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= 030789
         (171 letters)

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

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



>pdb|1OZN|A Chain A, 1.5a Crystal Structure Of The Nogo Receptor Ligand Binding
           Domain Reveals A Convergent Recognition Scaffold
           Mediating Inhibition Of Myelination
          Length = 285

 Score = 28.1 bits (61), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 9/21 (42%), Positives = 14/21 (66%)

Query: 137 NDDPVIFDTSIVPWWAWIKRF 157
           ND+P + D    P WAW+++F
Sbjct: 233 NDNPWVCDCRARPLWAWLQKF 253


>pdb|1P8T|A Chain A, Crystal Structure Of Nogo-66 Receptor
          Length = 285

 Score = 28.1 bits (61), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 9/21 (42%), Positives = 14/21 (66%)

Query: 137 NDDPVIFDTSIVPWWAWIKRF 157
           ND+P + D    P WAW+++F
Sbjct: 232 NDNPWVCDCRARPLWAWLQKF 252


>pdb|3KJ4|A Chain A, Structure Of Rat Nogo Receptor Bound To 1d9 Antagonist
           Antibody
 pdb|3KJ4|D Chain D, Structure Of Rat Nogo Receptor Bound To 1d9 Antagonist
           Antibody
          Length = 286

 Score = 28.1 bits (61), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 9/21 (42%), Positives = 14/21 (66%)

Query: 137 NDDPVIFDTSIVPWWAWIKRF 157
           ND+P + D    P WAW+++F
Sbjct: 232 NDNPWVCDCRARPLWAWLQKF 252


>pdb|1SQF|A Chain A, The Crystal Structure Of E. Coli Fmu Binary Complex With
           S- Adenosylmethionine At 2.1 A Resolution
 pdb|1SQG|A Chain A, The Crystal Structure Of The E. Coli Fmu Apoenzyme At 1.65
           A Resolution
          Length = 429

 Score = 26.6 bits (57), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 93  DPKWVNGTWDLKQFQKNGQTDWDAVIDAEARR-RKWLENSPESSSND 138
           D ++++ +W LK+ QK     W ++++A  +R   WL  +    S D
Sbjct: 140 DARYLHPSWLLKRLQKAYPEQWQSIVEANNQRPPMWLRINRTHHSRD 186


  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
   0.312    0.127    0.387 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,982,928
Number of Sequences: 62578
Number of extensions: 196235
Number of successful extensions: 276
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 271
Number of HSP's gapped (non-prelim): 7
length of query: 171
length of database: 14,973,337
effective HSP length: 92
effective length of query: 79
effective length of database: 9,216,161
effective search space: 728076719
effective search space used: 728076719
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)