BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= psy7686
         (243 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

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



>pdb|1CF7|A Chain A, Structural Basis Of Dna Recognition By The Heterodimeric
          Cell Cycle Transcription Factor E2f-Dp
          Length = 76

 Score =  106 bits (264), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 53/69 (76%), Positives = 60/69 (86%)

Query: 8  SRFEKSLGLLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67
          SR EKSLGLLTTKFVSLLQ+A +GVL LK AA+ L V+QKRRIYDITNVLEGIGLIEK +
Sbjct: 6  SRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVLEGIGLIEKKS 65

Query: 68 KNIIRWKAL 76
          KN I+WK +
Sbjct: 66 KNSIQWKGV 74


>pdb|2RCC|A Chain A, Crystal Structure Of Putative Class I Ribonucleotide
          Reductase (Np_241368.1) From Bacillus Halodurans At
          1.90 A Resolution
 pdb|2RCC|B Chain B, Crystal Structure Of Putative Class I Ribonucleotide
          Reductase (Np_241368.1) From Bacillus Halodurans At
          1.90 A Resolution
 pdb|2RCC|C Chain C, Crystal Structure Of Putative Class I Ribonucleotide
          Reductase (Np_241368.1) From Bacillus Halodurans At
          1.90 A Resolution
          Length = 346

 Score = 28.1 bits (61), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 10/28 (35%), Positives = 16/28 (57%)

Query: 46 QKRRIYDITNVLEGIGLIEKNNKNIIRW 73
          QKR+IYD T      G++   + N++ W
Sbjct: 6  QKRKIYDTTASNASTGILNGKSSNVLNW 33


>pdb|3SP1|A Chain A, Crystal Structure Of Cysteinyl-Trna Synthetase (Cyss) From
           Borrelia Burgdorferi
 pdb|3SP1|B Chain B, Crystal Structure Of Cysteinyl-Trna Synthetase (Cyss) From
           Borrelia Burgdorferi
          Length = 501

 Score = 27.7 bits (60), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 28/113 (24%), Positives = 52/113 (46%), Gaps = 22/113 (19%)

Query: 55  NVLEGIGLIEKNNKNIIRWKALKNKNEE-------EYDLEQSKLIELRDEI-SDMRNHEA 106
           NV +G+ L+         W+ +K+ N          +  ++   + LR+EI  +++NH+ 
Sbjct: 400 NVAQGLALL---------WEIIKSDNLSFVSKLRLAFIFDEIMSLNLREEILKNLQNHDV 450

Query: 107 VIDEHIRKCQQSLRNIQEEEVNRKQCYIPTDVILGMFPDSSLMCLKAPYGTKL 159
           VIDE+++   +  R I + E N K+     D I   F     + +    GTK+
Sbjct: 451 VIDENMKALIEE-RRIAKCEKNFKRA----DEIRDFFAKKGFVLVDTKEGTKV 498


>pdb|1Z45|A Chain A, Crystal Structure Of The Gal10 Fusion Protein Galactose
           MutarotaseUDP-Galactose 4-Epimerase From Saccharomyces
           Cerevisiae Complexed With Nad, Udp-Glucose, And
           Galactose
          Length = 699

 Score = 27.3 bits (59), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 21/33 (63%)

Query: 164 ISTDENKIKLHVKSSHPEEPVNILLLDTEPKKE 196
           I+T  N++ L VK+ HP+  + + +L TEP  +
Sbjct: 613 INTLNNELTLIVKAFHPDSNITLEVLSTEPTYQ 645


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.316    0.135    0.390 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,365,486
Number of Sequences: 62578
Number of extensions: 302010
Number of successful extensions: 740
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 730
Number of HSP's gapped (non-prelim): 20
length of query: 243
length of database: 14,973,337
effective HSP length: 96
effective length of query: 147
effective length of database: 8,965,849
effective search space: 1317979803
effective search space used: 1317979803
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)