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= 043637
         (693 letters)

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

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



>pdb|3FUB|A Chain A, Crystal Structure Of Gdnf-Gfralpha1 Complex
 pdb|3FUB|C Chain C, Crystal Structure Of Gdnf-Gfralpha1 Complex
          Length = 281

 Score = 30.0 bits (66), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 17/83 (20%), Positives = 38/83 (45%), Gaps = 17/83 (20%)

Query: 456 RGQSEEAMTSFSEMQWETRPSKFTFETLLAACANISSLEQGKQI-------------HCF 502
           R +  +A+  F    ++  P+K ++  L  +C +I+  E+ +Q              +C 
Sbjct: 45  RRKCHKALRQF----FDKVPAKHSYGMLFCSCRDIACTERRRQTIVPVCSYEERERPNCL 100

Query: 503 VIRNCYEINVVCRGALVEVYTKC 525
            +++  + N +CR  L + +T C
Sbjct: 101 SLQDSCKTNYICRSRLADFFTNC 123


>pdb|2V5E|A Chain A, The Structure Of The Gdnf:coreceptor Complex: Insights
           Into Ret Signalling And Heparin Binding
          Length = 200

 Score = 29.6 bits (65), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 17/83 (20%), Positives = 38/83 (45%), Gaps = 17/83 (20%)

Query: 456 RGQSEEAMTSFSEMQWETRPSKFTFETLLAACANISSLEQGKQI-------------HCF 502
           R +  +A+  F    ++  P+K ++  L  +C +I+  E+ +Q              +C 
Sbjct: 40  RRKCHKALRQF----FDKVPAKHSYGMLFCSCRDIACTERRRQTIVPVCSYEERERPNCL 95

Query: 503 VIRNCYEINVVCRGALVEVYTKC 525
            +++  + N +CR  L + +T C
Sbjct: 96  SLQDSCKTNYICRSRLADFFTNC 118


>pdb|1ZQ7|A Chain A, X-Ray Crystal Structure Of Protein Q8pzk8 From
           Methanosarcina Mazei. Northeast Structural Genomics
           Consortium Target Mar9.
 pdb|1ZQ7|B Chain B, X-Ray Crystal Structure Of Protein Q8pzk8 From
           Methanosarcina Mazei. Northeast Structural Genomics
           Consortium Target Mar9.
 pdb|1ZQ7|C Chain C, X-Ray Crystal Structure Of Protein Q8pzk8 From
           Methanosarcina Mazei. Northeast Structural Genomics
           Consortium Target Mar9.
 pdb|1ZQ7|D Chain D, X-Ray Crystal Structure Of Protein Q8pzk8 From
           Methanosarcina Mazei. Northeast Structural Genomics
           Consortium Target Mar9
          Length = 207

 Score = 29.3 bits (64), Expect = 8.1,   Method: Composition-based stats.
 Identities = 15/42 (35%), Positives = 23/42 (54%)

Query: 139 VSANQITYANVLRSSAEELELGVSKQLHGLIVKRGFCGNVIL 180
           V    +T    + +S +EL   V    HGLIVK+G+C  ++L
Sbjct: 101 VEVTILTQPEKINASPKELPDKVEIGKHGLIVKQGYCQGLLL 142


>pdb|1QNI|A Chain A, Crystal Structure Of Nitrous Oxide Reductase From
           Pseudomonas Nautica, At 2.4a Resolution
 pdb|1QNI|B Chain B, Crystal Structure Of Nitrous Oxide Reductase From
           Pseudomonas Nautica, At 2.4a Resolution
 pdb|1QNI|C Chain C, Crystal Structure Of Nitrous Oxide Reductase From
           Pseudomonas Nautica, At 2.4a Resolution
 pdb|1QNI|D Chain D, Crystal Structure Of Nitrous Oxide Reductase From
           Pseudomonas Nautica, At 2.4a Resolution
 pdb|1QNI|E Chain E, Crystal Structure Of Nitrous Oxide Reductase From
           Pseudomonas Nautica, At 2.4a Resolution
 pdb|1QNI|F Chain F, Crystal Structure Of Nitrous Oxide Reductase From
           Pseudomonas Nautica, At 2.4a Resolution
          Length = 581

 Score = 28.9 bits (63), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 21/45 (46%), Gaps = 8/45 (17%)

Query: 573 GIKPDHITFHGILLACIHEGNVKLALQFFDSMRCKYGIIPQLEHY 617
           G+ P H TF G        GN    L F DS  CK+ I   ++HY
Sbjct: 320 GLGPLHTTFDG-------RGNAYTTL-FIDSQVCKWNIADAIKHY 356


  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
   0.324    0.138    0.426 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,981,449
Number of Sequences: 62578
Number of extensions: 826459
Number of successful extensions: 2144
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2142
Number of HSP's gapped (non-prelim): 5
length of query: 693
length of database: 14,973,337
effective HSP length: 106
effective length of query: 587
effective length of database: 8,340,069
effective search space: 4895620503
effective search space used: 4895620503
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: 55 (25.8 bits)