br /> yefM:Gene<br /> yegZ:Gene<br /> yejM:Gene<br /> yfaS_1:Gene<br /> yfdT:Gene<br /> yffL:Gene<br /> yffN:Gene<br /> yffP:Gene<br /> yffQ:Gene<br /> yffM:Gene<br /> yffO:Gene<br /> yffR:Gene<br /> yffS:Gene<br /> ygdT:Gene<br /> ygiA:Gene<br /> ygiD:Gene<br /> ygiT:Gene<br /> yhbV:Gene<br /> yhhQ:Gene<br /> yi82_1:Gene<br /> ylbE_2:Gene<br /> yibJ:Gene<br /> yibV:Gene<br /> yigP:Gene<br /> yjgX_1:Gene<br /> yjbS:Gene<br /> yjbT:Gene<br /> yjdP:Gene<br /> yjhW:Gene<br /> yjjL:Gene<br /> ykfM:Gene<br /> ykgO:Gene<br /> ylbG:Gene<br /> ylcH:Gene<br /> ylcI:Gene<br /> yliL:Gene<br /> ymfK:Gene<br /> ymgI:Gene<br /> ymgJ:Gene<br /> yncK_2:Gene<br /> yncL:Gene<br /> yneM:Gene<br /> ynhF:Gene<br /> yoaI:Gene<br /> yojO:Gene<br /> ypaB:Gene<br /> ypfM:Gene<br /> ypjK:Gene<br /> yqgD:Gene<br /> yraL:Gene<br /> yrbB:Gene<br /> yrfF:Gene<br /> yrhD:Gene<br /> ytcA:Gene<br /> ytjA:Gene<br /> ysaA:Gene<br /> &lt;/essentialGenes&gt;<br /> <br /> == Evidence ==<br /> Add evidence for nonessentiality here:<br /> &lt;protect&gt;&lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| id=&quot;M48ae3191b3b22&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Gene!!Reference(s)!!Comments<br /> |- <br /> |<br /> [[folA]]<br /> |<br /> PMID:8423162<br /> |<br /> <br /> |- <br /> |<br /> micF<br /> |<br /> PMID:15466019<br /> |<br /> <br /> |- <br /> |<br /> rpsF, rpsI, rpsM, rpsO, rpsQ, and rpsT<br /> |<br /> PMID:17277072<br /> |<br /> precise gene knockout by recombineering <br /> |- <br /> |<br /> accD, degS, dpiA, dpiB, entD, etk,eutD, eutK, eutM, eutR, eutS, fldA, folD, ftnA, ftnB, ftsN, ftsX, gatA, glcA, gpsA, gsp, hflB, intZ, kup, lolA, lyx, mraY, mreD, mug, murA, murB, murF, nadD, pgmB, pptA, ptrA, purB, qmcA, queC, queF, raiA, ravA, rimN, rlmG, rluE, rluF, rplP, rplV, rpsG, rsmE, rsmF, rutA, trpH, ubiD, uspB, xni, yabQ, yadR, ybfK, ychO, ydiL, yejM, yffL yffN, yffP, yffQ, ygiA, ygiD, yhbV, yibJ, yigP, yjjL, ypjK, yraL, yrbB, yrfF, ysaA<br /> |<br /> PMID:13129938<br /> |<br /> accD listed as N* <br /> |- <br /> |<br /> ryeC, ryeD, rygC, rygD<br /> |<br /> PMID:18710431<br /> |<br /> <br /> |- <br /> |<br /> dsrA<br /> |<br /> PMID:8670904<br /> |<br /> <br /> |- <br /> |<br /> csrA<br /> |<br /> PMID:8366066<br /> |<br /> <br /> |- <br /> |<br /> csrB<br /> |<br /> PMID:11567002<br /> |<br /> <br /> |- <br /> |<br /> csrC<br /> |<br /> PMID:12694612<br /> |<br /> <br /> |- <br /> |<br /> csrD<br /> |<br /> PMID:16980588<br /> |<br /> <br /> |- <br /> |<br /> C0067, C0293, C0299, C0343, C0362, C0465, C0664, C0719, alaT, alaU, alaV, alaW, alaX, argQ, argV, argW, argY, argZ, asnT, asnU, asnV, asnW, aspT, aspU, aspV, bcsB, cydA, cydC, dicA, dicF, entS, fadJ, fadK, feoC,fruL, gadY,gcvB,ghrA, ghrB, glnW, gltT, gltU, gltV, gltW, glyU, glyV, glyW, glyX, glyY, gmm, gsiA, gsiB, gsiD,gspB, hofM, hspQ, isrA, isrB, isrC, kilR, ldrA, ldrB, ldrC, ldrD, leuP, leuQ, leuT, lysQ, lysV, lysW, lysY, lysZ, mdtQ, metT, metU, metV, metW, metY, metZ, micA, micC, minD, minE, mnmG, mokB, mokC, nepI, omrA, omrB, pagP, pheU, pheV, proK, proL, psrD, psrN, psrO, racR, rdlA, rdlB, rdlC, rdlD, rhaA, rhaB, rhaD, rhaM, rnc, rpoE, rprA, rseX, rutD,rutF, rutR, rybA, rydB, rydC, ryeA, ryeB, ryeE, ryfA, ryfB, ryfC, ryfD, ryhA, ryhB, ryiA, ryjA, ryjB, ryjC, selC, serW, serX, sgrS, skp, sokA, sokB, sokC, spf, sraA, sroA, sroB, sroC, sroD, sroF, sroG, sroH, ssrS, tadA, tdcF, tff, thrT, thrV, thrW, tisA, tisB, rttR, tpke70, tp2, tyrU, tyrV, ubiB<br /> valT, valU, valV, valW, valX, valY, valZ, waaU, wzyE, yafF, yagG, ybhU, yccB, ydfB, ydfN, ydgU, yffM, yffO, yffR, yffS, ygiD, ygiT, yhhQ, yibV, yjbS, yjbT, yjdP, yjhW, ykfM, ykgO, ylbG, ylcH, ylcI, yliL, ymfK, ymgI, ymgJ, yncL, yneM, ynhF, yoaI, yojO, ypaB, ypfM, yqgD, yrhD, ytcA, ytjA<br /> <br /> |<br /> <br /> |<br /> Covered by deletions (see PEC) <br /> |- <br /> |<br /> suhB<br /> |<br /> PMID:17652087<br /> |<br /> precise gene knockout by recombineering <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22&amp;page=136300&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || ||<br /> |}<br /> &lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22--&gt;&lt;/protect&gt;<br /> Add evidence for essentiality here:<br /> &lt;protect&gt;&lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| id=&quot;Y48ae47a0bea4a&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Gene!!Reference(s)!!Comments<br /> |- <br /> |<br /> nusA<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> rpoD<br /> |<br /> <br /> |<br /> Ts mutants and depletion studies <br /> |- <br /> |<br /> nusE<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> nusG<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> ffh<br /> |<br /> PMID:7559342<br /> |<br /> <br /> |- <br /> |<br /> rpsU<br /> |<br /> PMID:17277072<br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a&amp;page=136300&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || ||<br /> |}<br /> &lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a--&gt;&lt;/protect&gt;<br /> <br /> == See also ==<br /> [[Image:PEC search essentials.jpg|thumb]]<br /> * Baba et al [http://www.nature.com/msb/journal/v2/n1/suppinfo/msb4100050_S1.html supplemental data]<br /> * Gerdes et al [http://www.integratedgenomics.com/online_material/gerdes/supplementary_table.html supplemental data]<br /> * [http://www.shigen.nig.ac.jp/ecoli/pec/ PEC] ([[PEC|EcoliWiki page]]). PEC is a curated database that focuses on phenotypes of ''E. coli'' genes. To display essential genes, go to the [http://www.shigen.nig.ac.jp/ecoli/pec/genes.jsp PEC gene search] and uncheck nonessential, unknown, and Kohara phage (See figure).<br /> * Kato (2007)&lt;ref name='PMID:17700540'/&gt; identified 303 essential genes<br /> <br /> == References ==<br /> {{RefHelp}}<br /> &lt;references/&gt;</div> Bubunenm https://ecoliwiki.org/colipedia/index.php?title=Essential_genes&diff=1373898 Essential genes 2012-12-10T18:01:43Z <p>Bubunenm: Table edited by Bubunenm via TableEdit</p> <hr /> <div>== Introduction and caveats ==<br /> A number of studies have attempted to determine the minimum number of essential genes in ''E. coli''&lt;ref name='PMID:13129938'/&gt;&lt;ref name='PMID:16738554'/&gt;&lt;ref name='PMID:17700540'/&gt;. Although some essentiality has been rigorously tested for individual genes, much of the data comes from determining what is not essential. Any genes that were annotated after these studies were done will be missing from the supplemental data tables that list whether genes are essential or nonessential.<br /> <br /> This page displays a list of ''E. coli'' genes that '''may''' be essential. A more accurate description of this list might be &quot;Genes that have not been shown to be nonessential&quot;. The list is generated by a wiki extension that starts with the members of the Gene Lists for [[:Category:Gene List:MG1655|MG1655]] and removes<br /> * all genes where Keio deletions have been isolated, <br /> * all ins genes that are from insertion elements. <br /> === Manually curating nonessential genes ===<br /> The extension is displayed on this page between a pair of tags that allow addition of nonessential genes from manual curation. Placing a gene page name between the tags '''''removes''''' that gene from the list of candidates for essentiality.<br /> &lt;pre&gt;<br /> &lt;nowiki&gt;<br /> &lt;essentialGenes&gt;<br /> nonessential gene 1:Gene<br /> nonessential gene 2:Gene<br /> etc.<br /> &lt;/essentialGenes&gt;<br /> &lt;/nowiki&gt;<br /> &lt;/pre&gt;<br /> Manual curation so far includes:<br /> * Pseudogenes were recognized by the presence of a gene name with an underscore and a number. <br /> * tRNA genes that can be mutated to nonsense suppressors are marked as nonessential. Note that in many cases these are redundant and not all copies of a tRNA isoacceptor can be simultaneously deleted. <br /> * Similarly, although ribosomal RNA genes are not on this list, at least one of each rRNA is needed for viability.<br /> * Genes where Tn insertions were found by Gerdes et al. &lt;ref name='PMID:13129938'/&gt; were added for to the list of nonessentials.<br /> * Checking what [[PEC]] has to say about the genes<br /> * Limited checking of the literature for specific genes<br /> Community curation is still needed to improve the quality of this list.<br /> <br /> === Missing essential genes ===<br /> In some cases, the Keio collection reports a deletion strain for an essential gene. These often reflect trapping of duplications that provide a second complementing copy of the gene. To add back an essential gene, go to its gene page and edit the alleles table to remove any alleles with the PMID:16738554 code (that's how the extension recognizes the presence of the deletion strain on the list. To update the list on this page, you will need to clear the cache by clicking edit and then saving. See [[rpoD:Gene]] for an example.<br /> <br /> == The list (Edit this)==<br /> &lt;essentialGenes&gt;<br /> List nonessential gene pages here<br /> C0067:Gene<br /> C0293:Gene<br /> C0299:Gene<br /> C0343:Gene<br /> C0362:Gene<br /> C0465:Gene<br /> C0664:Gene<br /> C0719:Gene<br /> accD:Gene<br /> acpH:Gene<br /> adrA:Gene<br /> alaT:Gene<br /> alaU:Gene<br /> alaV:Gene<br /> alaW:Gene<br /> alaX:Gene<br /> araA:Gene<br /> araB:Gene<br /> araD:Gene<br /> arpB_2:Gene<br /> argQ:Gene<br /> argV:Gene<br /> argW:Gene<br /> argY:Gene<br /> argZ:Gene<br /> asnT:Gene<br /> asnU:Gene<br /> asnV:Gene<br /> asnW:Gene<br /> aspT:Gene<br /> aspU:Gene<br /> aspV:Gene<br /> bcsB:Gene<br /> csrA:Gene<br /> csrB:Gene<br /> csrC:Gene<br /> csrD:Gene<br /> cydA:Gene<br /> cydC:Gene<br /> degS:Gene<br /> dicA:Gene<br /> dicF:Gene<br /> dinQ:Gene<br /> dpiA:Gene<br /> dpiB:Gene<br /> dsbD:Gene<br /> dsrA:Gene<br /> efeU_2:Gene<br /> entD:Gene<br /> entS:Gene<br /> etk:Gene<br /> eutD:Gene<br /> eutK:Gene<br /> eutM:Gene<br /> eutR:Gene<br /> eutS:Gene<br /> fadJ:Gene<br /> fadK:Gene<br /> feoC:Gene<br /> fldA:Gene<br /> folA:Gene<br /> folD:Gene<br /> fruL:Gene<br /> ftnA:Gene<br /> ftnB:Gene<br /> ftsN:Gene<br /> ftsX:Gene<br /> gadY:Gene<br /> gapC_1:Gene<br /> gatA:Gene<br /> gatR_2:Gene<br /> gcvB:Gene<br /> gfcB:Gene<br /> ghrA:Gene<br /> ghrB:Gene<br /> glcA:Gene<br /> glnU:Gene<br /> glnV:Gene<br /> glnW:Gene<br /> glnX:Gene<br /> gltT:Gene<br /> gltU:Gene<br /> gltV:Gene<br /> gltW:Gene<br /> glyU:Gene<br /> glyV:Gene<br /> glyW:Gene<br /> glyX:Gene<br /> glyY:Gene<br /> gmm:Gene<br /> gpsA:Gene<br /> gsp:Gene<br /> gspB:Gene<br /> gsiA:Gene<br /> gsiB:Gene<br /> gsiD:Gene<br /> hflB:Gene<br /> hofM:Gene<br /> hspQ:Gene<br /> ileT:Gene<br /> ileU:Gene<br /> ileV:Gene<br /> ileX:Gene<br /> ileY:Gene<br /> ilvG_2:Gene<br /> isrA:Gene<br /> isrB:Gene<br /> isrC:Gene<br /> istR-1:Gene<br /> istR-2:Gene<br /> intZ:Gene<br /> kilR:Gene<br /> kup:Gene<br /> lafU:Gene<br /> lacZ:Gene<br /> ldrA:Gene<br /> ldrB:Gene<br /> ldrC:Gene<br /> ldrD:Gene<br /> leuP:Gene<br /> leuQ:Gene<br /> leuT:Gene<br /> leuV:Gene<br /> leuX:Gene<br /> lfhA:Gene<br /> lolA:Gene<br /> lomR_2:Gene<br /> lysT:Gene<br /> lysQ:Gene<br /> lysV:Gene<br /> lysW:Gene<br /> lysY:Gene<br /> lysZ:Gene<br /> lyx:Gene<br /> mazE:Gene<br /> mazF:Gene<br /> mdtQ:Gene<br /> metT:Gene<br /> metU:Gene<br /> metV:Gene<br /> metW:Gene<br /> metY:Gene<br /> metZ:Gene<br /> micA:Gene<br /> micC:Gene<br /> micF:Gene<br /> minD:Gene<br /> minE:Gene<br /> mnmG:Gene<br /> mokB:Gene<br /> mokC:Gene<br /> mraY:Gene<br /> mreD:Gene<br /> molR_3:Gene<br /> mug:Gene<br /> murA:Gene<br /> murB:Gene<br /> murF:Gene<br /> nadD:Gene<br /> nepI:Gene<br /> omrA:Gene<br /> omrB:Gene<br /> oriC:Gene<br /> orn:Gene<br /> oxyS:Gene<br /> pagP:Gene<br /> pgmB:Gene<br /> pheU:Gene<br /> pheV:Gene<br /> pinE:Gene<br /> pptA:Gene<br /> proK:Gene<br /> proL:Gene<br /> psrD:Gene<br /> psrN:Gene<br /> psrO:Gene<br /> ptrA:Gene<br /> purB:Gene<br /> qmcA:Gene<br /> queC:Gene<br /> queF:Gene<br /> racR:Gene<br /> raiA:Gene<br /> ravA:Gene<br /> rcnA:Gene<br /> rdlA:Gene<br /> rdlB:Gene<br /> rdlC:Gene<br /> rdlD:Gene<br /> rhaA:Gene<br /> rhaB:Gene<br /> rhaD:Gene<br /> rhaM:Gene<br /> rimN:Gene<br /> rlmG:Gene<br /> rlmL:Gene<br /> rluE:Gene<br /> rluF:Gene<br /> rnc:Gene<br /> rnlA:Gene<br /> rpoE:Gene<br /> rplP:Gene<br /> rplV:Gene<br /> rprA:Gene<br /> rpsF:Gene<br /> rpsG:Gene<br /> rpsI:Gene<br /> rpsM:Gene<br /> rpsO:Gene<br /> rpsQ:Gene<br /> rpsT:Gene<br /> rrfA:Gene<br /> rrfB:Gene<br /> rrfC:Gene<br /> rrfD:Gene<br /> rrfE:Gene<br /> rrfF:Gene<br /> rrfG:Gene<br /> rrfH:Gene<br /> rrsA:Gene<br /> rrsB:Gene<br /> rrsC:Gene<br /> rrsD:Gene<br /> rrsE:Gene<br /> rrsF:Gene<br /> rrsG:Gene<br /> rrsH:Gene<br /> rrlA:Gene<br /> rrlB:Gene<br /> rrlC:Gene<br /> rrlD:Gene<br /> rrlE:Gene<br /> rrlF:Gene<br /> rrlG:Gene<br /> rrlH:Gene<br /> rseX:Gene<br /> rsmE:Gene<br /> rsmF:Gene<br /> rttR:Gene<br /> rutA:Gene<br /> rutD:Gene<br /> rutF:Gene<br /> rutR:Gene<br /> rybA:Gene<br /> rydB:Gene<br /> rydC:Gene<br /> ryeA:Gene<br /> ryeB:Gene<br /> ryeE:Gene<br /> rybB:Gene<br /> ryeC:Gene<br /> ryeD:Gene<br /> ryfA:Gene<br /> ryfB:Gene<br /> ryfC:Gene<br /> ryfD:Gene<br /> rygC:Gene<br /> rygD:Gene<br /> rygE:Gene<br /> ryhA:Gene<br /> ryhB:Gene<br /> ryiA:Gene<br /> glmZ:Gene<br /> ryjA:Gene<br /> ryjB:Gene<br /> ryjC:Gene<br /> selC:Gene<br /> serU:Gene<br /> serV:Gene<br /> serW:Gene<br /> serX:Gene<br /> sgrS:Gene<br /> skp:Gene<br /> sokA:Gene<br /> sokB:Gene<br /> sokC:Gene<br /> spf:Gene<br /> sraA:Gene<br /> sroA:Gene<br /> sroB:Gene<br /> sroC:Gene<br /> sroD:Gene<br /> sroF:Gene<br /> sroG:Gene<br /> sroH:Gene<br /> ssrA:Gene<br /> ssrS:Gene<br /> tadA:Gene<br /> tdcF:Gene<br /> tff:Gene<br /> thrT:Gene<br /> thrV:Gene<br /> thrW:Gene<br /> tisA:Gene<br /> tisB:Gene<br /> tp2:Gene<br /> tpke70:Gene<br /> trpH:Gene<br /> tusB:Gene<br /> tusC:Gene<br /> tusD:Gene<br /> tusE:Gene<br /> tyrT:Gene<br /> tyrU:Gene<br /> tyrV:Gene<br /> ubiB:Gene<br /> ubiD:Gene<br /> uof:Gene<br /> uspB:Gene<br /> valT:Gene<br /> valU:Gene<br /> valV:Gene<br /> valW:Gene<br /> valX:Gene<br /> valY:Gene<br /> valZ:Gene<br /> ves:Gene<br /> waaU:Gene<br /> wbbL_1:Gene<br /> wzyE:Gene<br /> xni:Gene<br /> yabQ:Gene<br /> yadR:Gene<br /> yafF:Gene<br /> yagG:Gene<br /> ybhU:Gene<br /> ybfK:Gene<br /> yccB:Gene<br /> yceM:Gene<br /> ycgH_2:Gene<br /> ychE_2:Gene<br /> ychG_1:Gene<br /> ychO:Gene<br /> ychS:Gene<br /> yciY:Gene<br /> yciZ:Gene<br /> ydbA_2:Gene<br /> ydfB:Gene<br /> ydfN:Gene<br /> ydgU:Gene<br /> ydiL:Gene<br /> yedN_1:Gene<br /> yedS_3:Gene<br /> yeeL_1:Gene<br /> yefM:Gene<br /> yegZ:Gene<br /> yejM:Gene<br /> yfaS_1:Gene<br /> yfdT:Gene<br /> yffL:Gene<br /> yffN:Gene<br /> yffP:Gene<br /> yffQ:Gene<br /> yffM:Gene<br /> yffO:Gene<br /> yffR:Gene<br /> yffS:Gene<br /> ygdT:Gene<br /> ygiA:Gene<br /> ygiD:Gene<br /> ygiT:Gene<br /> yhbV:Gene<br /> yhhQ:Gene<br /> yi82_1:Gene<br /> ylbE_2:Gene<br /> yibJ:Gene<br /> yibV:Gene<br /> yigP:Gene<br /> yjgX_1:Gene<br /> yjbS:Gene<br /> yjbT:Gene<br /> yjdP:Gene<br /> yjhW:Gene<br /> yjjL:Gene<br /> ykfM:Gene<br /> ykgO:Gene<br /> ylbG:Gene<br /> ylcH:Gene<br /> ylcI:Gene<br /> yliL:Gene<br /> ymfK:Gene<br /> ymgI:Gene<br /> ymgJ:Gene<br /> yncK_2:Gene<br /> yncL:Gene<br /> yneM:Gene<br /> ynhF:Gene<br /> yoaI:Gene<br /> yojO:Gene<br /> ypaB:Gene<br /> ypfM:Gene<br /> ypjK:Gene<br /> yqgD:Gene<br /> yraL:Gene<br /> yrbB:Gene<br /> yrfF:Gene<br /> yrhD:Gene<br /> ytcA:Gene<br /> ytjA:Gene<br /> ysaA:Gene<br /> &lt;/essentialGenes&gt;<br /> <br /> == Evidence ==<br /> Add evidence for nonessentiality here:<br /> &lt;protect&gt;&lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| id=&quot;M48ae3191b3b22&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Gene!!Reference(s)!!Comments<br /> |- <br /> |<br /> [[folA]]<br /> |<br /> PMID:8423162<br /> |<br /> <br /> |- <br /> |<br /> micF<br /> |<br /> PMID:15466019<br /> |<br /> <br /> |- <br /> |<br /> rpsF, rpsI, rpsM, rpsO, rpsQ, and rpsT<br /> |<br /> PMID:7751274<br /> |<br /> <br /> |- <br /> |<br /> accD, degS, dpiA, dpiB, entD, etk,eutD, eutK, eutM, eutR, eutS, fldA, folD, ftnA, ftnB, ftsN, ftsX, gatA, glcA, gpsA, gsp, hflB, intZ, kup, lolA, lyx, mraY, mreD, mug, murA, murB, murF, nadD, pgmB, pptA, ptrA, purB, qmcA, queC, queF, raiA, ravA, rimN, rlmG, rluE, rluF, rplP, rplV, rpsG, rsmE, rsmF, rutA, trpH, ubiD, uspB, xni, yabQ, yadR, ybfK, ychO, ydiL, yejM, yffL yffN, yffP, yffQ, ygiA, ygiD, yhbV, yibJ, yigP, yjjL, ypjK, yraL, yrbB, yrfF, ysaA<br /> |<br /> PMID:13129938<br /> |<br /> accD listed as N* <br /> |- <br /> |<br /> ryeC, ryeD, rygC, rygD<br /> |<br /> PMID:18710431<br /> |<br /> <br /> |- <br /> |<br /> dsrA<br /> |<br /> PMID:8670904<br /> |<br /> <br /> |- <br /> |<br /> csrA<br /> |<br /> PMID:8366066<br /> |<br /> <br /> |- <br /> |<br /> csrB<br /> |<br /> PMID:11567002<br /> |<br /> <br /> |- <br /> |<br /> csrC<br /> |<br /> PMID:12694612<br /> |<br /> <br /> |- <br /> |<br /> csrD<br /> |<br /> PMID:16980588<br /> |<br /> <br /> |- <br /> |<br /> C0067, C0293, C0299, C0343, C0362, C0465, C0664, C0719, alaT, alaU, alaV, alaW, alaX, argQ, argV, argW, argY, argZ, asnT, asnU, asnV, asnW, aspT, aspU, aspV, bcsB, cydA, cydC, dicA, dicF, entS, fadJ, fadK, feoC,fruL, gadY,gcvB,ghrA, ghrB, glnW, gltT, gltU, gltV, gltW, glyU, glyV, glyW, glyX, glyY, gmm, gsiA, gsiB, gsiD,gspB, hofM, hspQ, isrA, isrB, isrC, kilR, ldrA, ldrB, ldrC, ldrD, leuP, leuQ, leuT, lysQ, lysV, lysW, lysY, lysZ, mdtQ, metT, metU, metV, metW, metY, metZ, micA, micC, minD, minE, mnmG, mokB, mokC, nepI, omrA, omrB, pagP, pheU, pheV, proK, proL, psrD, psrN, psrO, racR, rdlA, rdlB, rdlC, rdlD, rhaA, rhaB, rhaD, rhaM, rnc, rpoE, rprA, rseX, rutD,rutF, rutR, rybA, rydB, rydC, ryeA, ryeB, ryeE, ryfA, ryfB, ryfC, ryfD, ryhA, ryhB, ryiA, ryjA, ryjB, ryjC, selC, serW, serX, sgrS, skp, sokA, sokB, sokC, spf, sraA, sroA, sroB, sroC, sroD, sroF, sroG, sroH, ssrS, tadA, tdcF, tff, thrT, thrV, thrW, tisA, tisB, rttR, tpke70, tp2, tyrU, tyrV, ubiB<br /> valT, valU, valV, valW, valX, valY, valZ, waaU, wzyE, yafF, yagG, ybhU, yccB, ydfB, ydfN, ydgU, yffM, yffO, yffR, yffS, ygiD, ygiT, yhhQ, yibV, yjbS, yjbT, yjdP, yjhW, ykfM, ykgO, ylbG, ylcH, ylcI, yliL, ymfK, ymgI, ymgJ, yncL, yneM, ynhF, yoaI, yojO, ypaB, ypfM, yqgD, yrhD, ytcA, ytjA<br /> <br /> |<br /> <br /> |<br /> Covered by deletions (see PEC) <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22&amp;page=136300&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || ||<br /> |}<br /> &lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22--&gt;&lt;/protect&gt;<br /> Add evidence for essentiality here:<br /> &lt;protect&gt;&lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| id=&quot;Y48ae47a0bea4a&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Gene!!Reference(s)!!Comments<br /> |- <br /> |<br /> nusA<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> rpoD<br /> |<br /> <br /> |<br /> Ts mutants and depletion studies <br /> |- <br /> |<br /> nusE<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> nusG<br /> |<br /> PMID:17277072<br /> |<br /> <br /> |- <br /> |<br /> ffh<br /> |<br /> PMID:7559342<br /> |<br /> <br /> |- <br /> |<br /> rpsU<br /> |<br /> PMID:17277072<br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a&amp;page=136300&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || ||<br /> |}<br /> &lt;!--box uid=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a--&gt;&lt;/protect&gt;<br /> <br /> == See also ==<br /> [[Image:PEC search essentials.jpg|thumb]]<br /> * Baba et al [http://www.nature.com/msb/journal/v2/n1/suppinfo/msb4100050_S1.html supplemental data]<br /> * Gerdes et al [http://www.integratedgenomics.com/online_material/gerdes/supplementary_table.html supplemental data]<br /> * [http://www.shigen.nig.ac.jp/ecoli/pec/ PEC] ([[PEC|EcoliWiki page]]). PEC is a curated database that focuses on phenotypes of ''E. coli'' genes. To display essential genes, go to the [http://www.shigen.nig.ac.jp/ecoli/pec/genes.jsp PEC gene search] and uncheck nonessential, unknown, and Kohara phage (See figure).<br /> * Kato (2007)&lt;ref name='PMID:17700540'/&gt; identified 303 essential genes<br /> <br /> == References ==<br /> {{RefHelp}}<br /> &lt;references/&gt;</div> Bubunenm