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= 042872
         (381 letters)

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

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



>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase
 pdb|2V1X|B Chain B, Crystal Structure Of Human Recq-Like Dna Helicase
 pdb|2WWY|A Chain A, Structure Of Human Recq-Like Helicase In Complex With A
           Dna Substrate
 pdb|2WWY|B Chain B, Structure Of Human Recq-Like Helicase In Complex With A
           Dna Substrate
          Length = 591

 Score = 59.3 bits (142), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 46/182 (25%), Positives = 68/182 (37%), Gaps = 65/182 (35%)

Query: 220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ--------------------- 258
           +F    FRPLQ +    ++A ++ F+++PTGGGKSLCYQ                     
Sbjct: 39  VFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLISLME 98

Query: 259 DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDK 318
           DQ++ L  + GI AT LN+  +      V  E+                           
Sbjct: 99  DQLMVLK-QLGISATMLNASSSKEHVKWVHAEMVN-----------------------KN 134

Query: 319 PSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEA 378
              KL+YVTPE+I  ++ F   L+  +                      R+     VDE 
Sbjct: 135 SELKLIYVTPEKIAKSKMFMSRLEKAYE--------------------ARRFTRIAVDEV 174

Query: 379 HC 380
           HC
Sbjct: 175 HC 176


>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
          Length = 523

 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 39/132 (29%), Positives = 54/132 (40%), Gaps = 45/132 (34%)

Query: 221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLN--------------- 265
           FG + FRP Q +     ++ +DC V++PTGGGKSLCYQ   + LN               
Sbjct: 21  FGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLISLMKD 80

Query: 266 -----LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPS 320
                   G+ A  LNS QT  Q   V+   R G +                        
Sbjct: 81  QVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQI------------------------ 116

Query: 321 CKLLYVTPERIV 332
            +LLY+ PER++
Sbjct: 117 -RLLYIAPERLM 127


>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
          Length = 523

 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 39/131 (29%), Positives = 51/131 (38%), Gaps = 45/131 (34%)

Query: 221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLN--------------- 265
           FG + FRP Q +     ++ +DC V+ PTGGGKSLCYQ   + LN               
Sbjct: 21  FGYQQFRPGQEEIIDTVLSGRDCLVVXPTGGGKSLCYQIPALLLNGLTVVVSPLISLXKD 80

Query: 266 -----LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPS 320
                   G+ A  LNS QT  Q   V    R G +                        
Sbjct: 81  QVDQLQANGVAAACLNSTQTREQQLEVXTGCRTGQI------------------------ 116

Query: 321 CKLLYVTPERI 331
            +LLY+ PER+
Sbjct: 117 -RLLYIAPERL 126


>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In
           Complex With Adp
          Length = 245

 Score = 29.6 bits (65), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 30/125 (24%), Positives = 55/125 (44%), Gaps = 15/125 (12%)

Query: 217 NVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLK----FGIPA 272
           N++  G +   P+Q QA    +  ++     PTG GK+L +   I+ + LK     G  A
Sbjct: 43  NILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPIL-MQLKQPANKGFRA 101

Query: 273 TFLN-SQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCK----LLYVT 327
             ++ +++  SQ    L ++ +G     H     +I     A++K  P       +L  T
Sbjct: 102 LIISPTRELASQIHRELIKISEGTGFRIH-----MIHKAAVAAKKFGPKSSKKFDILVTT 156

Query: 328 PERIV 332
           P R++
Sbjct: 157 PNRLI 161


  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
   0.320    0.135    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,766,711
Number of Sequences: 62578
Number of extensions: 350716
Number of successful extensions: 777
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 773
Number of HSP's gapped (non-prelim): 5
length of query: 381
length of database: 14,973,337
effective HSP length: 101
effective length of query: 280
effective length of database: 8,652,959
effective search space: 2422828520
effective search space used: 2422828520
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)