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= psy8798
         (114 letters)

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

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



>pdb|2RJB|A Chain A, Crystal Structure Of Uncharacterized Protein Ydcj (Sf1787)
           From Shigella Flexneri Which Includes Domain Duf1338.
           Northeast Structural Genomics Consortium Target Sfr276
 pdb|2RJB|B Chain B, Crystal Structure Of Uncharacterized Protein Ydcj (Sf1787)
           From Shigella Flexneri Which Includes Domain Duf1338.
           Northeast Structural Genomics Consortium Target Sfr276
 pdb|2RJB|C Chain C, Crystal Structure Of Uncharacterized Protein Ydcj (Sf1787)
           From Shigella Flexneri Which Includes Domain Duf1338.
           Northeast Structural Genomics Consortium Target Sfr276
 pdb|2RJB|D Chain D, Crystal Structure Of Uncharacterized Protein Ydcj (Sf1787)
           From Shigella Flexneri Which Includes Domain Duf1338.
           Northeast Structural Genomics Consortium Target Sfr276
          Length = 455

 Score = 29.3 bits (64), Expect = 0.60,   Method: Compositional matrix adjust.
 Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 9/58 (15%)

Query: 53  PQGKFTVEEFEQIGTINSTAPHEFNLDQLEDKPWRKPGADITDYFNYGFTEETWRAHH 110
           P+ +  +EE+EQ G  N T   EF  + LE   W +              EET+RA H
Sbjct: 157 PRCRQLLEEYEQQGGFNETQAQEFVQEALETFRWHQLAT---------VDEETYRALH 205


>pdb|3MXL|A Chain A, Crystal Structure Of Nitrososynthase From Micromonospora
          Carbonacea Var. Africana
 pdb|3MXL|B Chain B, Crystal Structure Of Nitrososynthase From Micromonospora
          Carbonacea Var. Africana
 pdb|3MXL|C Chain C, Crystal Structure Of Nitrososynthase From Micromonospora
          Carbonacea Var. Africana
 pdb|3MXL|D Chain D, Crystal Structure Of Nitrososynthase From Micromonospora
          Carbonacea Var. Africana
          Length = 395

 Score = 28.1 bits (61), Expect = 1.4,   Method: Composition-based stats.
 Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 3/39 (7%)

Query: 41 LPAFSDIAQNPDPQGKFTVEEFEQ---IGTINSTAPHEF 76
          +P  S  A + D  G F VE FEQ   +G + +T P E 
Sbjct: 24 IPRISAEAADRDRTGTFPVEAFEQFAKLGLMGATVPAEL 62


>pdb|3NVN|B Chain B, Molecular Mechanism Of Guidance Cue Recognition
 pdb|3NVQ|B Chain B, Molecular Mechanism Of Guidance Cue Recognition
 pdb|3NVQ|F Chain F, Molecular Mechanism Of Guidance Cue Recognition
          Length = 476

 Score = 26.6 bits (57), Expect = 3.6,   Method: Composition-based stats.
 Identities = 16/32 (50%), Positives = 20/32 (62%), Gaps = 2/32 (6%)

Query: 10 LYGDQAGQNTGDPNTTEPPQPDPKEQSSFSEL 41
          LY DQAG N  +P +  PP   P+  SSFS+L
Sbjct: 45 LYRDQAG-NCTEPVSLAPP-ARPRPGSSFSKL 74


>pdb|3OT2|A Chain A, Crystal Structure Of A Putative Nuclease Belonging To
          Duf820 (Ava_3926) From Anabaena Variabilis Atcc 29413
          At 1.96 A Resolution
 pdb|3OT2|B Chain B, Crystal Structure Of A Putative Nuclease Belonging To
          Duf820 (Ava_3926) From Anabaena Variabilis Atcc 29413
          At 1.96 A Resolution
          Length = 187

 Score = 26.2 bits (56), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 11/26 (42%), Positives = 14/26 (53%)

Query: 47 IAQNPDPQGKFTVEEFEQIGTINSTA 72
          I Q P PQGK +  + E +  INS  
Sbjct: 32 IIQKPXPQGKHSAIQSECVSVINSVV 57


>pdb|1EER|B Chain B, Crystal Structure Of Human Erythropoietin Complexed To
          Its Receptor At 1.9 Angstroms
 pdb|1EER|C Chain C, Crystal Structure Of Human Erythropoietin Complexed To
          Its Receptor At 1.9 Angstroms
          Length = 227

 Score = 25.8 bits (55), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 13/68 (19%)

Query: 27 PPQPDPKEQSSFSELPAFSDIAQNPDPQGKFTVEEFEQIGTI------NSTAPHEFNLD- 79
          PP PDPK +S  + L      A+ P+    FT E  E +             P +++   
Sbjct: 5  PPNPDPKFESKAALL-----AARGPEELLCFT-ERLEDLVCFWEEAASAGVGPGQYSFSY 58

Query: 80 QLEDKPWR 87
          QLED+PW+
Sbjct: 59 QLEDEPWK 66


  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
   0.309    0.130    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,389,153
Number of Sequences: 62578
Number of extensions: 179834
Number of successful extensions: 240
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 238
Number of HSP's gapped (non-prelim): 6
length of query: 114
length of database: 14,973,337
effective HSP length: 77
effective length of query: 37
effective length of database: 10,154,831
effective search space: 375728747
effective search space used: 375728747
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 45 (21.9 bits)