RPS-BLAST 2.2.26 [Sep-21-2011]

Database: pdb70 
           27,921 sequences; 6,701,793 total letters

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

Query= psy408
         (132 letters)



>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
           programmed cell death; HET: DTP; 6.90A {Drosophila
           melanogaster} PDB: 3iz8_A*
          Length = 1221

 Score = 31.0 bits (69), Expect = 0.12
 Identities = 12/65 (18%), Positives = 25/65 (38%), Gaps = 6/65 (9%)

Query: 3   SVFNWVRDHRVHHKYSETDADPHNSKR-----GFFFAHVGWLMCRKHKDVIEKGRMVDMS 57
           S+ N ++  + +  Y   D DP   +       F       L+C K+ D++    M +  
Sbjct: 519 SILNTLQQLKFYKPYI-CDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDE 577

Query: 58  DVMAD 62
            +  +
Sbjct: 578 AIFEE 582



 Score = 28.7 bits (63), Expect = 0.73
 Identities = 21/114 (18%), Positives = 40/114 (35%), Gaps = 30/114 (26%)

Query: 8   VRDHRVHHK-----YSETDADPHNSK-----RGFFFAHVGWLMCRKHKDVIEKGRMVDM- 56
           + +    H+     Y+       +         +F++H+G      H   IE    + + 
Sbjct: 439 LENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH-----HLKNIEHPERMTLF 493

Query: 57  SDVMADPLVRFHEKHFFWFKLVLCFIIPTIVPYYYFGESLLVSVLTMNFFR-YI 109
             V  D   RF E+     K     I      +   G S+L ++  + F++ YI
Sbjct: 494 RMVFLD--FRFLEQ-----K-----IRHDSTAWNASG-SILNTLQQLKFYKPYI 534


>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3;
           winged-helix domain, helix-turn-helix, AAA+ ATPase
           domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A
           {Sulfolobus solfataricus}
          Length = 384

 Score = 27.0 bits (59), Expect = 2.2
 Identities = 13/90 (14%), Positives = 26/90 (28%), Gaps = 13/90 (14%)

Query: 34  AHVGWLMCRKHKDVIEKGRMVDMSDVMA-------DPLVRFHEKHFFWFKLVLCFIIPTI 86
           A     +  +   +   G ++    V         + L+   +   F +KL L  +I + 
Sbjct: 238 ARKAVNLLFRAAQLASGGGIIRKEHVDKAIVDYEQERLIEAVKALPFHYKLALRSLIESE 297

Query: 87  VP------YYYFGESLLVSVLTMNFFRYIL 110
                   Y           L+   F  I+
Sbjct: 298 DVMSAHKMYTDLCNKFKQKPLSYRRFSDII 327


>1mc0_A 3',5'-cyclic nucleotide phosphodiesterase 2A; GAF domain, 3',5'
           guanosine monophosphate, hydrolase; HET: PCG; 2.86A {Mus
           musculus} SCOP: d.110.2.1 d.110.2.1
          Length = 368

 Score = 26.1 bits (57), Expect = 4.6
 Identities = 6/34 (17%), Positives = 16/34 (47%)

Query: 47  VIEKGRMVDMSDVMADPLVRFHEKHFFWFKLVLC 80
           V+E  + + + D+ +D + +         + +LC
Sbjct: 86  VVEDKQCIQLKDLTSDDVQQLQNMLGCELQAMLC 119


  Database: pdb70
    Posted date:  Sep 4, 2012  3:40 AM
  Number of letters in database: 6,701,793
  Number of sequences in database:  27,921
  
Lambda     K      H
   0.331    0.142    0.493 

Gapped
Lambda     K      H
   0.267   0.0506    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,161,751
Number of extensions: 115541
Number of successful extensions: 226
Number of sequences better than 10.0: 1
Number of HSP's gapped: 225
Number of HSP's successfully gapped: 8
Length of query: 132
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 49
Effective length of database: 4,384,350
Effective search space: 214833150
Effective search space used: 214833150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 52 (24.3 bits)