RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780693|ref|YP_003065106.1| transcriptional regulator
protein [Candidatus Liberibacter asiaticus str. psy62]
         (235 letters)



>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix,
           two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}
          Length = 236

 Score = 80.7 bits (198), Expect = 3e-16
 Identities = 31/122 (25%), Positives = 50/122 (40%), Gaps = 4/122 (3%)

Query: 117 GIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLEL----FKKRSSAAR 172
           G+  PV   +     + F S    +    +++   A   ++    +L     K   +  +
Sbjct: 115 GVTIPVEGSYGSAMMLTFASPERKVDISGVLDPKKAVQLLMMVHYQLKIIAAKTVLNPKQ 174

Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG 232
            L+ RE  CL  A  G T+   A   G++  TV  YL  A  KLDA +  Q +A A   G
Sbjct: 175 MLSPREMLCLVWASKGKTASVTANLTGINARTVQHYLDKARAKLDAESVPQLVAIAKDRG 234

Query: 233 YI 234
            +
Sbjct: 235 LV 236


>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA
           binding motif, alpha/beta/alpha sandwich; HET: LAE;
           1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2
           d.110.5.1 PDB: 1h0m_A*
          Length = 234

 Score = 79.5 bits (195), Expect = 6e-16
 Identities = 31/165 (18%), Positives = 56/165 (33%), Gaps = 4/165 (2%)

Query: 74  DDFLFHFNSGLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVI 133
           D  +    S      W    E   +    +            +GI  P++          
Sbjct: 70  DPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFMSMFT 129

Query: 134 FTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARN----LTERETSCLQLAGDGY 189
             S+  ++  +  I+A  A   +      +   R++        L  +E + L+    G 
Sbjct: 130 MASDKPVIDLDREIDAVAAAATIGQIHARISFLRTTPTAEDAAWLDPKEATYLRWIAVGK 189

Query: 190 TSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234
           T EEIA+  G+  ++V   L  A  + D  ++    A AIR   I
Sbjct: 190 TMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234


>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein;
           NMR {Erwinia amylovora} SCOP: a.4.6.2
          Length = 99

 Score = 76.8 bits (189), Expect = 4e-15
 Identities = 20/80 (25%), Positives = 36/80 (45%)

Query: 155 QVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV 214
           + +   LE         + L+ +E+  L+L  +G+   EIA+KL  S+ T+++   SA +
Sbjct: 16  ESVAKLLEKISAGGYGDKRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMM 75

Query: 215 KLDAVNRIQAIAKAIRFGYI 234
           KL   N I  +         
Sbjct: 76  KLGVDNDIALLNYLSSVSMT 95


>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding
           domain, activator, antibiotic resistance, cytoplasm,
           DNA-binding; NMR {Staphylococcus aureus}
          Length = 91

 Score = 73.7 bits (181), Expect = 3e-14
 Identities = 24/70 (34%), Positives = 38/70 (54%)

Query: 165 KKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA 224
           KKR+     LTERE   L L   GY+++EIA    +++ TV  ++ +   KL+  +R QA
Sbjct: 21  KKRAELYEMLTEREMEILLLIAKGYSNQEIASASHITIKTVKTHVSNILSKLEVQDRTQA 80

Query: 225 IAKAIRFGYI 234
           +  A +   I
Sbjct: 81  VIYAFQHNLI 90


>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory
           proteins, LUXR family, structural genomics; 2.04A
           {Bacteroides thetaiotaomicron vpi-5482}
          Length = 258

 Score = 73.5 bits (180), Expect = 4e-14
 Identities = 35/196 (17%), Positives = 69/196 (35%), Gaps = 16/196 (8%)

Query: 53  ELHNYDLDSGDIPNILIETYGDDFLF-HFNSGLLPII----------WQSIQEETVIESS 101
                  +  +    +I++  +D ++   +   L               S+     ++  
Sbjct: 65  NFLGLTPE--EAALSVIDSMDEDCIYRRIHPEDLVEKRLMEYKFFQKTFSMSPGERLKYR 122

Query: 102 GQLSVRL---EGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVIT 158
           G+  +R+   +G       +   ++     N ++IF    L          +    Q+  
Sbjct: 123 GRCRLRMMNEKGVYQYIDNLVQIMQNTPAGNVWLIFCLYSLSADQRPEQGIYATITQMER 182

Query: 159 DFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218
             +E           L+ERE   L+    G +S+EIA  L +SV+TVN +  +   KL  
Sbjct: 183 GEVETLSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSV 242

Query: 219 VNRIQAIAKAIRFGYI 234
            N I+A   A     +
Sbjct: 243 GNSIEACRAAELMKLL 258


>2krf_A Transcriptional regulatory protein COMA; activator, competence,
           DNA-binding, transcription regulation component
           regulatory system; NMR {Bacillus subtilis}
          Length = 73

 Score = 71.1 bits (175), Expect = 2e-13
 Identities = 22/61 (36%), Positives = 33/61 (54%)

Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY 233
           LT RE   LQ    G+T++EIA+ L LS  ++   L S   KL+  +R +A+  A   G 
Sbjct: 13  LTPRECLILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFNKLNVGSRTEAVLIAKSDGV 72

Query: 234 I 234
           +
Sbjct: 73  L 73


>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR
           {Sinorhizobium meliloti}
          Length = 79

 Score = 69.4 bits (170), Expect = 7e-13
 Identities = 16/61 (26%), Positives = 27/61 (44%)

Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY 233
           L+ERE   L     G  ++ IA  L +S  TV  +  +   K+ A +    +  A+  G+
Sbjct: 17  LSERERQVLSAVVAGLPNKSIAYDLDISPRTVEVHRANVMAKMKAKSLPHLVRMALAGGF 76

Query: 234 I 234
            
Sbjct: 77  G 77


>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional
           regulator; 2.05A {Bacillus subtilis} SCOP: a.4.6.2
          Length = 74

 Score = 68.2 bits (167), Expect = 1e-12
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 165 KKRSSAARN-LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQ 223
           K++   ++  LT+RE    +L     T++EIA +L +S  TV  ++ +A  KL    R Q
Sbjct: 2   KEKEFQSKPLLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQ 61

Query: 224 AIAKAIRFGYI 234
           A+ + +R G +
Sbjct: 62  AVVELLRMGEL 72


>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA
           complex, two-component response regulator,
           helix-turn-helix, DNA bending; 2.12A {Escherichia coli}
           SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A
          Length = 82

 Score = 67.1 bits (164), Expect = 3e-12
 Identities = 15/59 (25%), Positives = 28/59 (47%)

Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG 232
           LT RE   L+L   G  ++ IA +L ++  TV  ++     K+   +R++A     +  
Sbjct: 22  LTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQER 80


>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein
           structure initiative; NMR {Salmonella typhimurium}
          Length = 61

 Score = 65.4 bits (160), Expect = 1e-11
 Identities = 19/58 (32%), Positives = 29/58 (50%)

Query: 177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234
           RE   L+L  +GYT+  I+EKL +S+ TV  +  +   KL      + +  A R   I
Sbjct: 2   RERQVLKLIDEGYTNHGISEKLHISIKTVETHRMNMMRKLQVHKVTELLNCARRMRLI 59


>3c57_A Two component transcriptional regulatory protein DEVR; response
           regulator, two-component regulatory system, DNA- binding
           protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A
           1zlj_A
          Length = 95

 Score = 64.1 bits (156), Expect = 2e-11
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 167 RSSAARN----LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRI 222
           R S  ++    LT++E + L L  +G T+++IA+++ L+  TV  Y+     KL    R 
Sbjct: 17  RGSHMQDPLSGLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRT 76

Query: 223 QAIAKAIRFGYI 234
           QA   A      
Sbjct: 77  QAAVFATELKRS 88


>3c3w_A Two component transcriptional regulatory protein DEVR; response
           regulator, two-component regulatory system, DNA- binding
           protein; 2.20A {Mycobacterium tuberculosis}
          Length = 225

 Score = 60.3 bits (145), Expect = 3e-10
 Identities = 19/62 (30%), Positives = 31/62 (50%)

Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG 232
            LT++E + L L  +G T+++IA+++ L+  TV  Y+     KL    R QA   A    
Sbjct: 149 GLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQAAVFATELK 208

Query: 233 YI 234
             
Sbjct: 209 RS 210


>3klo_A Transcriptional regulator VPST; REC domain, HTH domain,
           DNA-binding, transcription regulation; HET: C2E TAR;
           2.80A {Vibrio cholerae} PDB: 3kln_A*
          Length = 225

 Score = 58.9 bits (142), Expect = 9e-10
 Identities = 24/83 (28%), Positives = 47/83 (56%), Gaps = 5/83 (6%)

Query: 153 CYQVITDFLELFKKRSSAARN-----LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNA 207
             ++  +++  ++  +S   +     LT+RE   ++L G G ++ EIA+KL +S +TV  
Sbjct: 134 TRKLAQEYILHYRAGNSVVTSQMYAKLTKREQQIIKLLGSGASNIEIADKLFVSENTVKT 193

Query: 208 YLGSATVKLDAVNRIQAIAKAIR 230
           +L +   K++A NR+QA+  A  
Sbjct: 194 HLHNVFKKINAKNRLQALIWAKN 216


>1a04_A Nitrate/nitrite response regulator protein NARL; signal
           transduction protein, response regulators, two-
           component systems; 2.20A {Escherichia coli} SCOP:
           a.4.6.2 c.23.1.1 PDB: 1rnl_A
          Length = 215

 Score = 47.2 bits (111), Expect = 3e-06
 Identities = 15/60 (25%), Positives = 28/60 (46%)

Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG 232
            LT RE   L+L   G  ++ IA +L ++  TV  ++     K+   +R++A     +  
Sbjct: 154 QLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQER 213


>1yio_A Response regulatory protein; transcription regulation, DNA binding
           protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2
           c.23.1.1 PDB: 1zn2_A
          Length = 208

 Score = 41.9 bits (97), Expect = 1e-04
 Identities = 14/59 (23%), Positives = 27/59 (45%)

Query: 176 ERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234
            RE   LQL   G  +++IA +LG++  TV  +  +   KL+  +    +    ++   
Sbjct: 145 GREQQVLQLTIRGLMNKQIAGELGIAEVTVKVHRHNIMQKLNVRSLANLVHLVEKYESF 203


>3bil_A Probable LACI-family transcriptional regulator; structural
           genomics, unknown function, PSI-2, protein structure
           initiative; 2.50A {Corynebacterium glutamicum atcc
           13032}
          Length = 348

 Score = 36.6 bits (83), Expect = 0.005
 Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 3/46 (6%)

Query: 190 TSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIRFGYI 234
           T +++A + G+S+ T +  L  +  V      RIQ +A     GY 
Sbjct: 10  TLKDVARQAGVSIATASRALADNPAVAASTRERIQQLAS--DLGYR 53


>3jvd_A Transcriptional regulators; structural genomics, PSI-2, sugar
           binding protein, transcription regulation, protein
           structure initiative; 2.30A {Corynebacterium glutamicum}
          Length = 333

 Score = 36.3 bits (82), Expect = 0.006
 Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 190 TSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIRFGYI 234
           + +E+AE  G+   T +  L G   V      ++QA AK     Y+
Sbjct: 8   SLKEVAELAGVGYATASRALSGKGYVSPQTREKVQAAAK--ELNYV 51


>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein
           structure initiative II(PSI II), NYSGXRC, 11232D),
           structural genomics; 2.53A {Corynebacterium glutamicum}
          Length = 366

 Score = 36.2 bits (82), Expect = 0.007
 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 190 TSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIRFGYI 234
           T   IA KLG+S  TV+        +  +   RI   A+ +  GY+
Sbjct: 11  TLASIAAKLGISRTTVSNAYNRPEQLSAELRQRILDTAEDM--GYL 54


>2hsg_A Glucose-resistance amylase regulator; CCPA, transcriptional
           regulator, transcription regulator; 2.50A {Bacillus
           megaterium} SCOP: a.35.1.5 c.93.1.1 PDB: 1rzr_G 2jcg_A
           1zvv_A
          Length = 332

 Score = 35.8 bits (81), Expect = 0.008
 Identities = 11/46 (23%), Positives = 22/46 (47%), Gaps = 3/46 (6%)

Query: 190 TSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIRFGYI 234
           T  ++A +  +S+ TV+  + G+  VK     ++    +  R GY 
Sbjct: 4   TIYDVAREASVSMATVSRVVNGNPNVKPSTRKKVLETIE--RLGYR 47


>3e3m_A Transcriptional regulator, LACI family; structural genomics,
           DNA-binding, plasmid, transcription regulation, PSI-2;
           1.60A {Silicibacter pomeroyi}
          Length = 355

 Score = 35.9 bits (81), Expect = 0.009
 Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 190 TSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIRFGYI 234
           T  ++A+  G+S  TV+  L   + +  +   RI  + K     Y+
Sbjct: 14  TMRDVAKAAGVSRMTVSRALKKDSPISSETRERILKVVK--DMNYV 57


>2o20_A Catabolite control protein A; CCPA, transcriptional regulator,
           helix-turn-helix; 1.90A {Lactococcus lactis}
          Length = 332

 Score = 35.1 bits (79), Expect = 0.015
 Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 190 TSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIRFGYI 234
           T  ++A   G+S+ TV+  + G+A VK     ++          Y 
Sbjct: 7   TIYDVARVAGVSMATVSRVVNGNANVKEKTRQKVLEAIA--ELDYR 50


>3kjx_A Transcriptional regulator, LACI family; LACL family, protein
           structure initiative II(PSI II), NYSGXRC, structural
           genomics; 2.33A {Silicibacter pomeroyi}
          Length = 344

 Score = 35.1 bits (79), Expect = 0.015
 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 190 TSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIRFGYI 234
           T  +++E  G+S  TV+  L     V      R+ A AK    GY+
Sbjct: 12  TLRDVSEASGVSEMTVSRVLRNRGDVSDATRARVLAAAK--ELGYV 55


>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A
           {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1
           PDB: 1sc5_A
          Length = 239

 Score = 34.9 bits (79), Expect = 0.017
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 162 ELFKKRSSAARNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
           EL +K   A   L ERE   +QL   +   ++E+A+ L  SV  V+     A  +L
Sbjct: 176 ELTEKVKEAVSKLPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALERL 231


>3h5o_A Transcriptional regulator GNTR; transcription regulator,
           GNTR,chromobacterium violaceum, PSI, SGX, DNA-binding;
           2.30A {Chromobacterium violaceum}
          Length = 339

 Score = 34.3 bits (77), Expect = 0.022
 Identities = 9/46 (19%), Positives = 17/46 (36%), Gaps = 3/46 (6%)

Query: 190 TSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIRFGYI 234
           T  ++A+  G+S  TV+  L     V      ++          Y+
Sbjct: 6   TMHDVAKAAGVSAITVSRVLNQPQQVSEQLREKVMQAVD--ALAYV 49


>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding,
           transmembrane, transcription; 2.00A {Escherichia coli}
           SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A
          Length = 194

 Score = 34.4 bits (78), Expect = 0.025
 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 162 ELFKKRSSAARNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
           EL +       +L E     + L   DG + EEIA  +   V TV + +  A   +
Sbjct: 129 ELRQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRAREAI 184


>1jye_A Lactose operon repressor; gene regulation, protein stability,
           protein DNA-binding, transcription; 1.70A {Escherichia
           coli} SCOP: c.93.1.1 PDB: 1lbi_A 1lbg_A* 1lbh_A 1jyf_A
           3edc_A 1efa_A* 1jwl_A* 2pe5_A* 1tlf_A* 2p9h_A* 2paf_A*
           1cjg_A* 1l1m_A 1osl_A 2kei_A* 2kej_A* 2kek_A* 2bjc_A
           1lqc_A 1lcc_A* ...
          Length = 349

 Score = 34.1 bits (77), Expect = 0.027
 Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 190 TSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIRFGYI 234
           T  ++AE  G+S  TV+  +  ++ V      +++A        YI
Sbjct: 5   TLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMA--ELNYI 48


>2q1z_A RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc binding
           transcription factor; 2.40A {Rhodobacter sphaeroides 2}
           PDB: 2z2s_A
          Length = 184

 Score = 33.8 bits (76), Expect = 0.033
 Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
            L E + + ++ A     T  E+A + GL + T+ + +  A  +L
Sbjct: 135 RLPEAQRALIERAFFGDLTHRELAAETGLPLGTIKSRIRLALDRL 179


>3ctp_A Periplasmic binding protein/LACI transcriptional regulator;
           structural genomics, protein structure initiative; HET:
           XLF; 1.41A {Alkaliphilus metalliredigens qymf}
          Length = 330

 Score = 33.9 bits (76), Expect = 0.034
 Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 3/46 (6%)

Query: 190 TSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIRFGYI 234
              EIA++ G+S+ TV+ +L  +  V  DA  +IQ +       Y 
Sbjct: 4   NIREIAKRAGISIATVSRHLNNTGYVSEDAREKIQKVVD--ELNYT 47


>3dbi_A Sugar-binding transcriptional regulator, LACI family; structural
           genomics, protein structure initiative, PSI-2; HET: MSE;
           2.45A {Escherichia coli K12}
          Length = 338

 Score = 33.7 bits (76), Expect = 0.037
 Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 3/46 (6%)

Query: 190 TSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIRFGYI 234
           T  E+A++ G+S  TV+  L G+  V  +  +R+    +    GY 
Sbjct: 5   TMLEVAKRAGVSKATVSRVLSGNGYVSQETKDRVFQAVEES--GYR 48


>1qpz_A PURA, protein (purine nucleotide synthesis repressor);
           transcription regulation, DNA-binding, purine
           biosynthesis; HET: DNA HPA; 2.50A {Escherichia coli}
           SCOP: a.35.1.5 c.93.1.1 PDB: 1bdi_A* 1qp0_A* 1qp4_A*
           1pnr_A* 1wet_A* 1zay_A* 1vpw_A* 2pue_A* 2puf_A* 2pug_A*
           1bdh_A* 1qp7_A* 1qqa_A* 1qqb_A* 2puc_A* 2pua_A* 2pub_A*
           2pud_A* 1jfs_A* 1jh9_A* ...
          Length = 340

 Score = 33.3 bits (75), Expect = 0.042
 Identities = 10/46 (21%), Positives = 22/46 (47%), Gaps = 3/46 (6%)

Query: 190 TSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIRFGYI 234
           T +++A++  +S  TV+  +  +  V  +  N + A  K +   Y 
Sbjct: 2   TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKEL--HYS 45


>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 = 33.0 bits (75), Expect = 0.062
 Identities = 26/146 (17%), Positives = 52/146 (35%), Gaps = 55/146 (37%)

Query: 18  SPRLHL-------IQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILI- 69
           SP L +       +Q+ +          NS L  P  +Q+   L N         N+++ 
Sbjct: 336 SPMLSISNLTQEQVQDYVNK-------TNSHL--PAGKQVEISLVN----GAK--NLVVS 380

Query: 70  ---ETYGDDFLFHFNSGLLPIIWQSIQEETVIESS----GQLSVRLEGGLLPFAGIAFPV 122
              ++     L+  N  L     +  +  + ++ S     +  ++     LP   +A P 
Sbjct: 381 GPPQS-----LYGLNLTL-----RKAKAPSGLDQSRIPFSERKLKFSNRFLP---VASP- 426

Query: 123 RLGFHKNGYVIFTSEFLMLANEVIIE 148
              FH        S  L+ A+++I +
Sbjct: 427 ---FH--------SHLLVPASDLINK 441



 Score = 32.6 bits (74), Expect = 0.081
 Identities = 31/238 (13%), Positives = 56/238 (23%), Gaps = 106/238 (44%)

Query: 64  IPN---ILIETYGDDFLFHFNSGLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAG-IA 119
           +P     +     + F        LP   +    +    +  +L  +       F G ++
Sbjct: 22  VPTASFFIASQLQEQFNKI-----LPEPTEGFAADDEPTTPAELVGK-------FLGYVS 69

Query: 120 FPVRLGFHKNGY--VI------FTSEFLMLANEVIIEAH--------------GACYQVI 157
             V        +  V+      F + +L   N++    H                  ++I
Sbjct: 70  SLVEPS-KVGQFDQVLNLCLTEFENCYL-EGNDI----HALAAKLLQENDTTLVKTKELI 123

Query: 158 TDFLELFKKRSSAARNLTERETSCL-----------------QLAGDGYTSE-------- 192
            ++      R  A R   ++  S L                 Q   D Y  E        
Sbjct: 124 KNY---ITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTY 180

Query: 193 ---------EIAEKL----------------GLSVH-------TV--NAYLGSATVKL 216
                      AE L                GL++              YL S  +  
Sbjct: 181 HVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISC 238


>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding
           anti-sigma factor, oxidative stress, transcription
           regulation; 2.35A {Mycobacterium tuberculosis}
          Length = 92

 Score = 32.7 bits (75), Expect = 0.077
 Identities = 12/44 (27%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 174 LTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
           L+    + +Q +   G+++ +IA  LG++  TV + L  A   L
Sbjct: 38  LSAEHRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLHYAVRAL 81


>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics,
           midwest center for structura genomics, protein structure
           initiative; 2.50A {Fusobacterium nucleatum subsp}
          Length = 164

 Score = 32.6 bits (73), Expect = 0.091
 Identities = 10/44 (22%), Positives = 19/44 (43%)

Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
           N ++ E   L     GY+  EIA  L  ++ +++  +     K 
Sbjct: 109 NFSKFEKEVLTYLIRGYSYREIATILSKNLKSIDNTIQRIRKKS 152


>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding,
           transcription, transcription regulator, transcription
           regulation; 3.20A {Klebsiella pneumoniae}
          Length = 315

 Score = 31.5 bits (71), Expect = 0.18
 Identities = 7/26 (26%), Positives = 12/26 (46%)

Query: 187 DGYTSEEIAEKLGLSVHTVNAYLGSA 212
              T  +IA +LG+   T++  L   
Sbjct: 20  QDMTQAQIARELGIYRTTISRLLKRG 45


>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family,
           transcription regulation; NMR {Escherichia coli K12}
           SCOP: a.35.1.5 PDB: 1uxd_A
          Length = 65

 Score = 31.2 bits (71), Expect = 0.19
 Identities = 11/49 (22%), Positives = 17/49 (34%), Gaps = 6/49 (12%)

Query: 190 TSEEIAEKLGLSVHTV----NAYLGSATVKLDAVNRIQAIAKAIRFGYI 234
             +EIA   G+S  T     N       V    V ++ A+ +     Y 
Sbjct: 2   KLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVR--EHNYH 48


>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding;
           HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP:
           a.4.13.2
          Length = 243

 Score = 31.3 bits (70), Expect = 0.21
 Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 1/48 (2%)

Query: 170 AARNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
           A   L ERE   + L      T  E+A +LG+S   ++         +
Sbjct: 195 AIEELDERERLIVYLRYYKDQTQSEVASRLGISQVQMSRLEKKILQHI 242


>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET:
           CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A
          Length = 192

 Score = 30.8 bits (69), Expect = 0.32
 Identities = 13/50 (26%), Positives = 24/50 (48%)

Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRI 222
           ++ E     +++  DG + ++IA K GLS   V   L +A+   + V   
Sbjct: 9   SIREIGLRLMRMKNDGMSQKDIAAKEGLSQAKVTRALQAASAPEELVALF 58


>1dw9_A Cyanate lyase; cyanate degradation, structural genomics, PSI,
           protein structure initiative, midwest center for
           structural genomics, MCSG; HET: SO4; 1.65A {Escherichia
           coli} SCOP: a.35.1.4 d.72.1.1 PDB: 1dwk_A* 2ivq_A 2ivb_A
           2iu7_A 2iv1_A 2iuo_A 2ivg_A
          Length = 156

 Score = 30.5 bits (69), Expect = 0.35
 Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 1/39 (2%)

Query: 188 GYTSEEIAEKLGLS-VHTVNAYLGSATVKLDAVNRIQAI 225
             +  EIA+  GL+      A LG   +  DA   + A 
Sbjct: 26  DLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAK 64


>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding
           protein, binding protein; NMR {Enterobacteria phage P2}
           PDB: 2xcj_A
          Length = 99

 Score = 30.3 bits (68), Expect = 0.37
 Identities = 9/46 (19%), Positives = 21/46 (45%), Gaps = 4/46 (8%)

Query: 188 GYTSEEIAEKLGLSVHTVNAY-LGSATVKLDAVNRIQAIAKAIRFG 232
             + +++A+  G+   T++ Y  G +T   D +     I +  +F 
Sbjct: 17  YLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMN---ILQTPQFT 59


>2auw_A Hypothetical protein NE0471; alpha-beta structure, structural
           genomics, PSI, protein structure initiative; 1.85A
           {Nitrosomonas europaea} SCOP: a.35.1.10 d.331.1.1
          Length = 170

 Score = 29.1 bits (65), Expect = 0.86
 Identities = 7/21 (33%), Positives = 10/21 (47%)

Query: 188 GYTSEEIAEKLGLSVHTVNAY 208
             +    AE LG+S   V+ Y
Sbjct: 103 NLSLTTAAEALGISRRMVSYY 123


>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
           termination, ATP-binding, cytoplasm, hydrolase,
           membrane; 2.80A {Schizosaccharomyces pombe}
          Length = 508

 Score = 28.9 bits (64), Expect = 0.92
 Identities = 52/206 (25%), Positives = 80/206 (38%), Gaps = 51/206 (24%)

Query: 37  TINSALDFPRRQQLIC-ELHNYDLDSGDIPNILIET-YGDDFLF--HFNSGLLPIIWQSI 92
           T  + +D  +R+QL   ++  + LD  D  N+L +   GD  +   H    LLP      
Sbjct: 242 TPGTVMDLMKRRQLDARDIKVFVLDEAD--NMLDQQGLGDQSMRIKH----LLP------ 289

Query: 93  QEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGA 152
           +   ++  S   S R+E     FA  A  +RL          T E   L+ E I + +  
Sbjct: 290 RNTQIVLFSATFSERVEKYAERFAPNANEIRLK---------TEE---LSVEGIKQLYMD 337

Query: 153 C------YQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVN 206
           C      Y V+ +   L          LT  ++       D  T+EEIA ++    HTV 
Sbjct: 338 CQSEEHKYNVLVELYGL----------LTIGQSIIFCKKKD--TAEEIARRMTADGHTVA 385

Query: 207 AYLGSATVKLDAVNRIQAIAKAIRFG 232
              G+    L+   R  AI  + R G
Sbjct: 386 CLTGN----LEGAQR-DAIMDSFRVG 406


>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme,
           streptolydigin, antibiotic, transcription regulation;
           HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1
           a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F*
           2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H
           1ku2_A
          Length = 423

 Score = 29.1 bits (64), Expect = 0.92
 Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 5/38 (13%)

Query: 169 SAARNLTERETSCLQL-----AGDGYTSEEIAEKLGLS 201
            A   L+ERE   L+L      G  +T EE+    G++
Sbjct: 356 KALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVT 393


>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus
           islandicus rod-shaped virusorganism_taxid}
          Length = 55

 Score = 28.9 bits (64), Expect = 0.96
 Identities = 14/29 (48%), Positives = 18/29 (62%)

Query: 183 QLAGDGYTSEEIAEKLGLSVHTVNAYLGS 211
           +LA  GYT ++IA  LG+S   V  YL S
Sbjct: 26  ELAKMGYTVQQIANALGVSERKVRRYLES 54


>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A
           {Enterobacteria phage lambda}
          Length = 236

 Score = 28.8 bits (63), Expect = 1.0
 Identities = 7/21 (33%), Positives = 12/21 (57%)

Query: 188 GYTSEEIAEKLGLSVHTVNAY 208
           G + E +A+K+G+    V A 
Sbjct: 30  GLSQESVADKMGMGQSGVGAL 50


>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA
           complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1
          Length = 438

 Score = 29.1 bits (64), Expect = 1.0
 Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 5/38 (13%)

Query: 169 SAARNLTERETSCLQL-----AGDGYTSEEIAEKLGLS 201
            A   L+ERE   L+L      G  +T EE+    G++
Sbjct: 371 KALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVT 408


>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein
           fold, OPPF, structural genomics, oxford protein
           production facility; 2.80A {Neisseria gonorrhoeae}
          Length = 141

 Score = 28.7 bits (64), Expect = 1.0
 Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 4/42 (9%)

Query: 188 GYTSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKA 228
           G+T  E+A   GL    ++       +++      +Q +A A
Sbjct: 81  GFTQSELATAAGLPQPYLSRIENSKQSLQDK---TVQKLANA 119


>1gdt_A GD resolvase, protein (gamma delta resolvase); protein-DNA complex,
           double helix, overhanging base, DNA binding protein/DNA
           complex; 3.00A {Escherichia coli} SCOP: a.4.1.2 c.53.1.1
           PDB: 1zr4_A 1zr2_A 2gm4_A 1res_A 1ret_A
          Length = 183

 Score = 28.6 bits (63), Expect = 1.1
 Identities = 5/28 (17%), Positives = 13/28 (46%)

Query: 182 LQLAGDGYTSEEIAEKLGLSVHTVNAYL 209
           L +   G  +  I++ + ++  TV   +
Sbjct: 152 LNMWQQGLGASHISKTMNIARSTVYKVI 179


>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition,
           transcription regulation, helix-turn- helix motif; 3.00A
           {Mycobacterium tuberculosis H37RV}
          Length = 70

 Score = 28.3 bits (63), Expect = 1.4
 Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 1/49 (2%)

Query: 169 SAARNLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
           +   +LT  +   L L    G +  + A   G  V T+ + +  A   L
Sbjct: 11  TMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDAL 59


>2r0q_C Putative transposon TN552 DNA-invertase BIN3; site-specific
           recombinase, resolvase, DNA-binding protein, protein-DNA
           complex, DNA integration, DNA invertase, DNA
           recombination; 3.20A {Staphylococcus aureus}
          Length = 209

 Score = 28.4 bits (62), Expect = 1.5
 Identities = 5/34 (14%), Positives = 16/34 (47%)

Query: 182 LQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVK 215
           +++  +G    +IA+++ ++  TV        + 
Sbjct: 169 VEMLEEGQAISKIAKEVNITRQTVYRIKHDNGLS 202


>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class
           I, activator, RNA polymerase, holoenzyme, sigma70, open
           complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A
           {Escherichia coli k-12}
          Length = 613

 Score = 27.9 bits (61), Expect = 2.3
 Identities = 9/45 (20%), Positives = 17/45 (37%), Gaps = 5/45 (11%)

Query: 162 ELFKKRSSAARNLTERETSCLQL-----AGDGYTSEEIAEKLGLS 201
            L          LT RE   L++         +T EE+ ++  ++
Sbjct: 539 SLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 583


>2kfs_A Conserved hypothetical regulatory protein; WHTH, DNA binding,
           phosphorylation, DNA-binding protein; NMR {Mycobacterium
           tuberculosis}
          Length = 148

 Score = 27.6 bits (61), Expect = 2.9
 Identities = 8/22 (36%), Positives = 10/22 (45%)

Query: 189 YTSEEIAEKLGLSVHTVNAYLG 210
           Y    +AE LG+ V  V   L 
Sbjct: 32  YDLPRVAELLGVPVSKVAQQLR 53


>2rek_A Putative TETR-family transcriptional regulator; sulfur, SAD,
           structural genomics, PSI-2, protein structure
           initiative; 1.86A {Streptomyces coelicolor A3}
          Length = 199

 Score = 27.5 bits (60), Expect = 3.0
 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 3/57 (5%)

Query: 166 KRSSAARNLTE-RETSCLQLAGDGY--TSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219
           KR+ A RN     E +  ++A  G   + EEIA + G+   T++ +  S    L AV
Sbjct: 10  KRADARRNYDRIIEAAAAEVARHGADASLEEIARRAGVGSATLHRHFPSRWGLLQAV 66


>1y9q_A Transcriptional regulator, HTH_3 family; transcriptional
           regulaator, strucutral genomics, protein structure
           initiative, PSI; 1.90A {Vibrio cholerae} SCOP: a.35.1.8
           b.82.1.15
          Length = 192

 Score = 27.2 bits (59), Expect = 3.2
 Identities = 4/21 (19%), Positives = 9/21 (42%)

Query: 188 GYTSEEIAEKLGLSVHTVNAY 208
           G + +  A+  G+S   +   
Sbjct: 24  GLSLDATAQLTGVSKAMLGQI 44


>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 = 27.3 bits (59), Expect = 3.2
 Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 14/39 (35%)

Query: 192 EEIA-EKLGLSVHTVNAYLGSATVKLDAVNRIQAIA-KA 228
           E+ A +KL             A++KL A +   A+A KA
Sbjct: 18  EKQALKKL------------QASLKLYADDSAPALAIKA 44


>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein,
           structural genomics, PSI- 2, protein structure
           initiative; 3.00A {Corynebacterium diphtheriae}
          Length = 583

 Score = 27.1 bits (59), Expect = 3.3
 Identities = 15/98 (15%), Positives = 31/98 (31%), Gaps = 14/98 (14%)

Query: 141 LANEVIIEAHGACYQVITDFLELFKKRSSA----ARNLTERETSCLQL------AGDGYT 190
           +A   +I AH   + +     E+ +K   +     R L+  +                  
Sbjct: 473 VAGAPLIIAHDGVWLLGNACREILRKVEPSPFSPVRYLSTDQAELTNAAMLWLSEVGDLA 532

Query: 191 SEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKA 228
           + ++    G+S  T  A +      L    R+ A+   
Sbjct: 533 TSDLMAMCGVSRGTAKACVD----GLVDEERVVAVGGG 566


>1r71_A Transcriptional repressor protein KORB; INCP, plasmid partitioning,
           protein-DNA complex, heilx-turn- helix motif,
           transcription factor; HET: BRU; 2.20A {Escherichia coli}
           SCOP: a.4.14.1
          Length = 178

 Score = 27.3 bits (60), Expect = 3.3
 Identities = 6/37 (16%), Positives = 14/37 (37%)

Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYL 209
              E      +    G    +IA+++G S   +  ++
Sbjct: 37  TPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHV 73


>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition,
           protein-DNA complex, A10G mutant, DNA binding
           protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2
           PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C
          Length = 52

 Score = 27.4 bits (61), Expect = 3.3
 Identities = 7/34 (20%), Positives = 15/34 (44%)

Query: 176 ERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYL 209
             +    +L   G+  +++A   G+ V T+  Y 
Sbjct: 9   HEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYF 42


>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure,
           structural genomics, protein structure initiative; NMR
           {Corynebacterium glutamicum} SCOP: a.4.1.19
          Length = 97

 Score = 27.1 bits (60), Expect = 3.5
 Identities = 8/24 (33%), Positives = 14/24 (58%)

Query: 182 LQLAGDGYTSEEIAEKLGLSVHTV 205
           L    DG + ++IA  LG++  T+
Sbjct: 17  LYENSDGASLQQIANDLGINRVTL 40


>2o0m_A Transcriptional regulator, SORC family; structural genomics, PSI-2,
           protein structure initiative; 1.60A {Enterococcus
           faecalis V583} SCOP: c.124.1.8
          Length = 345

 Score = 27.2 bits (60), Expect = 3.5
 Identities = 8/58 (13%), Positives = 20/58 (34%), Gaps = 9/58 (15%)

Query: 155 QVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSA 212
            V  D L++ ++R    RN+   +               ++E +G++   +       
Sbjct: 10  AVAPDMLDVLQERFQILRNIYWMQ---------PIGRRSLSETMGITERVLRTETDVL 58


>2kyz_A Heavy metal binding protein; structural genomics, PSI-2, protein
           structure initiative, joint center structural genomics,
           JCSG; NMR {Thermotoga maritima}
          Length = 67

 Score = 26.9 bits (60), Expect = 3.6
 Identities = 6/43 (13%), Positives = 19/43 (44%), Gaps = 4/43 (9%)

Query: 192 EEIAEKLGLSVHTVNAYLGSATVKLDAVNRI-QAIAKAIRFGY 233
            +  E+LG+  + V+       V+ + ++ + + + +     Y
Sbjct: 20  SKALEELGVKNYEVSVEEKKVVVETENLDSVLKKLEEI---DY 59


>1s7o_A Hypothetical UPF0122 protein
           SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA
           binding protein, structural genomics; 2.31A
           {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3
          Length = 113

 Score = 27.2 bits (60), Expect = 3.7
 Identities = 12/44 (27%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 174 LTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
           LT+++ + ++L   D Y+  EIA++ G+S   V   +      L
Sbjct: 23  LTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKIL 66


>1u78_A TC3 transposase, transposable element TC3 transposase; transposon
           DNA, bipartite DNA-binding, HTH- motif, DNA binding
           protein/DNA complex; 2.69A {Caenorhabditis elegans}
           SCOP: a.4.1.2 a.4.1.2
          Length = 141

 Score = 27.1 bits (59), Expect = 4.0
 Identities = 8/39 (20%), Positives = 17/39 (43%), Gaps = 1/39 (2%)

Query: 172 RNLTERETS-CLQLAGDGYTSEEIAEKLGLSVHTVNAYL 209
             L++ E +    +     +  E++ K+  S H +  YL
Sbjct: 5   SALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYL 43


>2qrv_A DNA (cytosine-5)-methyltransferase 3A; DNA methyltransferase 3A
           (DNMT3A) and ITS regulatory factor; HET: DNA SAH; 2.89A
           {Homo sapiens}
          Length = 295

 Score = 26.8 bits (58), Expect = 4.6
 Identities = 9/66 (13%), Positives = 19/66 (28%), Gaps = 13/66 (19%)

Query: 172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAY--LGSATVKLDAVNRIQAIAKAI 229
             L   E   +      YT          ++  +     LG +      V  I+ +   +
Sbjct: 240 DILWCTEMERVFGFPVHYTDVS-------NMSRLARQRLLGRSWS----VPVIRHLFAPL 288

Query: 230 RFGYIC 235
           +  + C
Sbjct: 289 KEYFAC 294


>2ppx_A AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif,
           XRE-family, structural genomics, PSI-2, protein
           structure initiative; 2.00A {Agrobacterium tumefaciens
           str} SCOP: a.35.1.3
          Length = 99

 Score = 26.8 bits (59), Expect = 4.8
 Identities = 8/42 (19%), Positives = 17/42 (40%), Gaps = 1/42 (2%)

Query: 188 GYTSEEIAEKLGLSVHTVNAY-LGSATVKLDAVNRIQAIAKA 228
             T EE + +  + + T+  +  G +     A   ++ IA  
Sbjct: 43  KLTQEEFSARYHIPLGTLRDWEQGRSEPDQPARAYLKIIAVD 84


>2jvl_A TRMBF1; coactivator, helix-turn-helix, protein binding,
           transcription; NMR {Trichoderma reesei}
          Length = 107

 Score = 26.4 bits (58), Expect = 5.2
 Identities = 12/58 (20%), Positives = 24/58 (41%), Gaps = 11/58 (18%)

Query: 166 KRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRI 222
           K     R   E             T  E+ +++G +  TV +Y  G+AT   + ++++
Sbjct: 37  KAIEQGRQKFEP----------TMTQAELGKEIGETAATVASYERGTATPDQNILSKM 84


>3fmy_A HTH-type transcriptional regulator MQSA (YGIT/B3021);
           helix-turn-helix, DNA-binding, transcription regulation,
           DNA binding protein; HET: MEQ; 1.40A {Escherichia coli
           k-12}
          Length = 73

 Score = 26.8 bits (59), Expect = 5.2
 Identities = 6/21 (28%), Positives = 10/21 (47%)

Query: 188 GYTSEEIAEKLGLSVHTVNAY 208
             T +E +E  G  V+  + Y
Sbjct: 24  SLTQKEASEIFGGGVNAFSRY 44


>2hs5_A Putative transcriptional regulator GNTR; APC6050, rhodococcus SP.
           RHA1, structural genomics, PSI-2, protein structure
           initiative; 2.20A {Rhodococcus SP} SCOP: a.4.5.6
           a.78.1.1
          Length = 239

 Score = 26.5 bits (57), Expect = 5.5
 Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 14/57 (24%)

Query: 167 RSSAARNLTERETSCLQLA--------------GDGYTSEEIAEKLGLSVHTVNAYL 209
           R +A R L ER +   ++A              G   +  +I   L +S +TV    
Sbjct: 16  RLAAHRGLLERTSRTTRVAGILRDAIIDGTFRPGARLSEPDICAALDVSRNTVREAF 72


>2qwt_A Transcriptional regulator, TETR family; structural genomics, PSI-2,
           protein structure initiative; 2.30A {Mycobacterium
           vanbaalenii pyr-1}
          Length = 196

 Score = 26.3 bits (57), Expect = 6.0
 Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 3/57 (5%)

Query: 166 KRSSAARNLTE-RETSCLQLAGDGY--TSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219
            R+ AARN     E +    A +G     +EIA + G+   TV  +  +    + AV
Sbjct: 7   LRADAARNRARVLEVAYDTFAAEGLGVPMDEIARRAGVGAGTVYRHFPTKQALVVAV 63


>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing
           system, phosphoryltransferase, helix-turn-helix motif,
           transcription regulator; 3.20A {Streptococcus pneumoniae
           TIGR4}
          Length = 158

 Score = 26.2 bits (57), Expect = 6.4
 Identities = 9/36 (25%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

Query: 188 GYTSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRI 222
             T  E A  +G+S ++++ Y  G+++V  + ++ I
Sbjct: 14  DLTQLEFARIVGISRNSLSRYENGTSSVSTELIDII 49


>3mcz_A O-methyltransferase; adomet_mtases, S-adenosylmethionine-dependent
           methyltransfer structural genomics, PSI-2; HET: MSE;
           1.90A {Burkholderia thailandensis}
          Length = 352

 Score = 26.1 bits (57), Expect = 6.7
 Identities = 6/18 (33%), Positives = 8/18 (44%)

Query: 184 LAGDGYTSEEIAEKLGLS 201
           L   G T  E+A   G+ 
Sbjct: 52  LTQTGRTPAEVAASFGMV 69


>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus
           caldolyticus} SCOP: a.35.1.3
          Length = 77

 Score = 25.9 bits (57), Expect = 7.5
 Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 4/42 (9%)

Query: 188 GYTSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKA 228
           G + EE+A+  GL    ++    G   + L     I  I  A
Sbjct: 23  GVSQEELADLAGLHRTYISEVERGDRNISLI---NIHKICAA 61


>1y10_A Hypothetical protein RV1264/MT1302; adenylyl cyclase fold, lyase;
           HET: 1PE; 2.30A {Mycobacterium tuberculosis} PDB:
           1y11_A*
          Length = 407

 Score = 26.1 bits (57), Expect = 7.9
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 7/56 (12%)

Query: 183 QLAGDG---YTSEEIAEKLGLSVHTVNAY---LGSATV-KLDAVNRIQAIAKAIRF 231
            L GD     ++ EI+E  G+ +  +      +G A V   DAV  ++A  +A   
Sbjct: 58  HLVGDDGTYVSAREISENYGVDLELLQRVQRAVGLARVDDPDAVVHMRADGEAAAR 113


>3gpv_A Transcriptional regulator, MERR family; protein structure
           initiative II(PSI II), NYSGXRC, structural genomics;
           1.90A {Bacillus thuringiensis serovarkonkukian}
          Length = 148

 Score = 25.8 bits (56), Expect = 8.4
 Identities = 5/20 (25%), Positives = 11/20 (55%)

Query: 189 YTSEEIAEKLGLSVHTVNAY 208
           YT  ++A+   L++  +  Y
Sbjct: 17  YTIGQVAKMQHLTISQIRYY 36


>1r4p_A Sltii A subunit, shiga-like toxin type II A subunit; AB5 toxin;
           HET: 1PS; 1.77A {Escherichia coli} SCOP: d.165.1.2 PDB:
           2ga4_A*
          Length = 297

 Score = 25.7 bits (56), Expect = 8.8
 Identities = 8/41 (19%), Positives = 17/41 (41%), Gaps = 3/41 (7%)

Query: 197 KLGLSVHTVNAYLGSATVKLDA---VNRIQAIAKAIRFGYI 234
            L  S   +  + G+   +  +   +  +   A+A+RF  I
Sbjct: 134 SLVSSYLALMEFSGNTMTRDASRAVLRFVTVTAEALRFRQI 174


>1vi0_A Transcriptional regulator; structural genomics; HET: MSE DCC; 1.65A
           {Bacillus subtilis} SCOP: a.4.1.9 a.121.1.1
          Length = 206

 Score = 25.7 bits (55), Expect = 8.9
 Identities = 6/35 (17%), Positives = 16/35 (45%)

Query: 187 DGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNR 221
                 +IA++ G++  T+  Y  +    L ++ +
Sbjct: 27  HQSQVSKIAKQAGVADGTIYLYFKNKEDILISLFK 61


>3dp7_A SAM-dependent methyltransferase; structural genomics, protein
           structure initiative, NEW YORK structural genomix
           research, nysgxrc; 2.33A {Bacteroides vulgatus atcc
           8482}
          Length = 363

 Score = 25.6 bits (55), Expect = 9.2
 Identities = 8/20 (40%), Positives = 13/20 (65%)

Query: 182 LQLAGDGYTSEEIAEKLGLS 201
           L    +GYT +EI+ + GL+
Sbjct: 44  LSGKREGYTLQEISGRTGLT 63


>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca
           cleavage, DNA damage, DNA repair, DNA replication,
           DNA-BIND hydrolase; 1.37A {Thermotoga maritima}
          Length = 196

 Score = 25.9 bits (56), Expect = 9.3
 Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 7/44 (15%)

Query: 173 NLTERETSCLQ-----LAGDGY--TSEEIAEKLGLSVHTVNAYL 209
           +LTER+   L      +  +GY  +  EIA +  ++      +L
Sbjct: 2   DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHL 45


>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434}
           SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A
           2r63_A 1sq8_A
          Length = 69

 Score = 25.8 bits (57), Expect = 9.8
 Identities = 8/41 (19%), Positives = 17/41 (41%), Gaps = 3/41 (7%)

Query: 188 GYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKA 228
           G    E+A+K+G +  ++       T +      +  +A A
Sbjct: 14  GLNQAELAQKVGTTQQSIEQLENGKTKRPR---FLPELASA 51


  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
   0.321    0.138    0.395 

Gapped
Lambda     K      H
   0.267   0.0463    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,951,534
Number of extensions: 88086
Number of successful extensions: 637
Number of sequences better than 10.0: 1
Number of HSP's gapped: 636
Number of HSP's successfully gapped: 100
Length of query: 235
Length of database: 5,693,230
Length adjustment: 89
Effective length of query: 146
Effective length of database: 3,535,514
Effective search space: 516185044
Effective search space used: 516185044
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.6 bits)