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= psy11625
         (314 letters)

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

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



>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
           Transcriptional Activator Complex
          Length = 387

 Score = 34.7 bits (78), Expect = 0.067,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 34/53 (64%), Gaps = 8/53 (15%)

Query: 220 MEKRRRARINNCLNELKSLI--LEAMRKDPARHSKLEKADILEMTVKHLQNVQ 270
           +EKRRR ++N+ ++EL SL+    AM +      KL+K  +L M V+H++ ++
Sbjct: 20  IEKRRRDKMNSFIDELASLVPTCNAMSR------KLDKLTVLRMAVQHMKTLR 66


>pdb|4H10|A Chain A, Intermolecular Recognition Revealed By The Complex
           Structure Of Human Clock-bmal1 Basic Helix-loop-helix
           Domains With E-box Dna
          Length = 73

 Score = 32.0 bits (71), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 34/53 (64%), Gaps = 8/53 (15%)

Query: 220 MEKRRRARINNCLNELKSLI--LEAMRKDPARHSKLEKADILEMTVKHLQNVQ 270
           +EKRRR ++N+ ++EL SL+    AM +      KL+K  +L M V+H++ ++
Sbjct: 16  IEKRRRDKMNSFIDELASLVPTCNAMSR------KLDKLTVLRMAVQHMKTLR 62


>pdb|4ATI|A Chain A, Mitf:m-Box Complex
 pdb|4ATI|B Chain B, Mitf:m-Box Complex
 pdb|4ATK|A Chain A, Mitf:e-Box Complex
 pdb|4ATK|B Chain B, Mitf:e-Box Complex
          Length = 118

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 37/60 (61%), Gaps = 4/60 (6%)

Query: 214 QSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQ 273
           + N  ++E+RRR  IN+ + EL +LI ++   DP    +  K  IL+ +V +++ +QR+Q
Sbjct: 28  KDNHNLIERRRRFNINDRIKELGTLIPKS--NDP--DMRWNKGTILKASVDYIRKLQREQ 83


>pdb|2DB7|A Chain A, Crystal Structure Of Hypothetical Protein Ms0332
 pdb|2DB7|B Chain B, Crystal Structure Of Hypothetical Protein Ms0332
          Length = 64

 Score = 28.1 bits (61), Expect = 6.0,   Method: Composition-based stats.
 Identities = 10/20 (50%), Positives = 15/20 (75%)

Query: 291 GFGDCAVEINRYISRLDGLD 310
           GF +C  E+ RY+S ++GLD
Sbjct: 23  GFRECLAEVARYLSIIEGLD 42


>pdb|3F3M|A Chain A, Six Crystal Structures Of Two Phosphopantetheine
           Adenylyltransferases Reveal An Alternative Ligand
           Binding Mode And An Associated Structural Change
          Length = 168

 Score = 28.1 bits (61), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 227 RINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQLS 275
           R  +  +E+   +L+  +K+    S  E+ D++E +VKHL NV+  Q S
Sbjct: 25  RSTDRFDEIHVCVLKNSKKE-GTFSLEERMDLIEQSVKHLPNVKVHQFS 72


  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
   0.315    0.129    0.367 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,149,880
Number of Sequences: 62578
Number of extensions: 169839
Number of successful extensions: 462
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 459
Number of HSP's gapped (non-prelim): 9
length of query: 314
length of database: 14,973,337
effective HSP length: 99
effective length of query: 215
effective length of database: 8,778,115
effective search space: 1887294725
effective search space used: 1887294725
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)