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= 001771
         (1015 letters)

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

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



>pdb|2J7N|A Chain A, Structure Of The Rnai Polymerase From Neurospora Crassa
 pdb|2J7N|B Chain B, Structure Of The Rnai Polymerase From Neurospora Crassa
 pdb|2J7O|A Chain A, Structure Of The Rnai Polymerase From Neurospora Crassa
          Length = 1022

 Score = 56.6 bits (135), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 45/144 (31%), Positives = 70/144 (48%), Gaps = 14/144 (9%)

Query: 607 YLQHRLSILMKEEKKSLQAG-KLPVTESYYLMGTVDPTGILKSNEVCI----ILKDGQVS 661
           YLQ     L K +  +L++   + V  S Y+    D  G+L+ NEV +      +D + S
Sbjct: 510 YLQDIAWDLQKRKCDTLKSKLNIRVGRSAYIYMIADFWGVLEENEVHVGFSSKFRDEEES 569

Query: 662 WE-----KVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIAG 716
           +       VLV R+P     DI  ++A +  EL       K  I F   G   LA +++G
Sbjct: 570 FTLLSDCDVLVARSPAHFPSDIQRVRAVFKPELHSL----KDVIIFSTKGDVPLAKKLSG 625

Query: 717 GDFDGDMYFVSRNPELLKHFKESE 740
           GD+DGDM +V  +PE++  F  +E
Sbjct: 626 GDYDGDMAWVCWDPEIVDGFVNAE 649


>pdb|1VLL|A Chain A, Crystal Structure Of Alanine Dehydrogenase (Af1665) From
           Archaeoglobus Fulgidus At 2.80 A Resolution
 pdb|1VLL|B Chain B, Crystal Structure Of Alanine Dehydrogenase (Af1665) From
           Archaeoglobus Fulgidus At 2.80 A Resolution
          Length = 334

 Score = 35.0 bits (79), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 49/105 (46%), Gaps = 9/105 (8%)

Query: 598 LSGISLDEPYLQH-------RLSILMKEEKKSLQAGKLPVTESYYLMGTVDPTGILKSNE 650
           ++ I  D P  Q        +  I++ + +++   G++ V  S  ++G  D    +   E
Sbjct: 225 INAIGADGPGKQELDVEILKKAKIVVDDLEQAKHGGEINVAVSKGVIGVEDVHATI--GE 282

Query: 651 VCIILKDGQVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGT 695
           V   LKDG+ S E++ ++ + GL   D+ V K  Y   L   VG+
Sbjct: 283 VIAGLKDGRESDEEITIFDSTGLAIQDVAVAKVVYENALSKNVGS 327


>pdb|1OMO|A Chain A, Alanine Dehydrogenase Dimer WBOUND NAD (ARCHAEAL)
 pdb|1OMO|B Chain B, Alanine Dehydrogenase Dimer WBOUND NAD (ARCHAEAL)
          Length = 322

 Score = 35.0 bits (79), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 49/105 (46%), Gaps = 9/105 (8%)

Query: 598 LSGISLDEPYLQH-------RLSILMKEEKKSLQAGKLPVTESYYLMGTVDPTGILKSNE 650
           ++ I  D P  Q        +  I++ + +++   G++ V  S  ++G  D    +   E
Sbjct: 213 INAIGADGPGKQELDVEILKKAKIVVDDLEQAKHGGEINVAVSKGVIGVEDVHATI--GE 270

Query: 651 VCIILKDGQVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGT 695
           V   LKDG+ S E++ ++ + GL   D+ V K  Y   L   VG+
Sbjct: 271 VIAGLKDGRESDEEITIFDSTGLAIQDVAVAKVVYENALSKNVGS 315


>pdb|2DUM|A Chain A, Crystal Structure Of Hypothetical Protein, Ph0823
 pdb|2DUM|B Chain B, Crystal Structure Of Hypothetical Protein, Ph0823
 pdb|2DUM|C Chain C, Crystal Structure Of Hypothetical Protein, Ph0823
 pdb|2DUM|D Chain D, Crystal Structure Of Hypothetical Protein, Ph0823
          Length = 170

 Score = 30.0 bits (66), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 868 YNTVKSYEAVDR-SVTEIWKLPCFDDGVPEACMTKWKGYYDQYRWEMKEAIDKCTVEREE 926
           Y  V+ +E  ++  V E+  L   D+G  E  M  +  +YD    E+K+  +K    +EE
Sbjct: 19  YRAVEVFEKRNKMEVGEVILLHVIDEGTLEELMDGYSFFYDNAEIELKDIKEKL---KEE 75

Query: 927 AAELVIEKYKQI 938
           A+  + EK +++
Sbjct: 76  ASRKLQEKAEEV 87


>pdb|3DWB|A Chain A, Structure Of Human Ece-1 Complexed With Phosphoramidon
          Length = 670

 Score = 29.6 bits (65), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 7/75 (9%)

Query: 924 REEAAELVIEKYKQILYGAAEFEQSTRTLEEIYNEALAIYNITYDLAASRRQVSYCSFAW 983
           R+ A E     Y  I  G   F    + L++++N+  A+ ++ ++ A     + + +F+W
Sbjct: 390 RKSAKEKADAIYNMI--GYPNFIMDPKELDKVFNDYTAVPDLYFENA-----MRFFNFSW 442

Query: 984 RVAGSALRKFYARRQ 998
           RV    LRK   R Q
Sbjct: 443 RVTADQLRKAPNRDQ 457


  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    0.134    0.392 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,142,127
Number of Sequences: 62578
Number of extensions: 1216477
Number of successful extensions: 3002
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 2997
Number of HSP's gapped (non-prelim): 12
length of query: 1015
length of database: 14,973,337
effective HSP length: 108
effective length of query: 907
effective length of database: 8,214,913
effective search space: 7450926091
effective search space used: 7450926091
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: 56 (26.2 bits)