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= psy2694
         (262 letters)

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

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



>pdb|3HY5|A Chain A, Crystal Structure Of Cralbp
          Length = 316

 Score = 80.5 bits (197), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 39/122 (31%), Positives = 66/122 (54%), Gaps = 2/122 (1%)

Query: 17  FLTRFLYARKMNVDKSFDLLCNYITYRTNHAEFFDNLTVSNRQIQCAIKDGLPGVLSNRD 76
           F  RF+ ARK NV ++++LL  Y+ +R  + E FD+L  S   ++C I+ G PGVLS+RD
Sbjct: 94  FFLRFIRARKFNVGRAYELLRGYVNFRLQYPELFDSL--SPEAVRCTIEAGYPGVLSSRD 151

Query: 77  RKGRRILVFFANNWDHTRYTLEIIYKSLIXXXXXXXXXXXXXMNGLIFIVDWGNLTLRQT 136
           + GR +++F   NW     T + I ++               +NG   I ++   T++Q 
Sbjct: 152 KYGRVVMLFNIENWQSQEITFDEILQAYCFILEKLLENEETQINGFCIIENFKGFTMQQA 211

Query: 137 SN 138
           ++
Sbjct: 212 AS 213


>pdb|3HX3|A Chain A, Crystal Structure Of Cralbp Mutant R234w
          Length = 316

 Score = 77.8 bits (190), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 39/122 (31%), Positives = 64/122 (52%), Gaps = 2/122 (1%)

Query: 17  FLTRFLYARKMNVDKSFDLLCNYITYRTNHAEFFDNLTVSNRQIQCAIKDGLPGVLSNRD 76
           F  RF+ ARK NV ++++LL  Y+ +R  + E FD+L  S   ++C I+ G PGVLS+RD
Sbjct: 94  FFLRFIRARKFNVGRAYELLRGYVNFRLQYPELFDSL--SPEAVRCTIEAGYPGVLSSRD 151

Query: 77  RKGRRILVFFANNWDHTRYTLEIIYKSLIXXXXXXXXXXXXXMNGLIFIVDWGNLTLRQT 136
           + GR + +F   NW     T + I ++               +NG   I ++   T +Q 
Sbjct: 152 KYGRVVXLFNIENWQSQEITFDEILQAYCFILEKLLENEETQINGFCIIENFKGFTXQQA 211

Query: 137 SN 138
           ++
Sbjct: 212 AS 213


>pdb|1OIP|A Chain A, The Molecular Basis Of Vitamin E Retention: Structure Of
           Human Alpha-tocopherol Transfer Protein
 pdb|1OIZ|A Chain A, The Molecular Basis Of Vitamin E Retention: Structure Of
           Human Alpha-Tocopherol Transfer Protein
 pdb|1OIZ|B Chain B, The Molecular Basis Of Vitamin E Retention: Structure Of
           Human Alpha-Tocopherol Transfer Protein
          Length = 278

 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 54/114 (47%), Gaps = 2/114 (1%)

Query: 14  TDEFLTRFLYARKMNVDKSFDLLCNYITYRTNHAEFFDNLTVSNRQIQCAIKDGLPGVLS 73
           TD FL RFL AR  ++D ++ LL NY  +R    E   +L    R I   +K G  GVL 
Sbjct: 48  TDSFLLRFLRARDFDLDLAWRLLKNYYKWRAECPEISADL--HPRSIIGLLKAGYHGVLR 105

Query: 74  NRDRKGRRILVFFANNWDHTRYTLEIIYKSLIXXXXXXXXXXXXXMNGLIFIVD 127
           +RD  G ++L++   +WD   +T   +++  +              NG+  I D
Sbjct: 106 SRDPTGSKVLIYRIAHWDPKVFTAYDVFRVSLITSELIVQEVETQRNGIKAIFD 159


>pdb|1R5L|A Chain A, Crystal Structure Of Human Alpha-tocopherol Transfer
           Protein Bound To Its Ligand
          Length = 262

 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 54/114 (47%), Gaps = 2/114 (1%)

Query: 14  TDEFLTRFLYARKMNVDKSFDLLCNYITYRTNHAEFFDNLTVSNRQIQCAIKDGLPGVLS 73
           TD FL RFL AR  ++D ++ LL NY  +R    E   +L    R I   +K G  GVL 
Sbjct: 32  TDSFLLRFLRARDFDLDLAWRLLKNYYKWRAECPEISADL--HPRSIIGLLKAGYHGVLR 89

Query: 74  NRDRKGRRILVFFANNWDHTRYTLEIIYKSLIXXXXXXXXXXXXXMNGLIFIVD 127
           +RD  G ++L++   +WD   +T   +++  +              NG+  I D
Sbjct: 90  SRDPTGSKVLIYRIAHWDPKVFTAYDVFRVSLITSELIVQEVETQRNGIKAIFD 143


  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
   0.325    0.140    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,080,523
Number of Sequences: 62578
Number of extensions: 159906
Number of successful extensions: 450
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 442
Number of HSP's gapped (non-prelim): 4
length of query: 262
length of database: 14,973,337
effective HSP length: 97
effective length of query: 165
effective length of database: 8,903,271
effective search space: 1469039715
effective search space used: 1469039715
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)