<?xml version="1.0" encoding="UTF-8"?><xmi:XMI xmlns:pos="http:///org/u_compare/shared/label/penn/pos.ecore" xmlns:grammatical="http:///org/u_compare/shared/label/penn/function/grammatical.ecore" xmlns:general="http:///org/u_compare/shared/label/penn/pos/general.ecore" xmlns:cas="http:///uima/cas.ecore" xmlns:stanford="http:///org/u_compare/shared/label/stanford.ecore" xmlns:semantic2="http:///uk/ac/nactem/semantic.ecore" xmlns:bioie="http:///org/u_compare/shared/label/penn/pos/bioie.ecore" xmlns:function="http:///org/u_compare/shared/label/penn/function.ecore" xmlns:tcas="http:///uima/tcas.ecore" xmlns:bio="http:///org/u_compare/shared/semantic/bio.ecore" xmlns:syntactic="http:///org/u_compare/shared/syntactic.ecore" xmlns:comparable="http:///org/u_compare/shared/comparable.ecore" xmlns:examples="http:///org/apache/uima/examples.ecore" xmlns:label="http:///org/u_compare/shared/label.ecore" xmlns:xmi="http://www.omg.org/XMI" xmlns:general2="http:///org/u_compare/shared/label/penn/bracket/general.ecore" xmlns:shared="http:///org/u_compare/shared.ecore" xmlns:fragment="http:///org/u_compare/shared/document/fragment.ecore" xmlns:document="http:///org/u_compare/shared/document.ecore" xmlns:bracket="http:///org/u_compare/shared/label/penn/bracket.ecore" xmlns:text="http:///org/u_compare/shared/label/penn/function/text.ecore" xmlns:structure="http:///org/u_compare/shared/document/structure.ecore" xmlns:text2="http:///org/u_compare/shared/document/text.ecore" xmlns:release="http:///org/u_compare/shared/label/penn/pos/release.ecore" xmlns:semantic="http:///org/u_compare/shared/semantic.ecore" xmlns:nontext="http:///org/u_compare/shared/document/nontext.ecore" xmlns:conll="http:///org/u_compare/shared/label/conll.ecore" xmlns:chemical="http:///org/u_compare/shared/semantic/chemical.ecore" xmlns:semantic3="http:///org/u_compare/shared/label/penn/function/semantic.ecore" xmlns:release2="http:///org/u_compare/shared/label/penn/bracket/release.ecore" xmlns:coindex="http:///org/u_compare/shared/label/penn/coindex.ecore" xmi:version="2.0"><cas:NULL xmi:id="0"/><cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="Characterization of the MetR binding sites for the glyA gene of Escherichia coli. &#10;Sequence analysis of the glyA control region of Escherichia coli identified two regions with homology to the consensus binding sequence for MetR, a lysR family regulatory protein. Gel shift assays and DNase I protection assays verified that both sites bind MetR. Homocysteine, a coregulator for MetR, increased MetR binding to the glyA control region. The MetR binding sites were cloned into the pBend2 vector. Although the DNA did not show any significant intrinsic bend, MetR binding resulted in a bending angle of about 33 degrees. MetR-induced bending was independent of homocysteine. To verify that the MetR binding sites play a functional role in glyA expression, site-directed mutagenesis was used to alter the two binding sites in a lambda glyA-lacZ gene fusion phage. Changing the binding sites toward the consensus MetR binding sequence caused an increase in glyA-lacZ expression. Changing either binding site away from the consensus sequence caused a decrease in expression, suggesting that both sites are required for normal glyA regulation. "/><cas:FSArray xmi:id="509" elements="513 522"/><cas:FSArray xmi:id="516" elements="26"/><cas:FSArray xmi:id="525" elements="37"/><cas:FSArray xmi:id="531" elements="535 544"/><cas:FSArray xmi:id="538" elements="48"/><cas:FSArray xmi:id="547" elements="366"/><cas:FSArray xmi:id="553" elements="557 566"/><cas:FSArray xmi:id="560" elements="55"/><cas:FSArray xmi:id="569" elements="66"/><cas:FSArray xmi:id="575" elements="579 588"/><cas:FSArray xmi:id="582" elements="77"/><cas:FSArray xmi:id="591" elements="84"/><cas:FSArray xmi:id="597" elements="600"/><cas:FSArray xmi:id="603" elements="91"/><cas:FSArray xmi:id="609" elements="614 623 632"/><cas:FSArray xmi:id="617" elements="109"/><cas:FSArray xmi:id="626" elements="120"/><cas:FSArray xmi:id="635" elements="102"/><cas:FSArray xmi:id="641" elements="644"/><cas:FSArray xmi:id="647" elements="138"/><cas:FSArray xmi:id="653" elements="657 666"/><cas:FSArray xmi:id="660" elements="410"/><cas:FSArray xmi:id="669" elements="443"/><cas:FSArray xmi:id="675" elements="678"/><cas:FSArray xmi:id="681" elements="160"/><cas:FSArray xmi:id="687" elements="690"/><cas:FSArray xmi:id="693" elements="149"/><cas:FSArray xmi:id="699" elements="702"/><cas:FSArray xmi:id="705" elements="167"/><cas:FSArray xmi:id="711" elements="715 724"/><cas:FSArray xmi:id="718" elements="454"/><cas:FSArray xmi:id="727" elements="476"/><cas:FSArray xmi:id="733" elements="736"/><cas:FSArray xmi:id="739" elements="178"/><cas:FSArray xmi:id="745" elements="749 758"/><cas:FSArray xmi:id="752" elements="188"/><cas:FSArray xmi:id="761" elements="206"/><cas:FSArray xmi:id="767" elements="771 780"/><cas:FSArray xmi:id="774" elements="213"/><cas:FSArray xmi:id="783" elements="199"/><cas:FSArray xmi:id="792" elements="0 26 37 48 55 66 77 84 91 102 109 120 127 138 149 160 167 178 188 199 206 213 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"/><tcas:DocumentAnnotation xmi:id="8" sofa="1" begin="0" end="1137" language="x-unspecified"/><tcas:DocumentAnnotation xmi:id="21" sofa="1" begin="0" end="1137"/><examples:SourceDocumentInformation xmi:id="13" sofa="1" begin="0" end="1137" uri="/7608086.txt" offsetInSource="0" documentSize="1137" lastSegment="true"/><semantic:LinkedAnnotationSet xmi:id="513" linkingRelation="519" linkedAnnotations="516"/><semantic:LinkedAnnotationSet xmi:id="522" linkingRelation="528" linkedAnnotations="525"/><semantic:LinkedAnnotationSet xmi:id="535" linkingRelation="541" linkedAnnotations="538"/><semantic:LinkedAnnotationSet xmi:id="544" linkingRelation="550" linkedAnnotations="547"/><semantic:LinkedAnnotationSet xmi:id="557" linkingRelation="563" linkedAnnotations="560"/><semantic:LinkedAnnotationSet xmi:id="566" linkingRelation="572" linkedAnnotations="569"/><semantic:LinkedAnnotationSet xmi:id="579" linkingRelation="585" linkedAnnotations="582"/><semantic:LinkedAnnotationSet xmi:id="588" linkingRelation="594" linkedAnnotations="591"/><semantic:LinkedAnnotationSet xmi:id="600" linkingRelation="606" linkedAnnotations="603"/><semantic:LinkedAnnotationSet xmi:id="614" linkingRelation="620" linkedAnnotations="617"/><semantic:LinkedAnnotationSet xmi:id="623" linkingRelation="629" linkedAnnotations="626"/><semantic:LinkedAnnotationSet xmi:id="632" linkingRelation="638" linkedAnnotations="635"/><semantic:LinkedAnnotationSet xmi:id="644" linkingRelation="650" linkedAnnotations="647"/><semantic:LinkedAnnotationSet xmi:id="657" linkingRelation="663" linkedAnnotations="660"/><semantic:LinkedAnnotationSet xmi:id="666" linkingRelation="672" linkedAnnotations="669"/><semantic:LinkedAnnotationSet xmi:id="678" linkingRelation="684" linkedAnnotations="681"/><semantic:LinkedAnnotationSet xmi:id="690" linkingRelation="696" linkedAnnotations="693"/><semantic:LinkedAnnotationSet xmi:id="702" linkingRelation="708" linkedAnnotations="705"/><semantic:LinkedAnnotationSet xmi:id="715" linkingRelation="721" linkedAnnotations="718"/><semantic:LinkedAnnotationSet xmi:id="724" linkingRelation="730" linkedAnnotations="727"/><semantic:LinkedAnnotationSet xmi:id="736" linkingRelation="742" linkedAnnotations="739"/><semantic:LinkedAnnotationSet xmi:id="749" linkingRelation="755" linkedAnnotations="752"/><semantic:LinkedAnnotationSet xmi:id="758" linkingRelation="764" linkedAnnotations="761"/><semantic:LinkedAnnotationSet xmi:id="771" linkingRelation="777" linkedAnnotations="774"/><semantic:LinkedAnnotationSet xmi:id="780" linkingRelation="786" linkedAnnotations="783"/><shared:ExternalReference xmi:id="34" namespace="GREC Concepts" ID="Transcription_Binding_Site"/><shared:ExternalReference xmi:id="45" namespace="GREC Concepts" ID="Protein"/><shared:ExternalReference xmi:id="63" namespace="GREC Concepts" ID="Protein"/><shared:ExternalReference xmi:id="74" namespace="GREC Concepts" ID="Transcription_Binding_Site"/><shared:ExternalReference xmi:id="99" namespace="GREC Concepts" ID="Gene"/><shared:ExternalReference xmi:id="117" namespace="GREC Concepts" ID="Transcription_Binding_Site"/><shared:ExternalReference xmi:id="135" namespace="GREC Concepts" ID="Virus"/><shared:ExternalReference xmi:id="146" namespace="GREC Concepts" ID="Transcription_Binding_Site"/><shared:ExternalReference xmi:id="157" namespace="GREC Concepts" ID="Gene"/><shared:ExternalReference xmi:id="175" namespace="GREC Concepts" ID="Transcription_Binding_Site"/><shared:ExternalReference xmi:id="185" namespace="GREC Concepts" ID="Gene_Expression"/><shared:ExternalReference xmi:id="196" namespace="GREC Concepts" ID="Transcription_Binding_Site"/><shared:ExternalReference xmi:id="221" namespace="GREC Concepts" ID="Gene"/><shared:ExternalReference xmi:id="352" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="363" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="374" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="385" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="396" namespace="GREC" ID="Gene_Expression"/><shared:ExternalReference xmi:id="407" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="418" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="429" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="440" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="451" namespace="GREC" ID="Gene_Expression"/><shared:ExternalReference xmi:id="462" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="473" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="484" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="495" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="506" namespace="GREC" ID="Regulation"/><shared:ExternalReference xmi:id="519" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="528" namespace="GREC Concepts" ID="Destination"/><shared:ExternalReference xmi:id="541" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="550" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="563" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="572" namespace="GREC Concepts" ID="Destination"/><shared:ExternalReference xmi:id="585" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="594" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="606" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="620" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="629" namespace="GREC Concepts" ID="Location"/><shared:ExternalReference xmi:id="638" namespace="GREC Concepts" ID="Instrument"/><shared:ExternalReference xmi:id="650" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="663" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="672" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="684" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="696" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="708" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="721" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="730" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="742" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="755" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="764" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="777" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="786" namespace="GREC Concepts" ID="Manner"/><semantic:EventAnnotation xmi:id="344" sofa="1" begin="335" end="339" externalReference="352" linkedAnnotationSets="509"/><semantic:EventAnnotation xmi:id="355" sofa="1" begin="384" end="393" externalReference="363" linkedAnnotationSets="531"/><semantic:EventAnnotation xmi:id="366" sofa="1" begin="399" end="406" externalReference="374" linkedAnnotationSets="553"/><semantic:EventAnnotation xmi:id="377" sofa="1" begin="569" end="577" externalReference="385" linkedAnnotationSets="575"/><semantic:EventAnnotation xmi:id="388" sofa="1" begin="741" end="751" externalReference="396" linkedAnnotationSets="597"/><semantic:EventAnnotation xmi:id="399" sofa="1" begin="788" end="796" externalReference="407" linkedAnnotationSets="609"/><semantic:EventAnnotation xmi:id="410" sofa="1" begin="860" end="868" externalReference="418" linkedAnnotationSets="641"/><semantic:EventAnnotation xmi:id="421" sofa="1" begin="930" end="936" externalReference="429" linkedAnnotationSets="653"/><semantic:EventAnnotation xmi:id="432" sofa="1" begin="940" end="948" externalReference="440" linkedAnnotationSets="675"/><semantic:EventAnnotation xmi:id="443" sofa="1" begin="962" end="972" externalReference="451" linkedAnnotationSets="687"/><semantic:EventAnnotation xmi:id="454" sofa="1" begin="974" end="982" externalReference="462" linkedAnnotationSets="699"/><semantic:EventAnnotation xmi:id="465" sofa="1" begin="1036" end="1042" externalReference="473" linkedAnnotationSets="711"/><semantic:EventAnnotation xmi:id="476" sofa="1" begin="1045" end="1053" externalReference="484" linkedAnnotationSets="733"/><semantic:EventAnnotation xmi:id="487" sofa="1" begin="1100" end="1108" externalReference="495" linkedAnnotationSets="745"/><semantic:EventAnnotation xmi:id="498" sofa="1" begin="1125" end="1135" externalReference="506" linkedAnnotationSets="767"/><comparable:IDArray xmi:id="789" array="792" idType="t"/><semantic2:NucleicAcids xmi:id="26" sofa="1" begin="324" end="334" externalReference="34"/><semantic2:NucleicAcids xmi:id="66" sofa="1" begin="410" end="433" externalReference="74"/><semantic2:NucleicAcids xmi:id="91" sofa="1" begin="736" end="740" externalReference="99"/><semantic2:NucleicAcids xmi:id="109" sofa="1" begin="797" end="818" externalReference="117"/><semantic2:NucleicAcids xmi:id="138" sofa="1" begin="869" end="886" externalReference="146"/><semantic2:NucleicAcids xmi:id="149" sofa="1" begin="952" end="961" externalReference="157"/><semantic2:NucleicAcids xmi:id="167" sofa="1" begin="998" end="1002" externalReference="175"/><semantic2:NucleicAcids xmi:id="188" sofa="1" begin="1085" end="1095" externalReference="196"/><semantic2:NucleicAcids xmi:id="213" sofa="1" begin="1120" end="1124" externalReference="221"/><semantic2:Proteins xmi:id="37" sofa="1" begin="340" end="344" externalReference="45"/><semantic2:Proteins xmi:id="55" sofa="1" begin="394" end="398" externalReference="63"/><semantic2:LivingSystems xmi:id="127" sofa="1" begin="822" end="858" externalReference="135"/><semantic2:Processes xmi:id="178" sofa="1" begin="1057" end="1067" externalReference="185"/><semantic2:EventArgumentSpan xmi:id="48" sofa="1" begin="346" end="358"/><semantic2:EventArgumentSpan xmi:id="77" sofa="1" begin="556" end="568"/><semantic2:EventArgumentSpan xmi:id="84" sofa="1" begin="581" end="596"/><semantic2:EventArgumentSpan xmi:id="102" sofa="1" begin="753" end="778"/><semantic2:EventArgumentSpan xmi:id="120" sofa="1" begin="819" end="858"/><semantic2:EventArgumentSpan xmi:id="160" sofa="1" begin="952" end="972"/><semantic2:EventArgumentSpan xmi:id="199" sofa="1" begin="1113" end="1119"/><semantic2:EventArgumentSpan xmi:id="206" sofa="1" begin="1113" end="1135"/><cas:View sofa="1" members="509 516 525 531 538 547 553 560 569 575 582 591 597 603 609 617 626 635 641 647 653 660 669 675 681 687 693 699 705 711 718 727 733 739 745 752 761 767 774 783 792 8 21 13 513 522 535 544 557 566 579 588 600 614 623 632 644 657 666 678 690 702 715 724 736 749 758 771 780 34 45 63 74 99 117 135 146 157 175 185 196 221 352 363 374 385 396 407 418 429 440 451 462 473 484 495 506 519 528 541 550 563 572 585 594 606 620 629 638 650 663 672 684 696 708 721 730 742 755 764 777 786 344 355 366 377 388 399 410 421 432 443 454 465 476 487 498 789 26 66 91 109 138 149 167 188 213 37 55 127 178 48 77 84 102 120 160 199 206"/></xmi:XMI>