RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781147|ref|YP_003065560.1| transcriptional regulator
[Candidatus Liberibacter asiaticus str. psy62]
         (83 letters)



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

 Score = 50.3 bits (120), Expect = 9e-08
 Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 6/85 (7%)

Query: 2   PRRK----RDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57
           PRRK    R    ++D I  +       F ++R +   TQ E+    G  Q ++S +E  
Sbjct: 47  PRRKAAMDRAAARIADKIALKA--GGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENS 104

Query: 58  KSTINIDNMIILAHTLDTPLWKLLK 82
           K ++    +  LA+ L     ++  
Sbjct: 105 KQSLQDKTVQKLANALGVSPLEVRA 129


>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional
          regulator, transcription regulator; 1.69A {Aeromonas
          hydrophila} SCOP: a.35.1.3
          Length = 74

 Score = 50.2 bits (120), Expect = 1e-07
 Identities = 15/59 (25%), Positives = 31/59 (52%)

Query: 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80
          F    R +R    L+Q+ +   +G  +S++  +E G+  +++ N++ LA  LD    +L
Sbjct: 14 FGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPREL 72


>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein
          structure initiative, midwest center for structural
          genomics; 1.80A {Silicibacter pomeroyi}
          Length = 86

 Score = 50.2 bits (120), Expect = 1e-07
 Identities = 12/57 (21%), Positives = 26/57 (45%)

Query: 18 ERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLD 74
          E +      R  R +A LTQ ++  R    QS+++++ET +  +++          +
Sbjct: 11 EHVYLCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDVIEFAKWMAACE 67


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

 Score = 49.8 bits (119), Expect = 1e-07
 Identities = 16/65 (24%), Positives = 33/65 (50%)

Query: 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78
          +  F    + IR +  ++Q+E+ +  G  +++ISE+E G   I++ N+  +   LD P  
Sbjct: 8  KRKFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPAS 67

Query: 79 KLLKP 83
             + 
Sbjct: 68 TFFRK 72


>1adr_A P22 C2 repressor; transcription regulation; NMR {Bacteriophage
          P22} SCOP: a.35.1.2
          Length = 76

 Score = 47.5 bits (113), Expect = 7e-07
 Identities = 16/63 (25%), Positives = 28/63 (44%)

Query: 20 MIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWK 79
           +     R  RK+ K+ Q  +    G +   IS+ E  ++  N +N++ L+  L      
Sbjct: 4  QLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDY 63

Query: 80 LLK 82
          LLK
Sbjct: 64 LLK 66


>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix,
          DNA-binding, transcription, transcription regulation;
          1.53A {Enterobacteria phage P22} SCOP: a.35.1.2
          Length = 68

 Score = 47.5 bits (113), Expect = 7e-07
 Identities = 16/59 (27%), Positives = 27/59 (45%)

Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLK 82
             R  RK+ K+ Q  +    G +   IS+ E  ++  N +N++ L+  L      LLK
Sbjct: 8  ERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLK 66


>2wiu_B HTH-type transcriptional regulator HIPB; transferase
          transcription complex, bacterial persistence, serine
          kinase, mercury derivative, SAD; 2.35A {Escherichia
          coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B*
          Length = 88

 Score = 46.5 bits (110), Expect = 1e-06
 Identities = 11/60 (18%), Positives = 23/60 (38%)

Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLKP 83
          N  + +R++   TQ E+  + G  Q+ IS  E       +     +  +L+  +      
Sbjct: 15 NAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAK 74


>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix
          XRE-family like protei transcription regulator, PSI-2;
          2.60A {Staphylococcus aureus subsp}
          Length = 111

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 4/68 (5%)

Query: 18 ERMIFVNNF----RNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73
          E + F +N     + +R +  LTQKE+ +    +   I  +E   + I    +       
Sbjct: 16 ENLYFQSNAMKTLKELRTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAF 75

Query: 74 DTPLWKLL 81
          +     + 
Sbjct: 76 NVKYDDIF 83


>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 = 46.4 bits (110), Expect = 2e-06
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTP 76
               +RK   L+++++ + TG     +S  E+G+ST   D M+ +  T    
Sbjct: 7  EKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNILQTPQFT 59


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

 Score = 46.3 bits (109), Expect = 2e-06
 Identities = 13/61 (21%), Positives = 30/61 (49%)

Query: 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80
          +   N +++RK   LTQ E     G +++ +S  E G S+++ + + I+    +     +
Sbjct: 1  MIGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNVSYVDI 60

Query: 81 L 81
          +
Sbjct: 61 V 61


>1utx_A CYLR2; DNA-binding protein, transcriptional repressor, regulation
          of cytolysin operon, helix-turn-helix; 1.90A
          {Enterococcus faecalis} SCOP: a.35.1.3 PDB: 2gzu_A
          Length = 66

 Score = 46.1 bits (109), Expect = 2e-06
 Identities = 15/62 (24%), Positives = 35/62 (56%)

Query: 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80
          + +NN + IR++ K++Q E+      ++  I+ +E  K   ++   + +A+ L+TPL  +
Sbjct: 1  MIINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDI 60

Query: 81 LK 82
           +
Sbjct: 61 FQ 62


>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 = 44.9 bits (105), Expect = 5e-06
 Identities = 15/71 (21%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 11 LSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILA 70
          L+D + + +    N  +N+RK   L+       TG +++ + ++E G+S+  I  +  +A
Sbjct: 3  LTDVMFKSQ--IANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIA 60

Query: 71 HTLDTPLWKLL 81
            L+       
Sbjct: 61 SGLEASFSAFF 71


>3kz3_A Repressor protein CI; five helix bundle, DNA-binding,
          transcription, transcription regulation; 1.64A
          {Enterobacteria phage lambda}
          Length = 80

 Score = 43.0 bits (101), Expect = 2e-05
 Identities = 12/56 (21%), Positives = 26/56 (46%)

Query: 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81
          +   + E  L+ + + ++ G  QS ++ L  G + +N  N  +LA  L   + +  
Sbjct: 17 WEKKKNELGLSYESVADKMGMGQSAVAALFNGINALNAYNAALLAKILKVSVEEFS 72


>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein
          structure initiative, MI center for structural
          genomics, MCSG; 1.65A {Cytophaga hutchinsonii}
          Length = 73

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 8/62 (12%), Positives = 25/62 (40%)

Query: 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81
            N  +++  E   T   +       ++ +S+  T     +++ +  +A  L+  + +L+
Sbjct: 9  IFNRLKSVLAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVRELI 68

Query: 82 KP 83
            
Sbjct: 69 VS 70


>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 = 42.8 bits (101), Expect = 2e-05
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81
          +  ++ R +  L Q E+  + G  Q  I +LE GK T     +  LA  L   +  LL
Sbjct: 4  SRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGK-TKRPRFLPELASALGVSVDWLL 60


>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha,
          helix-turn-helix, structural genomics, NPPSFA; NMR
          {Homo sapiens} SCOP: a.35.1.12
          Length = 91

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 11/61 (18%), Positives = 25/61 (40%)

Query: 17 RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTP 76
          R  +      +  R+   LTQK++  +       I++ E+G++  N   +  +   +   
Sbjct: 9  RVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLK 68

Query: 77 L 77
          L
Sbjct: 69 L 69


>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure
          initiative, MI center for structural genomics, MCSG,
          transcription regulat; HET: MSE; 1.90A {Listeria
          innocua}
          Length = 114

 Score = 42.5 bits (100), Expect = 3e-05
 Identities = 12/63 (19%), Positives = 27/63 (42%)

Query: 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78
          +  F  N   ++KE  L   +I          ++   +G++  +I+ +I LA      + 
Sbjct: 7  QHQFAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYFHLSID 66

Query: 79 KLL 81
          +L+
Sbjct: 67 ELV 69


>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix,
          transcription/DNA complex; HET: DNA; 1.80A
          {Enterobacteria phage lambda} SCOP: a.35.1.2 PDB:
          1lrp_A 1rio_A 1lli_A*
          Length = 92

 Score = 42.3 bits (99), Expect = 3e-05
 Identities = 15/71 (21%), Positives = 30/71 (42%)

Query: 11 LSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILA 70
          L+   L +       +   + E  L+Q+ + ++ G  QS +  L  G + +N  N  +LA
Sbjct: 7  LTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLA 66

Query: 71 HTLDTPLWKLL 81
            L   + +  
Sbjct: 67 KILKVSVEEFS 77


>2bnm_A Epoxidase; oxidoreductase, cupin, HTH, cation-dependant, zinc,
          fosfomycin; 1.7A {Streptomyces wedmorensis} SCOP:
          a.35.1.3 b.82.1.10 PDB: 1zz7_A 1zz8_A 1zz9_A 1zzb_A
          1zz6_A 1zzc_A 2bnn_A 2bno_A
          Length = 198

 Score = 41.8 bits (97), Expect = 4e-05
 Identities = 12/67 (17%), Positives = 27/67 (40%), Gaps = 1/67 (1%)

Query: 18 ERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKS-TINIDNMIILAHTLDTP 76
              F    ++ R++ K+    + +  G     ++  E G+   + +  +  +AH L T 
Sbjct: 7  ASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTS 66

Query: 77 LWKLLKP 83
          +  L  P
Sbjct: 67 IGALTPP 73


>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein,
          xenobiotic response element family of transcriptional
          regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae
          PV}
          Length = 83

 Score = 41.5 bits (97), Expect = 5e-05
 Identities = 15/61 (24%), Positives = 29/61 (47%)

Query: 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81
           ++     R  A +TQKE+  R G  QS++S+ E  +  +++   +     + T  + LL
Sbjct: 15 LLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDPYALL 74

Query: 82 K 82
           
Sbjct: 75 S 75


>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA
          binding protein, transcription regulator; HET: CME;
          1.95A {Enterobacteria phage P2}
          Length = 84

 Score = 40.7 bits (95), Expect = 9e-05
 Identities = 16/61 (26%), Positives = 29/61 (47%)

Query: 17 RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTP 76
                V     +RKEA L+Q E+    G +QS IS++E+ +  ++   +  L   + + 
Sbjct: 6  HRYRCLVQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEVVASR 65

Query: 77 L 77
          L
Sbjct: 66 L 66


>3gn5_A HTH-type transcriptional regulator MQSA (YGIT/B3021); Zn-binding
           protein, HTH-XRE DNA binding motif, DNA-binding,
           transcription regulation; HET: MEQ; 2.15A {Escherichia
           coli k-12} PDB: 3gn5_B*
          Length = 133

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 14/76 (18%), Positives = 24/76 (31%)

Query: 3   RRKRDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTIN 62
                +     A +    +       +RK+  LTQKE     G   +  S  E G +  +
Sbjct: 53  DAFMAQVKAFRASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPH 112

Query: 63  IDNMIILAHTLDTPLW 78
              + +L      P  
Sbjct: 113 PSTIKLLRVLDKHPEL 128


>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus
          thuringiensis serovarisraelensis atcc 35646}
          Length = 293

 Score = 40.2 bits (92), Expect = 1e-04
 Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78
          +  + IR    LTQK++       QS +S +E+G    ++D +  +A  L  P+ 
Sbjct: 8  SEIKKIRVLRGLTQKQLSEN-ICHQSEVSRIESGAVYPSMDILQGIAAKLQIPII 61


>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 = 39.9 bits (93), Expect = 1e-04
 Identities = 10/59 (16%), Positives = 16/59 (27%), Gaps = 1/59 (1%)

Query: 24  NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINID-NMIILAHTLDTPLWKLL 81
             F +      L+        G ++  +S   T    I     +  L      P  K L
Sbjct: 93  EMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTIWLACLGWEATRPETKTL 151


>1zug_A Phage 434 CRO protein; gene regulating protein, transcription
          regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A
          3cro_L*
          Length = 71

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 1/58 (1%)

Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81
             +  R   K+TQ E+  + G  Q  I  +E G  T     +  +A  L+     L 
Sbjct: 6  ERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGV-TKRPRFLFEIAMALNCDPVWLQ 62


>3ivp_A Putative transposon-related DNA-binding protein; APC62618,
          structural genomics, PSI-2, protein structure
          initiative; HET: PG4; 2.02A {Clostridium difficile 630}
          Length = 126

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 8/60 (13%), Positives = 24/60 (40%)

Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLKP 83
             +  RK+  LT++++         +++ +E      ++  +  L   L+  + +   P
Sbjct: 15 LAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLLNVSVDEFFLP 74


>3clc_A Regulatory protein; protein-DNA complex, transcriptional
          regulator, helix-turn- helix, DNA-bending, plasmid,
          transcription regulator/DNA complex; 2.80A
          {Enterobacter SP}
          Length = 82

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 10/59 (16%), Positives = 28/59 (47%)

Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLK 82
             + IR E  +TQ+++  ++   +++IS +E     + I ++ ++   L+       +
Sbjct: 14 FVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFE 72


>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix,
          restriction- modification, transcription regulator;
          2.80A {Enterobacter SP} PDB: 3fya_A
          Length = 99

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 14/82 (17%), Positives = 34/82 (41%), Gaps = 7/82 (8%)

Query: 1  MPRRKRDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKST 60
          +PR    E  L   +           + IR E  +TQ+++  ++   +++IS +E     
Sbjct: 15 VPRGSHMESFLLSKV-------SFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRN 67

Query: 61 INIDNMIILAHTLDTPLWKLLK 82
          + I ++ ++   L+       +
Sbjct: 68 LTIKSLELIMKGLEVSDVVFFE 89


>1b0n_A Protein (SINR protein); transcription regulator, antagonist,
          sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1
          a.35.1.3
          Length = 111

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETG-KSTINIDNMIILAHTLDTPLWKLLK 82
             +  RKE   +  E+  + G A+S++S +E   ++  +I  +  ++  LD  +  LL 
Sbjct: 4  QRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTLLD 63

Query: 83 P 83
           
Sbjct: 64 E 64


>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 = 39.2 bits (91), Expect = 2e-04
 Identities = 13/59 (22%), Positives = 21/59 (35%)

Query: 18 ERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTP 76
               +   + IR+  KLTQ+E   R       + + E G+S  +      L      P
Sbjct: 27 ASAPRMPRIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQPARAYLKIIAVDP 85


>2awi_A PRGX; repressor, pheromone, DNA binding, regulatory domain,
          transcription; 2.25A {Enterococcus faecalis} SCOP:
          a.35.1.11 a.118.8.4 PDB: 2axv_A 2axu_A 2aw6_A 2axz_A
          2grl_A 2grm_A
          Length = 317

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 9/58 (15%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81
          +  + IR+E    Q ++ +    ++S   ++E     I+++ +   +  L    +++L
Sbjct: 6  SVLKQIRQELNYHQIDLYSG-IMSKSVYIKVEADSRPISVEELSKFSERLGVNFFEIL 62


>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT,
          structural genomics, PSI-2, protein structure
          initiative; NMR {Eubacterium rectale atcc 33656}
          Length = 94

 Score = 39.0 bits (90), Expect = 3e-04
 Identities = 12/66 (18%), Positives = 27/66 (40%)

Query: 17 RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTP 76
          +++ IF  N  +   +++ TQ EI    G +    +    G +   +  +  LA   +  
Sbjct: 5  KQKAIFSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNIN 64

Query: 77 LWKLLK 82
             L++
Sbjct: 65 KSDLIE 70


>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA
           binding motif, transcriptional regulator, bacter
           antitoxin, Zn binding protein, transcription
           regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB:
           3gn5_A* 3gn5_B*
          Length = 133

 Score = 38.6 bits (89), Expect = 4e-04
 Identities = 13/81 (16%), Positives = 26/81 (32%), Gaps = 2/81 (2%)

Query: 2   PRRKRDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKS-- 59
                 +     A +    +       +RK+  LTQKE     G   +  S  E G +  
Sbjct: 52  SDAFMAQVKAFRASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQP 111

Query: 60  TINIDNMIILAHTLDTPLWKL 80
             +   ++ +       L ++
Sbjct: 112 HPSTIKLLRVLDKHPELLNEI 132


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

 Score = 36.9 bits (84), Expect = 0.001
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78
          +   + E  L+Q+ + ++ G  QS +  L  G + +N  N  +LA  L   + 
Sbjct: 22 YEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVE 74


>3g7d_A PHPD; non heme Fe(II) dioxygenase, cupin, biosynthetic protein;
           1.80A {Streptomyces viridochromogenes} PDB: 3gbf_A
          Length = 443

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 7/64 (10%), Positives = 14/64 (21%), Gaps = 1/64 (1%)

Query: 21  IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELE-TGKSTINIDNMIILAHTLDTPLWK 79
              +           T+       G   + +     +  S   +  +  L   L      
Sbjct: 230 SAGSVLDLFLARRAHTRTSAAEAAGVPPADLEAALRSPASETGLTVLRTLGRALGFDYRV 289

Query: 80  LLKP 83
           LL  
Sbjct: 290 LLPA 293


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

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 10/48 (20%), Positives = 22/48 (45%)

Query: 30 RKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPL 77
          + E  +TQ E+    G   + ++  E G +T + + +  +   L+  L
Sbjct: 45 KFEPTMTQAELGKEIGETAATVASYERGTATPDQNILSKMERVLNVKL 92


>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 = 34.8 bits (80), Expect = 0.005
 Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 14 AILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73
          A +    +       +RK+  LTQKE     G   +  S  E G +  +  + I L   L
Sbjct: 4  ASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAXPHP-STIKLLRVL 62

Query: 74 DT 75
          D 
Sbjct: 63 DK 64


>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein
          structure initiative, midwest center for structural
          genomics; 2.00A {Lactobacillus plantarum WCFS1}
          Length = 78

 Score = 34.6 bits (79), Expect = 0.005
 Identities = 8/62 (12%), Positives = 18/62 (29%), Gaps = 1/62 (1%)

Query: 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELET-GKSTINIDNMIILAHTLDTPLWK 79
              +   +  +  LT   +    G  QS ++ +         I  +  +  TL   +  
Sbjct: 7  FVSEHLMELITQQNLTINRVATLAGLNQSTVNAMFEGRSKRPTITTIRKVCGTLGISVHD 66

Query: 80 LL 81
            
Sbjct: 67 FF 68


>3cec_A Putative antidote protein of plasmid maintenance system;
          ZP_00107635.1, structural genomics, joint center for
          structural genomics; HET: MSE; 1.60A {Nostoc
          punctiforme pcc 73102}
          Length = 104

 Score = 32.2 bits (73), Expect = 0.032
 Identities = 11/55 (20%), Positives = 19/55 (34%)

Query: 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81
           +I  +  +         G +   I E+  G+ +I +D  I L   L       L
Sbjct: 24 ADILDDLDINTANFAEILGVSNQTIQEVINGQRSITVDIAIRLGKALGNGPRLWL 78


>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2,
          protein structure initiative, northeast structural
          genomics consortium; 1.63A {Escherichia coli CFT073}
          SCOP: a.35.1.3 PDB: 2icp_A
          Length = 94

 Score = 31.9 bits (72), Expect = 0.040
 Identities = 12/55 (21%), Positives = 22/55 (40%)

Query: 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81
          +    E  ++ +E       A S  S L TGK+ +  +  I L+  + +     L
Sbjct: 14 QESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWL 68


>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical
          protein, JW0472, structural genomics, NPPSFA; 2.25A
          {Escherichia coli}
          Length = 113

 Score = 30.3 bits (68), Expect = 0.11
 Identities = 14/81 (17%), Positives = 25/81 (30%), Gaps = 10/81 (12%)

Query: 1  MPRRKRDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKST 60
          M +  R      D +L E +          +   L   E+       ++ +S L      
Sbjct: 1  MKQATRKPTTPGDILLYEYL----------EPLDLKINELAELLHVHRNSVSALINNNRK 50

Query: 61 INIDNMIILAHTLDTPLWKLL 81
          +  +    LA   DT +   L
Sbjct: 51 LTTEMAFRLAKVFDTTVDFWL 71


>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding
          protein; 1.00A {Staphylococcus aureus subsp}
          Length = 130

 Score = 29.7 bits (66), Expect = 0.16
 Identities = 7/46 (15%), Positives = 16/46 (34%)

Query: 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAH 71
           +  R+   +T  E+  RTG  +  +  +E  +     +       
Sbjct: 8  LKGRRERLGMTLTELEQRTGIKREMLVHIENNEFDQLPNKNYSEGF 53


>2o38_A Hypothetical protein; alpha-beta, helix-turn-helix, structural
          genomics, PSI-2, protein structure initiative; 1.83A
          {Rhodopseudomonas palustris CGA009} SCOP: a.35.1.13
          Length = 120

 Score = 28.9 bits (65), Expect = 0.26
 Identities = 12/60 (20%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 16 LRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGK-STINIDNMIILAHTLD 74
           + ++        +   A+L+Q     R G  Q  +S L   K    +++ ++ L + LD
Sbjct: 35 RQTKLRLAYALNAVIDRARLSQXXXXXRLGINQPKVSALRNYKLEGFSVERLMTLLNALD 94


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

 Score = 28.5 bits (63), Expect = 0.43
 Identities = 9/33 (27%), Positives = 15/33 (45%)

Query: 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETGK 58
          FR  R+E ++T  +    T    S +  +E G 
Sbjct: 12 FRKKREERRITLLDASLFTNINPSKLKRIEEGD 44


>3bg1_B Nucleoporin NUP145; NPC, transport, WD repeat, autocatalytic
           cleavage, mRNA transport, nuclear pore complex, nucleus,
           phosphoprotein; 3.00A {Saccharomyces cerevisiae} PDB:
           3bg0_B
          Length = 442

 Score = 26.4 bits (58), Expect = 1.6
 Identities = 12/46 (26%), Positives = 13/46 (28%), Gaps = 4/46 (8%)

Query: 10  HLSDAILRERMI--FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53
            L+D    E  I   V   R I      T   I NR       I  
Sbjct: 386 FLNDDKAAEDTIKRLVM--REITLLRASTNDHILNRLKIPSQLIFN 429


>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 = 24.9 bits (54), Expect = 4.2
 Identities = 5/27 (18%), Positives = 10/27 (37%), Gaps = 4/27 (14%)

Query: 22  FVNNFRNIRKEAKLTQKEIRNRTGFAQ 48
                R  +  + L Q    +R  F++
Sbjct: 389 LNLTLRKAKAPSGLDQ----SRIPFSE 411


>1nm8_A Carnitine O-acetyltransferase; two equally sized domains,
          anti-parallel beta-strand; 1.60A {Homo sapiens} SCOP:
          c.43.1.3 c.43.1.3 PDB: 1s5o_A* 2h3u_A* 2h3p_A* 1t7q_A*
          1t7n_A 1t7o_A* 1ndb_A 1ndf_A* 1ndi_A* 2h3w_A*
          Length = 616

 Score = 24.6 bits (53), Expect = 6.0
 Identities = 10/47 (21%), Positives = 20/47 (42%)

Query: 8  EPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54
          +P +S+         V+ F+      +  QK +  R    ++W+SE 
Sbjct: 34 QPIVSEEEWAHTKQLVDEFQASGGVGERLQKGLERRARKTENWLSEW 80


>1t1u_A Choline O-acetyltransferase; choline acetyltransferase; 1.55A
          {Rattus norvegicus} SCOP: c.43.1.3 c.43.1.3 PDB: 1q6x_A
          2fy2_A 2fy3_A 2fy4_A* 2fy5_A*
          Length = 639

 Score = 24.6 bits (53), Expect = 6.2
 Identities = 8/46 (17%), Positives = 18/46 (39%)

Query: 8  EPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53
          +  + +   R+    V  F       +  Q+++  R     +W+SE
Sbjct: 42 QHLVPEEQFRKSQAIVKRFGAPGGLGETLQEKLLERQEKTANWVSE 87


>3e7m_A Nitric oxide synthase, inducible; NOS, heme, tetrahydrobiopterin,
          oxidoreductase calmodulin-binding, FAD, FMN, iron,
          metal- binding, NADP; HET: HEM H4B AT2; 2.00A {Mus
          musculus} SCOP: d.174.1.1 PDB: 1r35_A* 3e67_A* 3e68_A*
          3e6l_A* 3e6n_A* 3e6o_A* 3e6t_A* 3e7i_A* 3e65_A* 3e7t_A*
          3eai_A* 3ebd_A* 3ebf_A* 1m8d_A* 1m8e_A* 1m8h_A* 1m8i_A*
          1m9t_A* 1qom_A* 1jwj_A* ...
          Length = 433

 Score = 23.9 bits (52), Expect = 8.0
 Identities = 12/41 (29%), Positives = 21/41 (51%)

Query: 1  MPRRKRDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIR 41
          + R  RD+P   + +L   + F+N +    KEAK+ +   R
Sbjct: 54 LTRGPRDKPTPLEELLPHAIEFINQYYGSFKEAKIEEHLAR 94


  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    0.135    0.398 

Gapped
Lambda     K      H
   0.267   0.0632    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 706,778
Number of extensions: 26867
Number of successful extensions: 148
Number of sequences better than 10.0: 1
Number of HSP's gapped: 146
Number of HSP's successfully gapped: 59
Length of query: 83
Length of database: 5,693,230
Length adjustment: 51
Effective length of query: 32
Effective length of database: 4,456,786
Effective search space: 142617152
Effective search space used: 142617152
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: 50 (23.2 bits)