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= psy11904
         (199 letters)

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

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



>pdb|2PSN|A Chain A, Crystal Structure Of Enolase1
 pdb|2PSN|B Chain B, Crystal Structure Of Enolase1
 pdb|2PSN|C Chain C, Crystal Structure Of Enolase1
 pdb|2PSN|D Chain D, Crystal Structure Of Enolase1
          Length = 434

 Score = 27.3 bits (59), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 71  DNWKSGSRNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQVGS--HYCQA 128
           D+W +  + T  +G + +G++  +T  K       +K  SC     KV+Q+GS     QA
Sbjct: 299 DDWGAWQKFTASAGIQVVGDDLTVTNPKRIAKAVNEK--SCNCLLLKVNQIGSVTESLQA 356

Query: 129 C 129
           C
Sbjct: 357 C 357


>pdb|3B97|A Chain A, Crystal Structure Of Human Enolase 1
 pdb|3B97|B Chain B, Crystal Structure Of Human Enolase 1
 pdb|3B97|C Chain C, Crystal Structure Of Human Enolase 1
 pdb|3B97|D Chain D, Crystal Structure Of Human Enolase 1
          Length = 433

 Score = 27.3 bits (59), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 71  DNWKSGSRNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQVGS--HYCQA 128
           D+W +  + T  +G + +G++  +T  K       +K  SC     KV+Q+GS     QA
Sbjct: 298 DDWGAWQKFTASAGIQVVGDDLTVTNPKRIAKAVNEK--SCNCLLLKVNQIGSVTESLQA 355

Query: 129 C 129
           C
Sbjct: 356 C 356


>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid
           Domain
          Length = 188

 Score = 26.9 bits (58), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 24/89 (26%), Positives = 37/89 (41%), Gaps = 18/89 (20%)

Query: 57  CSKCEKKLGKVITPDNWKSGSRNTIESGGRRIGENKALTAS-----------KARFNPYT 105
           CS C+ +LG + T    KSG         R  G + A +A            +A+ N Y 
Sbjct: 35  CSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYH 94

Query: 106 QKFESCKICRQKV------HQV-GSHYCQ 127
            K  +C  CR ++      H + GS +C+
Sbjct: 95  LKCFTCSTCRNRLVPGDRFHYINGSLFCE 123


>pdb|2DFY|X Chain X, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim
           Domains 1 And 2 With The Lim Interacting Domain Of Ldb1
 pdb|2DFY|C Chain C, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim
           Domains 1 And 2 With The Lim Interacting Domain Of Ldb1
          Length = 195

 Score = 26.9 bits (58), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 24/89 (26%), Positives = 37/89 (41%), Gaps = 18/89 (20%)

Query: 57  CSKCEKKLGKVITPDNWKSGSRNTIESGGRRIGENKALTAS-----------KARFNPYT 105
           CS C+ +LG + T    KSG         R  G + A +A            +A+ N Y 
Sbjct: 33  CSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYH 92

Query: 106 QKFESCKICRQKV------HQV-GSHYCQ 127
            K  +C  CR ++      H + GS +C+
Sbjct: 93  LKCFTCSTCRNRLVPGDRFHYINGSLFCE 121


>pdb|1DX8|A Chain A, Rubredoxin From Guillardia Theta
          Length = 70

 Score = 26.6 bits (57), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 9/32 (28%)

Query: 122 GSHYCQACAYKKGEHLVLVTADPEKGDKFALI 153
           G + C+AC Y           +PEKGDKFA I
Sbjct: 6   GKYECEACGY---------IYEPEKGDKFAGI 28


>pdb|1H7V|A Chain A, Rubredoxin From Guillardia Theta
          Length = 60

 Score = 26.6 bits (57), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 9/32 (28%)

Query: 122 GSHYCQACAYKKGEHLVLVTADPEKGDKFALI 153
           G + C+AC Y           +PEKGDKFA I
Sbjct: 6   GKYECEACGY---------IYEPEKGDKFAGI 28


>pdb|3QTP|A Chain A, Crystal Structure Analysis Of Entamoeba Histolytica
           Enolase
 pdb|3QTP|B Chain B, Crystal Structure Analysis Of Entamoeba Histolytica
           Enolase
          Length = 441

 Score = 26.6 bits (57), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 71  DNWKSGSRNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQVGS 123
           D+W + ++ T+E G  +I  +  L  + AR      K  +C     KV+Q+G+
Sbjct: 307 DDWAAWNKFTVEHGNFQIVGDDLLVTNPARVQMAMDK-NACNSVLIKVNQIGT 358


  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
   0.318    0.133    0.402 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,302,329
Number of Sequences: 62578
Number of extensions: 251488
Number of successful extensions: 535
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 531
Number of HSP's gapped (non-prelim): 16
length of query: 199
length of database: 14,973,337
effective HSP length: 94
effective length of query: 105
effective length of database: 9,091,005
effective search space: 954555525
effective search space used: 954555525
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: 49 (23.5 bits)