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= 041890
         (375 letters)

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

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



>pdb|1NAS|A Chain A, Sepiapterin Reductase Complexed With N-acetyl Serotonin
 pdb|1OAA|A Chain A, Mouse Sepiapterin Reductase Complexed With Nadp And
           Oxaloacetate
          Length = 259

 Score = 32.7 bits (73), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 17/56 (30%), Positives = 27/56 (48%)

Query: 293 REYHCWALYCMPEWAKGTDITISAAEQLRSWLLKYLDMNVANRFTTITRETAKNFE 348
           + Y  W LYC  + A+     + AAE+    +L Y    + N    + RET+K+ E
Sbjct: 161 QPYKGWGLYCAGKAARDMLYQVLAAEEPSVRVLSYAPGPLDNDMQQLARETSKDPE 216


>pdb|1SEP|A Chain A, Mouse Sepiapterin Reductase Complexed With Nadp And
           Sepiapterin
          Length = 261

 Score = 32.7 bits (73), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 17/56 (30%), Positives = 27/56 (48%)

Query: 293 REYHCWALYCMPEWAKGTDITISAAEQLRSWLLKYLDMNVANRFTTITRETAKNFE 348
           + Y  W LYC  + A+     + AAE+    +L Y    + N    + RET+K+ E
Sbjct: 163 QPYKGWGLYCAGKAARDMLYQVLAAEEPSVRVLSYAPGPLDNDMQQLARETSKDPE 218


>pdb|1ZAN|H Chain H, Crystal Structure Of Anti-Ngf Ad11 Fab
          Length = 224

 Score = 30.0 bits (66), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 21/43 (48%)

Query: 276 MMLLQDQNRDCYGWLINREYHCWALYCMPEWAKGTDITISAAE 318
           M  LQ ++   Y    +  Y    LY M  W +GT +T+S+A 
Sbjct: 82  MHSLQSEDTATYYCARDGGYSSSTLYAMDAWGQGTTVTVSSAS 124


>pdb|3U0T|D Chain D, Fab-Antibody Complex
 pdb|3U0T|B Chain B, Fab-Antibody Complex
          Length = 217

 Score = 29.3 bits (64), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 11/25 (44%), Positives = 18/25 (72%), Gaps = 1/25 (4%)

Query: 295 YHCWALYCMPE-WAKGTDITISAAE 318
           Y+C +LY +P  W +GT +T+S+A 
Sbjct: 94  YYCASLYSLPVYWGQGTTVTVSSAS 118


>pdb|1KEL|H Chain H, Catalytic Antibody 28b4 Fab Fragment Complexed With Hapten
           (1-[n-4'-Nitrobenzyl-N-4'-Carboxybutylamino]
           Methylphosphonic Acid)
 pdb|1KEM|H Chain H, Catalytic Antibody 28b4 Fab Fragment
          Length = 218

 Score = 28.9 bits (63), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 11/26 (42%), Positives = 17/26 (65%), Gaps = 2/26 (7%)

Query: 295 YHC--WALYCMPEWAKGTDITISAAE 318
           Y+C  W  Y M  W +GT +T+S+A+
Sbjct: 96  YYCARWGSYAMDYWGQGTSVTVSSAK 121


  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    0.137    0.452 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,926,604
Number of Sequences: 62578
Number of extensions: 440895
Number of successful extensions: 1785
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1779
Number of HSP's gapped (non-prelim): 8
length of query: 375
length of database: 14,973,337
effective HSP length: 100
effective length of query: 275
effective length of database: 8,715,537
effective search space: 2396772675
effective search space used: 2396772675
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: 52 (24.6 bits)