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= 041965
         (166 letters)

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

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



>pdb|2Q8O|A Chain A, Crystal Structure Of Mouse Gitr Ligand Dimer
 pdb|2Q8O|B Chain B, Crystal Structure Of Mouse Gitr Ligand Dimer
          Length = 136

 Score = 26.2 bits (56), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 3/45 (6%)

Query: 37 GPKYPGIHNPLDGTVRMLHDTSGTFKYYIKIVPTEYRYISKDVLP 81
           PK   ++   DG +++L   SGT+  Y +++P + +YI KD  P
Sbjct: 30 SPKPHCVNTTSDGKLKILQ--SGTYLIYGQVIPVDKKYI-KDNAP 71


>pdb|3FC0|A Chain A, 1.8 A Crystal Structure Of Murine Gitr Ligand Dimer
          Expressed In Drosophila Melanogaster S2 Cells
 pdb|3FC0|B Chain B, 1.8 A Crystal Structure Of Murine Gitr Ligand Dimer
          Expressed In Drosophila Melanogaster S2 Cells
          Length = 139

 Score = 26.2 bits (56), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 3/45 (6%)

Query: 37 GPKYPGIHNPLDGTVRMLHDTSGTFKYYIKIVPTEYRYISKDVLP 81
           PK   ++   DG +++L   SGT+  Y +++P + +YI KD  P
Sbjct: 33 SPKPHCVNTTSDGKLKILQ--SGTYLIYGQVIPVDKKYI-KDNAP 74


>pdb|2GFT|A Chain A, Crystal Structure Of The E263a Nucleophile Mutant Of
           Bacillus Licheniformis Endo-beta-1,4-galactanase In
           Complex With Galactotriose
 pdb|2GFT|B Chain B, Crystal Structure Of The E263a Nucleophile Mutant Of
           Bacillus Licheniformis Endo-beta-1,4-galactanase In
           Complex With Galactotriose
          Length = 399

 Score = 26.2 bits (56), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 14/57 (24%), Positives = 26/57 (45%)

Query: 22  AKNVNVSHVIHDLSFGPKYPGIHNPLDGTVRMLHDTSGTFKYYIKIVPTEYRYISKD 78
           A+ ++  HV +D+     YP  H  L     +L   + T+   + +  T Y Y ++D
Sbjct: 216 AETLHRHHVDYDVFASSYYPFWHGTLKNLTSVLTSVADTYGKKVMVAATSYTYTAED 272


>pdb|1R8L|A Chain A, The Structure Of Endo-Beta-1,4-Galactanase From Bacillus
           Licheniformis
 pdb|1R8L|B Chain B, The Structure Of Endo-Beta-1,4-Galactanase From Bacillus
           Licheniformis
 pdb|1UR0|A Chain A, The Structure Of Endo-Beta-1,4-Galactanase From Bacillus
           Licheniformis In Complex With Two Oligosaccharide
           Products.
 pdb|1UR0|B Chain B, The Structure Of Endo-Beta-1,4-Galactanase From Bacillus
           Licheniformis In Complex With Two Oligosaccharide
           Products.
 pdb|1UR4|A Chain A, The Structure Of Endo-Beta-1,4-Galactanase From Bacillus
           Licheniformis In Complex With Two Oligosaccharide
           Products.
 pdb|1UR4|B Chain B, The Structure Of Endo-Beta-1,4-Galactanase From Bacillus
           Licheniformis In Complex With Two Oligosaccharide
           Products.
 pdb|2CCR|A Chain A, Structure Of Beta-1,4-Galactanase
 pdb|2CCR|B Chain B, Structure Of Beta-1,4-Galactanase
 pdb|2J74|A Chain A, Structure Of Beta-1,4-Galactanase
 pdb|2J74|B Chain B, Structure Of Beta-1,4-Galactanase
          Length = 399

 Score = 26.2 bits (56), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 14/57 (24%), Positives = 26/57 (45%)

Query: 22  AKNVNVSHVIHDLSFGPKYPGIHNPLDGTVRMLHDTSGTFKYYIKIVPTEYRYISKD 78
           A+ ++  HV +D+     YP  H  L     +L   + T+   + +  T Y Y ++D
Sbjct: 216 AETLHRHHVDYDVFASSYYPFWHGTLKNLTSVLTSVADTYGKKVMVAETSYTYTAED 272


  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
   0.326    0.142    0.439 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,389,966
Number of Sequences: 62578
Number of extensions: 233432
Number of successful extensions: 619
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 615
Number of HSP's gapped (non-prelim): 7
length of query: 166
length of database: 14,973,337
effective HSP length: 92
effective length of query: 74
effective length of database: 9,216,161
effective search space: 681995914
effective search space used: 681995914
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: 47 (22.7 bits)