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= 017508
         (370 letters)

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

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



>pdb|3TTM|A Chain A, Crystal Structure Of Spud In Complex With Putrescine
 pdb|3TTM|B Chain B, Crystal Structure Of Spud In Complex With Putrescine
          Length = 346

 Score = 28.5 bits (62), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 29/131 (22%), Positives = 53/131 (40%), Gaps = 19/131 (14%)

Query: 29  SRAVSKMAVAQICESVGFQG----FKDSALDALSDIAIRYICDLGKTSSFQANLACRTEC 84
           S+ +S +A   IC ++G+ G     K  A +A + + ++Y            N+      
Sbjct: 204 SKYISDLANGNICVAIGYSGDIYQAKSRAEEAKNKVTVKY------------NIPKEGAG 251

Query: 85  NLFDIIRGIEDLEVLKGFMGAAEIGKCLVGSGIVKEIIDFVESKEEIPFAQPIPQYPVIR 144
           + FD++   +D E  +G +        L+   I+ EI D V+       A P+    +  
Sbjct: 252 SFFDMVAIPKDAENTEGALAFVNF---LMKPEIMAEITDVVQFPNGNAAATPLVSEAIRN 308

Query: 145 SRRLIPSFEEM 155
              + PS E M
Sbjct: 309 DPGIYPSEEVM 319


>pdb|3TTK|A Chain A, Crystal Structure Of Apo-Spud
 pdb|3TTK|B Chain B, Crystal Structure Of Apo-Spud
 pdb|3TTK|C Chain C, Crystal Structure Of Apo-Spud
          Length = 345

 Score = 28.5 bits (62), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 29/131 (22%), Positives = 53/131 (40%), Gaps = 19/131 (14%)

Query: 29  SRAVSKMAVAQICESVGFQG----FKDSALDALSDIAIRYICDLGKTSSFQANLACRTEC 84
           S+ +S +A   IC ++G+ G     K  A +A + + ++Y            N+      
Sbjct: 204 SKYISDLANGNICVAIGYSGDIYQAKSRAEEAKNKVTVKY------------NIPKEGAG 251

Query: 85  NLFDIIRGIEDLEVLKGFMGAAEIGKCLVGSGIVKEIIDFVESKEEIPFAQPIPQYPVIR 144
           + FD++   +D E  +G +        L+   I+ EI D V+       A P+    +  
Sbjct: 252 SFFDMVAIPKDAENTEGALAFVNF---LMKPEIMAEITDVVQFPNGNAAATPLVSEAIRN 308

Query: 145 SRRLIPSFEEM 155
              + PS E M
Sbjct: 309 DPGIYPSEEVM 319


>pdb|1U3C|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From
           Arabidopsis Thaliana
 pdb|1U3D|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From
           Arabidopsis Thaliana With Amppnp Bound
          Length = 509

 Score = 28.1 bits (61), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 2/50 (4%)

Query: 150 PSFEEMNETPPGKHIPSWLPAFPD-PHTYIYTPMWNERKSDPRADKIELA 198
           P FE     P G+++  WLP     P  +I+ P WN  +S  +A  IEL 
Sbjct: 419 PQFEGYKFDPNGEYVRRWLPELSRLPTDWIHHP-WNAPESVLQAAGIELG 467


  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
   0.317    0.135    0.394 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,621,619
Number of Sequences: 62578
Number of extensions: 453910
Number of successful extensions: 998
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 998
Number of HSP's gapped (non-prelim): 5
length of query: 370
length of database: 14,973,337
effective HSP length: 100
effective length of query: 270
effective length of database: 8,715,537
effective search space: 2353194990
effective search space used: 2353194990
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)