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= psy13858
         (70 letters)

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

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



>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
           Bound To Amppnp
          Length = 997

 Score = 62.0 bits (149), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 41/57 (71%), Gaps = 4/57 (7%)

Query: 1   MLSATVPNTLEFADWVGNTKKTKVYVVSTLKRPVPLKHFLYVG----PVLEKNQLFL 53
           +LSATVPNT EFA+W+G TK+  +YV+ST KRPVPL+  ++      PV+ +N  FL
Sbjct: 183 LLSATVPNTYEFANWIGRTKQKNIYVISTPKRPVPLEINIWAKKELIPVINQNSEFL 239


>pdb|2XGJ|A Chain A, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
           Processing And Surveillance
 pdb|2XGJ|B Chain B, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
           Processing And Surveillance
          Length = 1010

 Score = 47.0 bits (110), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 18/40 (45%), Positives = 27/40 (67%)

Query: 2   LSATVPNTLEFADWVGNTKKTKVYVVSTLKRPVPLKHFLY 41
           LSAT+PN +EFA+W+        ++V T  RP PL+H+L+
Sbjct: 229 LSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLF 268


>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
           Exosome
          Length = 1108

 Score = 47.0 bits (110), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 18/40 (45%), Positives = 27/40 (67%)

Query: 2   LSATVPNTLEFADWVGNTKKTKVYVVSTLKRPVPLKHFLY 41
           LSAT+PN +EFA+W+        ++V T  RP PL+H+L+
Sbjct: 327 LSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLF 366


>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In
           Complex With Unwound Dna
 pdb|2P6U|A Chain A, Apo Structure Of The Hel308 Superfamily 2 Helicase
          Length = 702

 Score = 28.1 bits (61), Expect = 1.4,   Method: Composition-based stats.
 Identities = 17/35 (48%), Positives = 19/35 (54%), Gaps = 6/35 (17%)

Query: 2   LSATVPNTLEFADWVGNTKKTKVYVVSTLKRPVPL 36
           LSAT PN  E A+W+        Y VS   RPVPL
Sbjct: 178 LSATAPNVTEIAEWLDAD-----YYVSDW-RPVPL 206


>pdb|1IXS|B Chain B, Structure Of Ruvb Complexed With Ruva Domain Iii
          Length = 318

 Score = 27.3 bits (59), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 5/44 (11%)

Query: 4  ATVPNTLEFADWVGNTK---KTKVYVVSTLKRPVPLKHFLYVGP 44
          A  P TL+  +++G  +   K +VY+ +   R  PL+H L  GP
Sbjct: 5  ALRPKTLD--EYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGP 46


>pdb|1HQC|A Chain A, Structure Of Ruvb From Thermus Thermophilus Hb8
 pdb|1HQC|B Chain B, Structure Of Ruvb From Thermus Thermophilus Hb8
          Length = 324

 Score = 26.9 bits (58), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 5/44 (11%)

Query: 4  ATVPNTLEFADWVGNTK---KTKVYVVSTLKRPVPLKHFLYVGP 44
          A  P TL+  +++G  +   K +VY+ +   R  PL+H L  GP
Sbjct: 5  ALRPKTLD--EYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGP 46


>pdb|1IXR|C Chain C, Ruva-Ruvb Complex
          Length = 312

 Score = 26.2 bits (56), Expect = 5.0,   Method: Composition-based stats.
 Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 5/44 (11%)

Query: 4  ATVPNTLEFADWVGNTK---KTKVYVVSTLKRPVPLKHFLYVGP 44
          A  P TL+  +++G  +   K +VY+ +   R  PL+H L  GP
Sbjct: 5  ALRPKTLD--EYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGP 46


>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
 pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
          Length = 715

 Score = 25.4 bits (54), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 6/35 (17%)

Query: 2   LSATVPNTLEFADWVGNTKKTKVYVVSTLKRPVPL 36
           LSAT+ N  + A W+G         V+T  RPVPL
Sbjct: 181 LSATISNYKQIAKWLGAEP------VATNWRPVPL 209


  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
   0.321    0.138    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,047,589
Number of Sequences: 62578
Number of extensions: 64960
Number of successful extensions: 157
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 154
Number of HSP's gapped (non-prelim): 9
length of query: 70
length of database: 14,973,337
effective HSP length: 40
effective length of query: 30
effective length of database: 12,470,217
effective search space: 374106510
effective search space used: 374106510
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)