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= psy17881
         (68 letters)

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

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



>pdb|3QKC|B Chain B, Crystal Structure Of Geranyl Diphosphate Synthase Small
          Subunit From Antirrhinum Majus
 pdb|3QKC|A Chain A, Crystal Structure Of Geranyl Diphosphate Synthase Small
          Subunit From Antirrhinum Majus
          Length = 273

 Score = 28.1 bits (61), Expect = 1.3,   Method: Composition-based stats.
 Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 13/62 (20%)

Query: 11 SATKEPMYRLRYQSPVNALLKQSHINPRNASRTPSATKEPMYRLRYQSP--------VNA 62
          S T+   YR   +S + + LK++        R P +  EPM+ L + +P        V A
Sbjct: 2  SLTRTQTYRATIESDIESYLKKA-----IPIRAPESVFEPMHHLTFAAPRTSASALCVAA 56

Query: 63 CE 64
          CE
Sbjct: 57 CE 58


>pdb|1PGJ|A Chain A, X-Ray Structure Of 6-Phosphogluconate Dehydrogenase From
           The Protozoan Parasite T. Brucei
 pdb|1PGJ|B Chain B, X-Ray Structure Of 6-Phosphogluconate Dehydrogenase From
           The Protozoan Parasite T. Brucei
          Length = 478

 Score = 27.7 bits (60), Expect = 1.9,   Method: Composition-based stats.
 Identities = 12/28 (42%), Positives = 16/28 (57%)

Query: 5   NASRTPSATKEPMYRLRYQSPVNALLKQ 32
           NAS  P  T+ P Y L+ +SP    +KQ
Sbjct: 301 NASNAPGITQSPGYTLKNKSPSGPEIKQ 328


>pdb|4G59|A Chain A, Crystal Structure Of The Murine Cytomegalovirus Mhc-I
           Homolog M152 With Ligand Rae-1 Gamma
 pdb|4G59|B Chain B, Crystal Structure Of The Murine Cytomegalovirus Mhc-I
           Homolog M152 With Ligand Rae-1 Gamma
          Length = 205

 Score = 27.3 bits (59), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 5/35 (14%)

Query: 19  RLRYQSP-----VNALLKQSHINPRNASRTPSATK 48
           RL+Y  P     ++  LKQS   PR+ SR+PS T+
Sbjct: 155 RLKYFIPECRQKIDEFLKQSKEKPRSTSRSPSITQ 189


>pdb|3POM|A Chain A, Crystal Structure Of The Unliganded Retinoblastoma Protein
           Pocket Domain
 pdb|3POM|B Chain B, Crystal Structure Of The Unliganded Retinoblastoma Protein
           Pocket Domain
          Length = 352

 Score = 26.2 bits (56), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 1/42 (2%)

Query: 24  SPVNALLKQSHINPRNASRTP-SATKEPMYRLRYQSPVNACE 64
           SP+  L+KQS + PR +  T  S   + +YRL Y      CE
Sbjct: 191 SPLFDLIKQSKLVPRGSKSTSLSLFYKKVYRLAYLRLNTLCE 232


  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
   0.314    0.125    0.364 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,915,871
Number of Sequences: 62578
Number of extensions: 54528
Number of successful extensions: 100
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 96
Number of HSP's gapped (non-prelim): 6
length of query: 68
length of database: 14,973,337
effective HSP length: 38
effective length of query: 30
effective length of database: 12,595,373
effective search space: 377861190
effective search space used: 377861190
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)