RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

Searching..................................................done

Query= gi|254780282|ref|YP_003064695.1| putative transcription
regulator protein [Candidatus Liberibacter asiaticus str. psy62]
         (299 letters)



>3mz1_A Putative transcriptional regulator; structural genomics, PSI-2,
           protein structure initiative, MI center for STR uctural
           genomics, MCSG; 1.88A {Sinorhizobium meliloti}
          Length = 300

 Score =  203 bits (516), Expect = 6e-53
 Identities = 67/286 (23%), Positives = 126/286 (44%), Gaps = 4/286 (1%)

Query: 8   LRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLH 67
           +R F  V  +G+FT A+  L++ +++++  I GLE  +  KL  R  R + +T  G+  +
Sbjct: 3   MRAFLRVVETGNFTRASASLNMPKATVTNLIQGLEAHLRTKLLNRTTRRVLVTPDGALYY 62

Query: 68  RVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLI 127
              + +   L+     L  +   P G+LR+ T       ++   L EF   YPDIQI L 
Sbjct: 63  ERAARLLSDLDELDGSLSTAQSLPKGRLRVETASAFANLVIIPALPEFHKKYPDIQIDLG 122

Query: 128 LDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELD 187
           + ++ ID   +  DCAIR    +   SLI R++  +   A A+  +L+    P    +L+
Sbjct: 123 VSDRTIDYLAENVDCAIRAG-TLTDQSLIARRITEMKFVACASRDFLERHPVPQHPSDLE 181

Query: 188 KHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDY 247
           K+  +    L     +        +  I       +  N   + +     G G+   P +
Sbjct: 182 KNCYVVGYFLPKTGQQMPFHFRRGNEEIEVSGRYTMAANESTTYLAAARAGLGVIQAPLF 241

Query: 248 IVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
           +V++   N  +V ++ D       +Y  YP     + +L+ F +++
Sbjct: 242 MVREDLRNGTMVPVLPDWQVEPMPIYLVYPPNRHLSSRLRVFADWV 287


>3hhg_A Transcriptional regulator, LYSR family; transcription factor,
           structural genomics, oxford protein production facility,
           OPPF; 3.20A {Neisseria meningitidis serogroup B}
          Length = 306

 Score =  182 bits (462), Expect = 1e-46
 Identities = 74/294 (25%), Positives = 130/294 (44%), Gaps = 9/294 (3%)

Query: 1   MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT 60
           M  + ++L VF  V  SGSF+ AAEQL ++ S++SR +  LE ++G+ L  R  R L+LT
Sbjct: 1   MKTNSEELTVFVQVVESGSFSRAAEQLAMANSAVSRIVKRLEEKLGVNLLNRTTRQLSLT 60

Query: 61  EQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYP 120
           E+G++  R    +  ++   + E+      P G L + + + +  +LL     +F   YP
Sbjct: 61  EEGAQYFRRAQRILQEMAAAETEMLAVHEIPQGVLSVDSAMPMVLHLLAPLAAKFNERYP 120

Query: 121 DIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREP 180
            I++ L+     I++     D A+R    +  S L  R L        A+P YL     P
Sbjct: 121 HIRLSLVSSEGYINLIERKVDIALRAG-ELDDSGLRARHLFDSRFRVIASPEYLAKHGTP 179

Query: 181 LSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSG 240
            S +EL  H  + F +  P  +  +  L     P           +S   +   C+ G G
Sbjct: 180 QSTEELAGHQCLGFTE--PGSLNTWAVLDAQGNPYKISPHFT--ASSGEILRSLCLSGCG 235

Query: 241 IALLPDYIVKD---NPNLVRIMEDVITP-SFTVYFCYPEALKNTGKLKAFRNFI 290
           I  L D++V +      L+ ++ +  +  +      Y        +L+ F +F+
Sbjct: 236 IVCLSDFLVDNDIAEGKLIPLLAEQTSDKTHPFNAVYYSDKAVNLRLRVFLDFL 289


>1ixc_A CBNR, LYSR-type regulatory protein; long alpha helix connecting DNA
           binding and regulatory domains, DNA binding protein;
           2.20A {Cupriavidus necator} SCOP: a.4.5.37 c.94.1.1 PDB:
           1iz1_A
          Length = 294

 Score =  148 bits (374), Expect = 1e-36
 Identities = 50/296 (16%), Positives = 104/296 (35%), Gaps = 6/296 (2%)

Query: 4   DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63
           ++ +L+ F  VA +G+   AA++LH+SQ  I+RQ+  LE ++G+ L  R  RG+ LT  G
Sbjct: 2   EFRQLKYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIELTAAG 61

Query: 64  SKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQ 123
                    +      +    + ++    G+L +A         L   L+ FL   P   
Sbjct: 62  HAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTAT 121

Query: 124 IQLILD--NKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPL 181
           + L     ++ ++  +         R   +   +    +    ++            +  
Sbjct: 122 VSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTC 181

Query: 182 SIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGI 241
            + +L    L  F     +       +        EPRI    V    + +   + G+  
Sbjct: 182 KLADLRAVELTLF-PRGGRPSFADEVIGLFKHAGIEPRI-ARVVEDATAALALTMAGAAS 239

Query: 242 ALLPDYIVK-DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296
           +++P  +     P++             +   + +  K    L  F   +   A+D
Sbjct: 240 SIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKE-KQPPILARFVEHVRRSAKD 294


>3fxq_A LYSR type regulator of TSAMBCD; transcriptional regulator, LTTR,
           TSAR, WHTH, DNA- binding, plasmid, transcription; 1.85A
           {Comamonas testosteroni} PDB: 3fxr_A* 3fxu_A* 3fzj_A
          Length = 305

 Score =  147 bits (372), Expect = 2e-36
 Identities = 53/294 (18%), Positives = 92/294 (31%), Gaps = 12/294 (4%)

Query: 4   DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63
               L+    +   GS   AA+ LHLSQ ++S  I  LE E+   L  R  RG++LT  G
Sbjct: 3   KLQTLQALICIEEVGSLRAAAQLLHLSQPALSAAIQQLEDELKAPLLVRTKRGVSLTSFG 62

Query: 64  SKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQ 123
               +    +  +    Q E+ +   +  G +  A +  +    L   L  F   +PD+ 
Sbjct: 63  QAFMKHARLIVTESRRAQEEIGQLRGRWEGHITFAASPAIALAALPLALASFAREFPDVT 122

Query: 124 IQLILDNKDI---DISMDYADCAI-RLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCRE 179
           + +           +     D A+    K    + L  + L    +       +      
Sbjct: 123 VNVRDGMYPAVSPQLRDGTLDFALTAAHKHDIDTDLEAQPLYVSDVVIVGQRQHP--MAN 180

Query: 180 PLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239
              + EL +                 N  A    P        L   S+L++        
Sbjct: 181 ATRLAELQECRWAFSSAPRGPGAIIRNAFARYGLP---EPKLGLVCESFLALPGVVAHSD 237

Query: 240 GIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
            +  +P  + +       L  I      P+ T+Y      L  T        +I
Sbjct: 238 LLTTMPRTLYERNAFKDQLCSIPLQDALPNPTIYVLRRHDLPVTPAAAGLIRWI 291


>3isp_A HTH-type transcriptional regulator RV1985C/MT2039; ROD shaped
           structure, DNA binding domain, regulatory domain,
           DNA-binding; 2.70A {Mycobacterium tuberculosis}
          Length = 303

 Score =  137 bits (346), Expect = 2e-33
 Identities = 47/299 (15%), Positives = 99/299 (33%), Gaps = 16/299 (5%)

Query: 3   FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ 62
            D  +L     V   GSF  AAE+LH++ S++S++I  LE +VG  L  R  +    T  
Sbjct: 6   LDGPQLAALAAVVELGSFDAAAERLHVTPSAVSQRIKSLEQQVGQVLVVRE-KPCRATTA 64

Query: 63  GSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDI 122
           G  L R+ ++          E+  ++     ++ IA   D               +  D+
Sbjct: 65  GIPLLRLAAQTALLESEALAEMGGNASLKRTRITIAVNADSMATWFSAVFDGLGDVLLDV 124

Query: 123 QIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYL-KNCREPL 181
           +I+    +  +      A  A+   +           L  +     A+  ++ ++  +  
Sbjct: 125 RIEDQDHSARLLRE-GVAMGAVTTERN-PVPGCRVHPLGEMRYLPVASRPFVQRHLSDGF 182

Query: 182 SIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGI 241
           +     K   + +       ++D        R I  P      V +          G G 
Sbjct: 183 TXXXXXKAPSLAWNR--DDGLQDMLVRKAFRRAITRPTH---FVPTTEGFTAAARAGLGW 237

Query: 242 ALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDW 297
            + P+ +      + + VR+ +        V   +     ++  +    + +   A   
Sbjct: 238 GMFPEKLAASPLADGSFVRVCD----IHLDVPLYWQCWKLDSPIIARITDTVRAAASGL 292


>3fzv_A Probable transcriptional regulator; LYSR, structural genomics,
           PSI-2, protein structure initiative; 2.71A {Pseudomonas
           aeruginosa PA01}
          Length = 306

 Score =  136 bits (343), Expect = 5e-33
 Identities = 52/297 (17%), Positives = 111/297 (37%), Gaps = 13/297 (4%)

Query: 2   SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYR-HARGLTLT 60
           S+   +L+ F      GS   A+ +L+++Q SIS  + GLE   G++LF R HA+G++LT
Sbjct: 3   SYTLRQLKYFVTTVECGSVAEASRKLYIAQPSISTAVKGLEESFGVQLFIRHHAQGVSLT 62

Query: 61  EQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYP 120
             G++ +R   E+       +      +   +G++ I     +    L G +  F   YP
Sbjct: 63  PAGARFYRKAQELLRMAHEFEQNALADNDVIAGQIDIGCFETVAPLYLPGLIAGFRQAYP 122

Query: 121 DIQIQLILDNKDI---DISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNC 177
            ++I++    +      ++    D A      + S+   +  +     HA     +    
Sbjct: 123 GVEIRIRDGEQQELVQGLTSGRFDLAFLYEHDLDSTIETEPLMPPQRPHALLPEGHRFAG 182

Query: 178 REPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL 237
           +  +S+++L    +I              +  ++   +G          S   +      
Sbjct: 183 QAQVSLRDLCLEPMILL-----DVQPSRTYFVSLFEELGLTPNIAFSSPSIEMVRGMVGQ 237

Query: 238 GSGIALLPDYIV----KDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
           G G +LL          D   +V +       +  +   + +  + T   + F ++ 
Sbjct: 238 GFGFSLLVTRPHSECTYDGKKVVMVDLAEPVSTSGLAAAWLKRAQLTKPARLFVDYC 294


>1uth_A LYSR-type regulatory protein; transcription regulation,
           transcriptional regulator; 2.2A {Burkholderia SP} SCOP:
           c.94.1.1 PDB: 1utb_A 1utb_B 1uth_B 2uyf_A 2uye_A
          Length = 315

 Score =  130 bits (328), Expect = 3e-31
 Identities = 49/296 (16%), Positives = 83/296 (28%), Gaps = 13/296 (4%)

Query: 2   SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE 61
             D + L VF  +    S + A E+L L+Q ++S  +  L T +   LF R ++G+  T 
Sbjct: 13  DIDLNLLVVFNQLLLDRSVSTAGEKLGLTQPAVSNSLKRLRTALNDDLFLRTSKGMEPTP 72

Query: 62  QGSKLHRVTSEVYHKLETTQIELQ-ESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYP 120
               L        + L+T             +    +A T       +   ++      P
Sbjct: 73  YALHLAEPVIYALNTLQTALTTRNSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAP 132

Query: 121 DIQIQLILDNKD---IDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNC 177
            IQI  +  N      D+     D A+ L  P   +   QR+L            +    
Sbjct: 133 HIQISTLRPNAGNLKEDMESGAVDLALGLL-PELQTGFFQRRLFRHRYVCMFRKDHPSAK 191

Query: 178 REPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL 237
                 Q  +  ++            D           G  R   L V  +++I      
Sbjct: 192 SPMSLKQFSELEHVGVVALNTGHGEVDGLL-----ERAGIKRRMRLVVPHFIAIGPILHS 246

Query: 238 GSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
              IA +P            L         P   +   +             R   
Sbjct: 247 TDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLF 302


>1al3_A Cys regulon transcriptional activator CYSB; LYSR family, cysteine
           biosynthesis, transcription regulation; 1.80A
           {Klebsiella aerogenes} SCOP: c.94.1.1
          Length = 324

 Score =  130 bits (326), Expect = 5e-31
 Identities = 65/294 (22%), Positives = 113/294 (38%), Gaps = 11/294 (3%)

Query: 4   DWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-LTE 61
              +LR    V     + +  AE L+ SQ  IS+Q+  LE E+GI++F R  + LT +T 
Sbjct: 2   KLQQLRYIVEVVNHNLNVSSTAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVTP 61

Query: 62  QGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPD 121
            G ++ R+  EV  K++  +    E +    G L +ATT    +  L G +K F+  YP 
Sbjct: 62  AGQEIIRIAREVLSKVDAIKSVAGEHTWPDKGSLYVATTHTQARYALPGVIKGFIERYPR 121

Query: 122 IQIQLILDNKDIDISM---DYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCR 178
           + + +   +            AD AI          L+       +      P +    +
Sbjct: 122 VSLHMHQGSPTQIAEAVSKGNADFAIATEALHLYDDLVMLPCYHWNRSIVVTPEHPLATK 181

Query: 179 EPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG 238
             +SI+EL ++ L+T+           + L T     G              I  Y  LG
Sbjct: 182 GSVSIEELAQYPLVTY----TFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLG 237

Query: 239 SGIALLPDYIVK--DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
            G+ ++    V    +P+LV++  + I    T    +  +      +  F    
Sbjct: 238 LGVGVIASMAVDPVSDPDLVKLDANGIFSHSTTKIGFRRSTFLRSYMYDFIQRF 291


>2h9b_A HTH-type transcriptional regulator BENM; LTTR, transcriptional
           activator, LYSR-type transcriptional regulator; 1.80A
           {Acinetobacter SP} PDB: 2h99_A 2f7a_A* 2f6p_A 2f78_A
           2f6g_A* 2f8d_A 2f97_A*
          Length = 312

 Score =  126 bits (317), Expect = 5e-30
 Identities = 48/294 (16%), Positives = 103/294 (35%), Gaps = 13/294 (4%)

Query: 4   DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63
           +   LR F  V    SFT AA++L ++Q  +SRQI  LE E+GI+L  R +R +  T +G
Sbjct: 2   ELRHLRYFVAVVEEQSFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPVKTTPEG 61

Query: 64  SKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQ 123
              ++   ++   ++      +         +RI     L   LL   +  +   +P+++
Sbjct: 62  HFFYQYAIKLLSNVDQMVSMTKR-IASVEKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLR 120

Query: 124 IQLILDNKDIDISM----DYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCRE 179
           I+L                      RL+    +      +   + +  +A+    +   +
Sbjct: 121 IELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKHSLLRNERLMVAVHASHPLNQMKDK 180

Query: 180 PLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239
            + + +L    ++ +                 D  +   +    +V      +     G 
Sbjct: 181 GVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTK--INEVREVQLALGLVAAGE 238

Query: 240 GIALLPDYIVKDNPN---LVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
           GI+L+P             V +++        +Y       ++T  + +    I
Sbjct: 239 GISLVPASTQSIQLFNLSYVPLLDPD--AITPIYIAVRNMEEST-YIYSLYETI 289


>2h98_A HTH-type transcriptional regulator CATM; BENM, LTTR; 1.80A
           {Acinetobacter SP} PDB: 2h9q_A* 2f7b_A 2f7c_A* 3glb_A*
          Length = 313

 Score =  120 bits (302), Expect = 3e-28
 Identities = 51/292 (17%), Positives = 93/292 (31%), Gaps = 9/292 (3%)

Query: 4   DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63
           +   LR F  V    S + AAE+L ++Q  +SRQI  LE E+GI+LF R  R   +TE G
Sbjct: 2   ELRHLRYFVTVVEEQSISKAAEKLCIAQPPLSRQIQKLEEELGIQLFERGFRPAKVTEAG 61

Query: 64  SKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQ 123
              ++   ++           +  +      LRI     L   LL   +  F    P+I 
Sbjct: 62  MFFYQHAVQILTHTAQASSMAKRIATVSQ-TLRIGYVSSLLYGLLPEIIYLFRQQNPEIH 120

Query: 124 IQLILDNKD---IDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLK-NCRE 179
           I+LI          +     D      K    +             A    H+L      
Sbjct: 121 IELIECGTKDQINALKQGKIDLGFGRLKITDPAIRRIMLHKEQLKLAIHKHHHLNQFAAT 180

Query: 180 PLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239
            + + ++    ++ +          F         +G       ++      +     G 
Sbjct: 181 GVHLSQIIDEPMLLYPVSQKPNFATFIQSL--FTELGLVPSKLTEIREIQLALGLVAAGE 238

Query: 240 GIALLPDYIVKDN-PNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
           G+ ++P   +     NL+ I          +         ++  +      +
Sbjct: 239 GVCIVPASAMDIGVKNLLYIPILDDDAYSPISLAVRNM-DHSNYIPKILACV 289


>2esn_A Probable transcriptional regulator; PA0477, APC5828,transcription,
           PSI, protein structure initiative, MCSG; 2.10A
           {Pseudomonas aeruginosa} SCOP: a.4.5.37 c.94.1.1
          Length = 310

 Score =  115 bits (288), Expect = 1e-26
 Identities = 37/298 (12%), Positives = 76/298 (25%), Gaps = 14/298 (4%)

Query: 2   SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE 61
             D + L VF  + R  +   AA +L +S S+ S  +  L   +  +LF R    +  T+
Sbjct: 9   RLDLNLLLVFDALYRHRNVGTAASELAISASAFSHALGRLRQGLDDELFLRQGNRMQPTQ 68

Query: 62  QGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPD 121
           +   L    +     L     E +      S +  +    D     L   L   L     
Sbjct: 69  RAEHLAAAVAAALRALGEGLEEWRPFVPGQSQRTFVFAATDYTAFALLPPLMNRLQHSAP 128

Query: 122 IQIQLILDNKDIDISMDYADCAIRL------RKPIQSSSLIQRKLVTIHMHAYAAPHYLK 175
                +++ +        A   I                +             A   + +
Sbjct: 129 GVRLRLVNAERKLSVEALASGRIDFALGYDEEHERLPEGIQAHDWFADRYVVVARRDHPR 188

Query: 176 NCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYC 235
               P     L + + +         + D           G  R   +Q+ + L+ +   
Sbjct: 189 LAGAPTLEGYLAERHAVVTPWNEDSGVIDRLL-----ARSGLRREVAVQLPTVLAALFLA 243

Query: 236 VLGSGIALLPDYIVK---DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
                +   P +  +   +   L         P + +                    +
Sbjct: 244 GSTDFLLTAPRHAARALAEAAGLALYPAPFDIPPYVLRLYSHVQHVGRDAHAWMIGQL 301


>3hhf_B Transcriptional regulator, LYSR family; transcription factor,
           structural genomics, oxford protein production facility,
           OPPF; 2.30A {Neisseria meningitidis serogroup B}
          Length = 213

 Score =  107 bits (267), Expect = 4e-24
 Identities = 42/205 (20%), Positives = 75/205 (36%), Gaps = 9/205 (4%)

Query: 90  KPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKP 149
            P G L + + + +  +LL     +F   YP I++ L+     I++     D A+R  + 
Sbjct: 4   IPQGVLSVDSAMPMVLHLLAPLAAKFNERYPHIRLSLVSSEGYINLIERKVDIALRAGEL 63

Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLA 209
              S L  R L        A+P YL     P S +EL  H  + F +          W  
Sbjct: 64  DD-SGLRARHLFDSRFRVIASPEYLAKHGTPQSTEELAGHQCLGFTE----PGSLNTWAV 118

Query: 210 TVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMED-VITP 265
              +            +S   +   C+ G GI  L D++V +      L+ ++ +     
Sbjct: 119 LDAQGNPYKISPHFTASSGEILRSLCLSGCGIVCLSDFLVDNDIAEGKLIPLLAEQTSDK 178

Query: 266 SFTVYFCYPEALKNTGKLKAFRNFI 290
           +      Y        +L+ F +F+
Sbjct: 179 THPFNAVYYSDKAVNLRLRVFLDFL 203


>3kos_A HTH-type transcriptional activator AMPR; alpha-beta sandwich,
           DNA-binding, transcription regulation; HET: MES; 1.83A
           {Citrobacter freundii} PDB: 3kot_A
          Length = 219

 Score = 99.0 bits (246), Expect = 1e-21
 Identities = 34/207 (16%), Positives = 74/207 (35%), Gaps = 12/207 (5%)

Query: 87  SSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRL 146
           ++ +   KL+I          L   L +F   YP I + +   N  +D + +  D  IR 
Sbjct: 6   ATKQTQEKLKIGVVGTFAIGCLFPLLSDFKRSYPHIDLHISTHNNRVDPAAEGLDYTIRY 65

Query: 147 RKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFN 206
                      + L +  M    +P      + P    ++ K  L+          E   
Sbjct: 66  G-GGAWHDTDAQYLCSALMSPLCSPTLASQIQTP---ADILKFPLLRSYR----RDEWAL 117

Query: 207 WLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVI 263
           W+ TV      P  + +  +S +++++    G G+A+ P  +      +  +V+     I
Sbjct: 118 WMQTVGEAPPSPTHNVMVFDSSVTMLEAAQAGMGVAIAPVRMFTHLLSSERIVQPFLTQI 177

Query: 264 TPSFTVYFCYPEALKNTGKLKAFRNFI 290
               + +    ++   T  ++ F  ++
Sbjct: 178 -DLGSYWITRLQSRPETPAMREFSRWL 203


>3fd3_A Chromosome replication initiation inhibitor protein; structural
           genomics, LYSR, PSI-2, protein structure initiative;
           HET: MSE P33 PG4; 1.70A {Agrobacterium tumefaciens str}
          Length = 208

 Score = 89.4 bits (221), Expect = 1e-18
 Identities = 29/212 (13%), Positives = 62/212 (29%), Gaps = 17/212 (8%)

Query: 93  GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISM---DYADCAIRLRKP 149
             L IAT  D         + +F        + + +D++D  +          A+     
Sbjct: 2   VTLNIATNADSLGTWFLDAVSKFTGGSD-YLVNIAVDDQDHTVEWLRGGRVLAAVTAH-D 59

Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYL-KNCREPLSIQELDKHNLITFGDLIPKCMEDFNWL 208
                     L  +  HA A+P ++ ++  + ++   L +   +TF        +     
Sbjct: 60  KPVQGCRVTPLGVLRYHATASPDFMARHFADGVTPAALARAPGLTFNQ-----KDRLQAS 114

Query: 209 ATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVITP 265
                   +       + S    ++  + G G  L P  +V +      LV +M      
Sbjct: 115 WIRTALGEDVSYPTHWLPSTDGFVKASLAGMGWGLNPVQLVAEHLAAGRLVELMPG---T 171

Query: 266 SFTVYFCYPEALKNTGKLKAFRNFIFLKARDW 297
              +   +        +L      +   AR  
Sbjct: 172 PLDIPLYWQVNRLAAERLAGLTANMVGTARVV 203


>1b9m_A Protein (mode); DNA-binding, gene regulation, winged helix turn
           helix, molybdate, OB fold; 1.75A {Escherichia coli}
           SCOP: a.4.5.8 b.40.6.2 b.40.6.2 PDB: 1b9n_A 1o7l_A
           1h9s_A 1h9r_A 1h9s_B
          Length = 265

 Score = 81.1 bits (199), Expect = 3e-16
 Identities = 32/198 (16%), Positives = 63/198 (31%), Gaps = 10/198 (5%)

Query: 1   MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-- 58
           +  D  ++ +   +A SGS +  A+   +S  S    I+ +       L  R   G    
Sbjct: 18  LFADPRRISLLKHIALSGSISQGAKDAGISYKSAWDAINEMNQLSEHILVERATGGKGGG 77

Query: 59  ---LTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQ----NLLQGN 111
              LT  G +L ++   +    +     L +    P   L  A +    Q    N   G 
Sbjct: 78  GAVLTRYGQRLIQLYDLLAQIQQKAFDVLSDDDALPLNSLLAAISRFSLQTSARNQWFGT 137

Query: 112 LKEFLLLYPDIQIQLILDNKDIDISMDYA-DCAIRLRKPIQSSSLIQRKLVTIHMHAYAA 170
           +           + ++L +    + +        RL        LI  K   + +    A
Sbjct: 138 ITARDHDDVQQHVDVLLADGKTRLKVAITAQSGARLGLDEGKEVLILLKAPWVGITQDEA 197

Query: 171 PHYLKNCREPLSIQELDK 188
                + + P  I  +++
Sbjct: 198 VAQNADNQLPGIISHIER 215


>3jv9_A OXYR, transcriptional regulator, LYSR family; LYSR-type
           transcriptional regulator, LTTR, redox, structural
           genomics, OPPF; 2.39A {Neisseria meningitidis}
          Length = 219

 Score = 77.8 bits (191), Expect = 3e-15
 Identities = 29/204 (14%), Positives = 64/204 (31%), Gaps = 5/204 (2%)

Query: 92  SGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--IDISMDYADCAIRLRKP 149
            G  ++     +   LL   +       P + + L  +      +        AI + +P
Sbjct: 3   EGAFKLGLIFTVAPYLLPKLIVSLRRTAPKMPLMLEENYTHTLTESLKRGDVDAIIVAEP 62

Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLA 209
            Q   ++   L            +     + +S + L +  ++   +      +  +  +
Sbjct: 63  FQEPGIVTEPLYDEPFFVIVPKGHSFEELDAVSPRMLGEEQVLLLTEGNCMRDQVLSSCS 122

Query: 210 TVD-RPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVK--DNPNLVRIMEDVITPS 266
            +  +   +   + LQ +S  +I      G  I++LP   +   D+     I  +   PS
Sbjct: 123 ELAAKQRIQGLTNTLQGSSINTIRHMVASGLAISVLPATALTENDHMLFSIIPFEGTPPS 182

Query: 267 FTVYFCYPEALKNTGKLKAFRNFI 290
             V   Y         L A +  I
Sbjct: 183 RRVVLAYRRNFVRPKALSAMKAAI 206


>1i6a_A OXYR, hydrogen peroxide-inducible genes activator; OXYR regulatory
           domain, oxidized form, transcription; 2.30A {Escherichia
           coli} SCOP: c.94.1.1 PDB: 1i69_A
          Length = 219

 Score = 73.5 bits (179), Expect = 5e-14
 Identities = 35/204 (17%), Positives = 62/204 (30%), Gaps = 9/204 (4%)

Query: 92  SGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--IDISMDYADCAIRLRKP 149
           SG L I     +G  LL   +      +P +++ L        +         A+ L   
Sbjct: 4   SGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDAVILALV 63

Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLA 209
            +S + I+  L    M       +    RE + + +L    L+   D      +   +  
Sbjct: 64  KESEAFIEVPLFDEPMLLAIYEDHPWANREAVPMADLAGEKLLMLEDGHCLRDQAMGFC- 122

Query: 210 TVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVITPS 266
                 G    +  +  S  ++      GSGI LLP   V        +V +      P 
Sbjct: 123 ---FEAGADEDTHFRATSLETLRNMVAAGSGITLLPALAVPPERKRDGVVYLPAIKPEPR 179

Query: 267 FTVYFCYPEALKNTGKLKAFRNFI 290
            T+   Y        + +     I
Sbjct: 180 RTIGLVYRPGSPLRSRYEQLAEAI 203


>2qsx_A Putative transcriptional regulator, LYSR family; the putative
           transcriptional regulator, PSI-2; 1.64A {Vibrio
           parahaemolyticus rimd 2210633}
          Length = 218

 Score = 73.2 bits (178), Expect = 6e-14
 Identities = 27/223 (12%), Positives = 73/223 (32%), Gaps = 13/223 (5%)

Query: 77  LETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDIS 136
           ++     L +++      L +  T       L  N+ +F   +P+I+++++  +  +   
Sbjct: 4   IQHATASLIQTN-TDQELLVVDVTPSFASLWLVPNINDFHQRHPNIRVKILTGDGAVKNI 62

Query: 137 MDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGD 196
              +D  +R   P+ +     + L    +      +  K        Q +  +  I    
Sbjct: 63  HGESDLHVRCL-PLSTHYEYSQLLCEETLLLIGNTNLPKLSD----NQAISHYPFIPQTT 117

Query: 197 LIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NP 253
                 + +      +          +    +    +   +  G+ALLPD++ +      
Sbjct: 118 ----RPQLWEQFKQENDLECPITYHSVGFEHFYLACEAVRMEKGLALLPDFMAQFSILRG 173

Query: 254 NLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296
           ++  I    +   +  Y   P     + K+  F +++  K   
Sbjct: 174 DIQHIGNLKLHSGYGYYVVIPNFRLTSRKVALFHDWLKDKLTH 216


>3ho7_A OXYR; beta-alpha-barrels, DNA-binding, transcription, transcriptio
           regulation; 1.58A {Porphyromonas gingivalis}
          Length = 232

 Score = 70.5 bits (172), Expect = 5e-13
 Identities = 26/213 (12%), Positives = 59/213 (27%), Gaps = 11/213 (5%)

Query: 83  ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--IDISMDYA 140
           E Q+S    +G+L IA    +   LL      +      ++I +        +   +   
Sbjct: 4   EEQQS---LTGRLNIAVLPTIAPYLLPRVFPIWKKELAGLEIHVSEMQTSRCLASLLSGE 60

Query: 141 DCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPK 200
                +    ++  L    L       Y +       ++ +   E++ H L    +    
Sbjct: 61  IDMAIIASKAETEGLEDDLLYYEEFLGYVSRCEPLFEQDVIRTTEVNPHRLWLLDEGHCF 120

Query: 201 CMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVK---DNPNLVR 257
             +   +           R +     S  + M+    G GI  +P   V+    +   + 
Sbjct: 121 RDQLVRFCQMKGL---HERQTAYSGGSMEAFMRLVESGQGITFIPQLTVEQLSPSQKELV 177

Query: 258 IMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
               +  P   V     +        +     +
Sbjct: 178 RPFGMPRPVREVRLAVRQDYSRRKLREQLIGLL 210


>2ijl_A AGR_C_4647P, molybdenum-binding transcriptional repressor;
           structural genomics, DNA-binding protein, PSI-2; 2.30A
           {Agrobacterium tumefaciens str}
          Length = 135

 Score = 70.5 bits (172), Expect = 5e-13
 Identities = 16/107 (14%), Positives = 34/107 (31%), Gaps = 8/107 (7%)

Query: 1   MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRH-----AR 55
                 K+ +  ++A +GS + A   + +S       +  L       +           
Sbjct: 22  ERLGHGKVELMQLIAETGSISAAGRAMDMSYRRAWLLVDALNHMFRQPVICSQRGGKQGG 81

Query: 56  GLTLTEQGSKLHRVTSEVYHKLETT---QIELQESSVKPSGKLRIAT 99
           G  LT  G++L      +  ++       I+  E++  P   L    
Sbjct: 82  GAALTVFGAELLERYRGMEERMNEALREDIDWLEANRNPQDALNRDR 128


>2ql3_A Probable transcriptional regulator, LYSR family protein; APC7314,
           rhodococcus SP. RHA1, structural genomics, PSI-2,
           protein structure initiative; HET: MSE; 2.05A
           {Rhodococcus SP}
          Length = 209

 Score = 68.2 bits (165), Expect = 2e-12
 Identities = 34/207 (16%), Positives = 65/207 (31%), Gaps = 13/207 (6%)

Query: 92  SGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD---IDISMDYADCAIRLRK 148
           +G + +     LG  +L   L  F   YP   ++   D ++     +     D AI    
Sbjct: 4   AGPIAVGCYPALGPTILPSMLYAFTAEYPRASVEFREDTQNRLRTQLEGGELDVAIVYDL 63

Query: 149 PIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWL 208
            +         +    M    A H L     P+ + +L +H ++             N  
Sbjct: 64  DLSPEWQTVPLMTREPMVVLGAEHPLAGVDGPVRLADLAEHPMVLL-----DAPPSTNHA 118

Query: 209 ATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKDNPN-----LVRIMEDVI 263
             V R  G       +  ++ +   +   G G  LL      D        +V+ + +  
Sbjct: 119 MDVCREAGFAPRVAYRTANFETARAFVGRGLGWTLLLQRPRVDVTYEGLPVVVKPIAEPK 178

Query: 264 TPSFTVYFCYPEALKNTGKLKAFRNFI 290
             S  V   + +    +   +AF  F+
Sbjct: 179 PASVAVVVAWHQEATLSRVARAFIRFV 205


>2hxr_A HTH-type transcriptional regulator CYNR; CYNR transcriptional
           regulator LYSR structural genomics, PSI-2, protein
           structure initiative; 2.05A {Escherichia coli K12} PDB:
           3hfu_A
          Length = 238

 Score = 57.1 bits (136), Expect = 4e-09
 Identities = 39/244 (15%), Positives = 73/244 (29%), Gaps = 22/244 (9%)

Query: 49  LFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLL 108
           ++ ++A                     +L   +  + + +    G LRIA T       +
Sbjct: 2   VWRQYAS----------------RALQELGAGKRAIHDVADLTRGSLRIAVTPTFTSYFI 45

Query: 109 QGNLKEFLLLY--PDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMH 166
              + +F   Y    +Q+Q +   K  D+             P+ S  L    L+T  + 
Sbjct: 46  GPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLA 105

Query: 167 AYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVN 226
              A H+     E +++  L    L+               +       G      ++ N
Sbjct: 106 LVVAQHHPLAVHEQVALSRLHDEKLVLL----SAEFATREQIDHYCEKAGLHPQVVIEAN 161

Query: 227 SYLSIMQYCVLGSGIALLPDYIVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAF 286
           S  ++++     S   LLP  I   +  L  I         T      +    T   KAF
Sbjct: 162 SISAVLELIRRTSLSTLLPAAIATQHDGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAF 221

Query: 287 RNFI 290
            +  
Sbjct: 222 LHMA 225


>2fyi_A HTH-type transcriptional regulator CBL; Lys-R family,
           cofactor-binding domain, cysteine biosynthesis; 2.80A
           {Escherichia coli K12} SCOP: c.94.1.1
          Length = 228

 Score = 55.6 bits (132), Expect = 1e-08
 Identities = 34/202 (16%), Positives = 62/202 (30%), Gaps = 3/202 (1%)

Query: 91  PSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPI 150
            SG L IATT    +  L   +K F  L+P+++++LI        ++     A       
Sbjct: 12  TSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASE 71

Query: 151 QSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLAT 210
           + S+  Q          ++      +    +S   L+                       
Sbjct: 72  RLSNDPQLVAFPWFRWHHSLLVPHDHPLTQISPLTLESIAKWPLITYRQGITGRSRIDDA 131

Query: 211 VDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD--NPNLVRIMEDVITPSFT 268
             R      I     +S +    Y  LG GI L+ +    +    NL+R+    +  + T
Sbjct: 132 FARKGLLADIVLSAQDSDVIKT-YVALGLGIGLVAEQSSGEQEEENLIRLDTRHLFDANT 190

Query: 269 VYFCYPEALKNTGKLKAFRNFI 290
           V+            +  F    
Sbjct: 191 VWLGLKRGQLQRNYVWRFLELC 212


>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein
           structure initiative; 2.20A {Thermoplasma acidophilum
           dsm 1728} SCOP: a.4.5.28 b.43.5.2
          Length = 230

 Score = 46.1 bits (109), Expect = 9e-06
 Identities = 31/201 (15%), Positives = 69/201 (34%), Gaps = 21/201 (10%)

Query: 1   MSFD-----WDKLRVFYVVARSG-----SFTHAAEQLHLSQSSISRQISGLETEVGI-KL 49
           MS +     +  ++     A +      + +  A+ L +SQ S SR I  LE    I + 
Sbjct: 1   MSLETDDQYYRAIKKIKEAAEASNRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRT 60

Query: 50  FYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQ 109
             +  + L +TE+G  +         ++   +  +  +    SG       +   Q ++Q
Sbjct: 61  VTKRGQILNITEKGLDVLYTEFADLSRILAIKNNVVITGTVTSGMGEGRYYVARKQYIIQ 120

Query: 110 GNLKEFLLLYP-DIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAY 168
              K  ++ Y   + I++   +      +      I +           R   ++     
Sbjct: 121 FQEKLGIIPYLGTLNIKVDQASLPELRKIRGFR-GIHIEGFKTED----RTFGSVK---- 171

Query: 169 AAPHYLKNCREPLSIQELDKH 189
           A P  ++N    + + E   +
Sbjct: 172 AFPAKIQNIPCFVIMPERTVY 192


>3oxn_A Putative transcriptional regulator, LYSR family; structural
           genomics, PSI-2, protein structure initiative; 2.70A
           {Vibrio parahaemolyticus}
          Length = 241

 Score = 45.0 bits (106), Expect = 2e-05
 Identities = 25/205 (12%), Positives = 50/205 (24%), Gaps = 11/205 (5%)

Query: 92  SGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--IDISMDYADCAIRLRKP 149
                IATT    Q +L   L       P++    +    D   D            R  
Sbjct: 18  DQTFTIATTDYAMQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPT 77

Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLA 209
                L    L  + +    +  +    +E  S+ +   H                  L 
Sbjct: 78  GPVEPLRSEILGRVGVLCLLSKQHPLANQEM-SLDDYLSHPHAMIAISDGVKALIEQALI 136

Query: 210 TVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVK---DNPNLVRIMEDVITPS 266
                    R   L+     + +        I  +P  +     +  +LV          
Sbjct: 137 D-----KPQRKMVLRAYHLEAALAIVDTLPIIITVPADLAYLVAERYDLVVKPLPFQFTP 191

Query: 267 FTVYFCYPEALKNTGKLKAFRNFIF 291
           F     +    +++   +  R+ + 
Sbjct: 192 FDYSMIWHARCEHSPAQEWLRSVVR 216


>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix
           prnai nucleotide-binding domain; HET: MSE; 1.80A
           {Sulfolobus solfataricus}
          Length = 244

 Score = 39.7 bits (92), Expect = 8e-04
 Identities = 15/85 (17%), Positives = 38/85 (44%), Gaps = 3/85 (3%)

Query: 8   LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSK 65
           +++  V+  +        A+ L  S+ ++  +I+ L+   GI       R + L E G  
Sbjct: 155 MKLLNVLYETKGTGITELAKMLDKSEKTLINKIAELKKF-GILTQKGKDRKVELNELGLN 213

Query: 66  LHRVTSEVYHKLETTQIELQESSVK 90
           + ++   V    ++++  ++E+  K
Sbjct: 214 VIKLNKSVIESSKSSEELVKENKGK 238


>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription
           regulator, activator, DNA-binding, repressor; HET: SAL;
           2.30A {Salmonella typhimurium} SCOP: a.4.5.28
          Length = 166

 Score = 36.0 bits (83), Expect = 0.011
 Identities = 17/78 (21%), Positives = 28/78 (35%), Gaps = 7/78 (8%)

Query: 8   LRVFYVVARSG---SFTHAAEQLHLSQSSISRQISGLE----TEVGIKLFYRHARGLTLT 60
               + + +     S    A+ + + Q S+ R +  LE             R A+ + LT
Sbjct: 56  WVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLT 115

Query: 61  EQGSKLHRVTSEVYHKLE 78
           E+   L     EV HK  
Sbjct: 116 EKAEPLIAEMEEVIHKTR 133


>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor,
           winged helix motif, DNA-binding; 1.40A {Methanobacterium
           thermoautotrophicum} PDB: 3bpx_A*
          Length = 138

 Score = 35.7 bits (82), Expect = 0.012
 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 6/77 (7%)

Query: 8   LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLFY----RHARGLTLTE 61
           +     + R         A   H+ + +I+R +  LE    I+       R    L +T 
Sbjct: 32  VACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDPENRRRYILEVTR 91

Query: 62  QGSKLHRVTSEVYHKLE 78
           +G ++  +  +V  + E
Sbjct: 92  RGEEIIPLILKVEERWE 108


>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural
           genomics, MI center for structural genomics, MCSG,
           unknown function; 1.78A {Listeria innocua}
          Length = 143

 Score = 35.4 bits (82), Expect = 0.016
 Identities = 11/76 (14%), Positives = 24/76 (31%), Gaps = 6/76 (7%)

Query: 9   RVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLFY----RHARGLTLTEQ 62
            V   +  +   +    A        +++R +  L  +  I        R    L+LT++
Sbjct: 41  SVLEGIEANEPISQKEIALWTKKDTPTVNRIVDVLLRKELIVREISTEDRRISLLSLTDK 100

Query: 63  GSKLHRVTSEVYHKLE 78
           G K      ++     
Sbjct: 101 GRKETTELRDIVEASC 116


>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine
           disulfide, MARR-family transcriptional regulator,
           DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB:
           3hse_A 3hrm_A
          Length = 140

 Score = 34.5 bits (79), Expect = 0.030
 Identities = 12/77 (15%), Positives = 29/77 (37%), Gaps = 6/77 (7%)

Query: 8   LRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGI----KLFYRHARGLTLTE 61
             V   +      +     E++ L   +++  +  LE +  +    +        ++LTE
Sbjct: 39  YIVLMAIENDEKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRTREEKDERNLQISLTE 98

Query: 62  QGSKLHRVTSEVYHKLE 78
           QG  +    +E+  K+ 
Sbjct: 99  QGKAIKSPLAEISVKVF 115


>1jgs_A Multiple antibiotic resistance protein MARR; transcription
           regulation, DNA-binding, repressor; HET: SAL; 2.30A
           {Escherichia coli} SCOP: a.4.5.28
          Length = 138

 Score = 32.9 bits (75), Expect = 0.083
 Identities = 8/75 (10%), Positives = 27/75 (36%), Gaps = 6/75 (8%)

Query: 8   LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKL----FYRHARGLTLTE 61
            +V   +  +   T     + L +   +++R +  L  +  ++       +    + LT 
Sbjct: 37  FKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTT 96

Query: 62  QGSKLHRVTSEVYHK 76
            G+ +     ++  +
Sbjct: 97  GGAAICEQCHQLVGQ 111


>2vh1_A FTSQ, cell division protein FTSQ; potra, membrane, septation, cell
           cycle, transmembrane, inner membrane; 2.7A {Escherichia
           coli}
          Length = 220

 Score = 32.8 bits (74), Expect = 0.094
 Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 3/63 (4%)

Query: 99  TTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDID-ISMDYAD-CAIRLRKPIQSSSLI 156
             ++LG+      L  F+ LYP +Q Q   D K I  + + Y    A+    P+      
Sbjct: 151 IKLNLGRGDTMKRLARFVELYPVLQQQAQTDGKRISYVDLRYDSGAAVGW-APLPPEEST 209

Query: 157 QRK 159
           Q++
Sbjct: 210 QQQ 212


>2fxa_A Protease production regulatory protein HPR; protease porduction,
           regulation, structural genomics, PSI, protein structure
           initiative; HET: PGE P6G 1PE; 2.40A {Bacillus subtilis}
           SCOP: a.4.5.28
          Length = 207

 Score = 32.7 bits (74), Expect = 0.11
 Identities = 11/76 (14%), Positives = 27/76 (35%), Gaps = 6/76 (7%)

Query: 9   RVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLE----TEVGIKLFYRHARGLTLTEQ 62
            + ++  +    S +  A+   +  S+       LE         +L  +    + LTE+
Sbjct: 52  HILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEE 111

Query: 63  GSKLHRVTSEVYHKLE 78
           G+++     E +    
Sbjct: 112 GTEVFWSLLEEFDPTR 127


>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for
           structural genomics, PSI, protein structure initiative,
           MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28
          Length = 145

 Score = 32.3 bits (73), Expect = 0.14
 Identities = 11/77 (14%), Positives = 27/77 (35%), Gaps = 6/77 (7%)

Query: 8   LRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFY----RHARGLTLTE 61
             +   +   G       +  L +++S+++  +  LE +  +        R A  L +T 
Sbjct: 36  FDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITR 95

Query: 62  QGSKLHRVTSEVYHKLE 78
           +G ++     E      
Sbjct: 96  KGEEVIEKVIERRENFI 112


>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
           photosynthetic reaction center, peripheral antenna; HET:
           CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
          Length = 154

 Score = 31.9 bits (71), Expect = 0.17
 Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 11/32 (34%)

Query: 105 QNL--LQGNLKEFLLLY-----PDIQIQLILD 129
           Q L  LQ +LK    LY     P + I+  ++
Sbjct: 20  QALKKLQASLK----LYADDSAPALAIKATME 47


>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance
           regulator, virulence determinant, transcriptional
           factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28
          Length = 142

 Score = 31.8 bits (72), Expect = 0.18
 Identities = 11/77 (14%), Positives = 24/77 (31%), Gaps = 6/77 (7%)

Query: 8   LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLF----YRHARGLTLTE 61
             V  ++             +L L   ++S  +  +E    IK       +    + LT+
Sbjct: 40  FLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTD 99

Query: 62  QGSKLHRVTSEVYHKLE 78
           +   +    S    K+ 
Sbjct: 100 KSETIRPELSNASDKVA 116


>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1,
           putative MARR-like transcription regulator, structural
           genomics; 2.38A {Bacillus cereus atcc 10987}
          Length = 139

 Score = 31.1 bits (70), Expect = 0.33
 Identities = 12/77 (15%), Positives = 30/77 (38%), Gaps = 6/77 (7%)

Query: 8   LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLF----YRHARGLTLTE 61
             V  V+A+SG  + +   E +    S+++  I  ++ +  +        +    + LT+
Sbjct: 36  FGVIQVLAKSGKVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTEKNPNDQRETLVYLTK 95

Query: 62  QGSKLHRVTSEVYHKLE 78
           +G +  +     Y    
Sbjct: 96  KGEETKKQVDVQYSDFL 112


>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator,
           APC5857, structural genomics, PSI, protein structure
           initiative; 1.80A {Pseudomonas aeruginosa} SCOP:
           a.4.5.28
          Length = 146

 Score = 30.4 bits (68), Expect = 0.45
 Identities = 10/59 (16%), Positives = 26/59 (44%), Gaps = 4/59 (6%)

Query: 24  AEQLHLSQSSISRQISGLETEVGIKLFY----RHARGLTLTEQGSKLHRVTSEVYHKLE 78
           A+ + +   +++R + GLE++  ++       R A+ + LT +   L      +   + 
Sbjct: 59  AQSVGVEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIADIEAIAASVR 117


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl reductase,
           beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae}
          Length = 2006

 Score = 29.5 bits (66), Expect = 0.85
 Identities = 22/187 (11%), Positives = 46/187 (24%), Gaps = 81/187 (43%)

Query: 166 HAYAAPHYLKNCREPLSIQELDKH-----------------------NLITFGDLIPKCM 202
           +    P  + +    L+ +++  +                       NL+  G   P+ +
Sbjct: 330 NNEGVPSPMLSISN-LTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGP--PQSL 386

Query: 203 EDFN-WLATVDRPIGE-----------PRISCLQVNSYLSIMQYCVLGSGIALLP---DY 247
              N  L     P G             + S    N +L +             P     
Sbjct: 387 YGLNLTLRKAKAPSGLDQSRIPFSERKLKFS----NRFLPVA-----------SPFHSHL 431

Query: 248 IVKDNPNLVRIMEDVITPSFTVYFCYPEALK------NTGKLKAFRNF-----------I 290
           +V  +     I +D++  + +  F   + ++        G     R             I
Sbjct: 432 LVPASD---LINKDLVKNNVS--FN-AKDIQIPVYDTFDG--SDLRVLSGSISERIVDCI 483

Query: 291 FLKARDW 297
                 W
Sbjct: 484 IRLPVKW 490


>2vh2_A FTSQ, cell division protein FTSQ; potra, cell cycle; 3.4A {Yersinia
           enterocolitica}
          Length = 255

 Score = 29.4 bits (65), Expect = 1.00
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 99  TTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYAD-CAIRLR 147
             ++LG++   G L+ F+ LYP +Q Q       +D  + Y    AI   
Sbjct: 177 VRLELGRDDRMGRLQRFIELYPMLQQQPDKRVSYVD--LRYETGAAIGWA 224


>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structural
           genomics, protein structure initiative; HET: GOL; 2.00A
           {Rhodococcus jostii RHA1}
          Length = 150

 Score = 28.4 bits (63), Expect = 2.0
 Identities = 12/77 (15%), Positives = 21/77 (27%), Gaps = 7/77 (9%)

Query: 9   RVFYVVARSG---SFTHAAEQLHLSQSSISRQISGLETEVGIKL----FYRHARGLTLTE 61
            V  +        +    A  + L  S I   +  LE    +        R  + +  TE
Sbjct: 43  SVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATE 102

Query: 62  QGSKLHRVTSEVYHKLE 78
           +G +L            
Sbjct: 103 EGRRLRDDAKARVDAAH 119


>1fjm_A Protein serine/threonine phosphatase-1 (alpha isoform, type 1);
           hydrolase, complex (hydrolase/toxin) complex; HET: ADD;
           2.10A {Oryctolagus cuniculus} SCOP: d.159.1.3
          Length = 330

 Score = 28.1 bits (62), Expect = 2.2
 Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 9/67 (13%)

Query: 158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFG--DLIPKCMEDFNWLATVD--- 212
           R+LVT+    ++AP+Y        ++  +D+  + +F       K    +   + ++   
Sbjct: 261 RQLVTL----FSAPNYCGEFDNAGAMMSVDETLMCSFQILKPADKNKGKYGQFSGLNPGG 316

Query: 213 RPIGEPR 219
           RPI  PR
Sbjct: 317 RPITPPR 323


>1z91_A Organic hydroperoxide resistance transcriptional regulator; OHRR,
           MARR family, bacterial transcription factor, DNA binding
           protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB:
           1z9c_A*
          Length = 147

 Score = 27.3 bits (60), Expect = 4.0
 Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 4/59 (6%)

Query: 24  AEQLHLSQSSISRQISGLETEVGIKLF----YRHARGLTLTEQGSKLHRVTSEVYHKLE 78
            EQL+L   +++  +  +E +  I          +  ++LTE G+ L     ++   + 
Sbjct: 61  GEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTIL 119


>2wus_R RODZ, putative uncharacterized protein; structural protein, cell
           WALL morphogenesis, bacterial cytos bacterial actin;
           2.90A {Thermotoga maritima}
          Length = 112

 Score = 27.3 bits (60), Expect = 4.8
 Identities = 10/73 (13%), Positives = 29/73 (39%), Gaps = 3/73 (4%)

Query: 44  EVGIKL-FYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLR-IATTI 101
           E+G      R  R +TL +     + +      ++E   ++  ++ V     ++  +  +
Sbjct: 7   ELGETFRKKREERRITLLDASLFTN-INPSKLKRIEEGDLKGLDAEVYIKSYIKRYSEFL 65

Query: 102 DLGQNLLQGNLKE 114
           +L  + +    +E
Sbjct: 66  ELSPDEMLKLYEE 78


>3pfd_A Acyl-COA dehydrogenase; structural genomics, seattle structural
           genomics center for infectious disease, ssgcid; HET:
           FDA; 2.10A {Mycobacterium thermoresistibile}
          Length = 393

 Score = 27.1 bits (60), Expect = 4.9
 Identities = 8/41 (19%), Positives = 17/41 (41%)

Query: 133 IDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHY 173
           +D ++ Y     +  +P+  +  +Q  L  + M   AA   
Sbjct: 271 LDAAIAYTKERKQFGRPVSDNQGVQFMLADMAMKIEAARLM 311


>1z05_A Transcriptional regulator, ROK family; structural genomics, PSI,
          protein structure initiative; 2.00A {Vibrio cholerae o1
          biovar eltor str} SCOP: a.4.5.63 c.55.1.10 c.55.1.10
          Length = 429

 Score = 27.2 bits (59), Expect = 5.4
 Identities = 7/38 (18%), Positives = 19/38 (50%), Gaps = 2/38 (5%)

Query: 9  RVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETE 44
          RV+ ++ + G  +    +++  L+ +SI++    L   
Sbjct: 43 RVYKLIDQKGPISRIDLSKESELAPASITKITRELIDA 80


>1qgc_4 Protein (inmunoglobuline); virus-antibody complex, icosahedral
           virus, virus/immune system complex; 30.00A {Mus
           musculus} SCOP: i.6.1.1
          Length = 438

 Score = 26.9 bits (59), Expect = 6.3
 Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 15/56 (26%)

Query: 57  LTLT-EQGSKLHRVTSEVYHKLETT-----------QIELQES---SVKPSGKLRI 97
           LTLT ++  + +  T E  HK  T+           ++ L ES    VKP G L++
Sbjct: 183 LTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNECEVMLVESGGGLVKPGGSLKL 238


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.323    0.138    0.410 

Gapped
Lambda     K      H
   0.267   0.0642    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,556,784
Number of extensions: 114819
Number of successful extensions: 354
Number of sequences better than 10.0: 1
Number of HSP's gapped: 322
Number of HSP's successfully gapped: 54
Length of query: 299
Length of database: 5,693,230
Length adjustment: 92
Effective length of query: 207
Effective length of database: 3,462,782
Effective search space: 716795874
Effective search space used: 716795874
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (25.5 bits)