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= 024930
         (260 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 = 37.7 bits (86), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 4/63 (6%)

Query: 55  DACKSHKEAERRRRQRINSHLSTLRTLLPN----TIKTDKASLLAEVVHHVKELRSQATD 110
           +A ++H + E+RRR ++NS +  L +L+P     + K DK ++L   V H+K LR     
Sbjct: 12  NAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNP 71

Query: 111 VAE 113
             E
Sbjct: 72  YTE 74


>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 = 36.6 bits (83), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 34/55 (61%), Gaps = 4/55 (7%)

Query: 55  DACKSHKEAERRRRQRINSHLSTLRTLLPN----TIKTDKASLLAEVVHHVKELR 105
           +A ++H + E+RRR ++NS +  L +L+P     + K DK ++L   V H+K LR
Sbjct: 8   NAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 62


>pdb|1ARB|A Chain A, The Primary Structure And Structural Characteristics Of
           Achromobacter Lyticus Protease I, A Lysine-Specific
           Serine Protease
 pdb|1ARC|A Chain A, The Primary Structure And Structural Characteristics Of
           Achromobacter Lyticus Protease I, A Lysine-specific
           Serine Protease
          Length = 268

 Score = 33.9 bits (76), Expect = 0.089,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 27/43 (62%), Gaps = 2/43 (4%)

Query: 14  YWSHQNGFVQEPNWPGTLINGEGSIMSSTSSASKVEKK-STSD 55
           YW++QN   + PN P +  NG+GS MS T S S V+   +TSD
Sbjct: 72  YWNYQNSTCRAPNTPASGANGDGS-MSQTQSGSTVKATYATSD 113


>pdb|1AN4|A Chain A, Structure And Function Of The BHLHZ DOMAIN OF USF
 pdb|1AN4|B Chain B, Structure And Function Of The BHLHZ DOMAIN OF USF
          Length = 65

 Score = 31.6 bits (70), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)

Query: 60  HKEAERRRRQRINSHLSTLRTLLPNTIK------TDKASLLAEVVHHVKELR 105
           H E ERRRR +IN+ +  L  ++P++          K  +L++   +++ELR
Sbjct: 9   HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60


>pdb|1EQ1|A Chain A, Nmr Structure Of An Exchangeable Apolipoprotein-Manduca
           Sexta Apolipophorin-Iii
          Length = 166

 Score = 30.4 bits (67), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 33/115 (28%), Positives = 49/115 (42%), Gaps = 7/115 (6%)

Query: 5   QSHHGSYQNYWSHQ-NGFVQEPN---WPGTLINGEGSIMSSTSSASKVEKKSTSDACKSH 60
           + H   +Q  +S Q N  V   N   +   L +G  S++   S+ S   + + SDA    
Sbjct: 13  EKHAKEFQKTFSEQFNSLVNSKNTQDFNKALKDGSDSVLQQLSAFSSSLQGAISDANGKA 72

Query: 61  KEAERRRRQRINSHLSTLRTLLPNTIKTDKA---SLLAEVVHHVKELRSQATDVA 112
           KEA  + RQ +      LR   P+  K   A    L A V   V+E +  A +VA
Sbjct: 73  KEALEQARQNVEKTAEELRKAHPDVEKEANAFKDKLQAAVQTTVQESQKLAKEVA 127


>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 = 28.9 bits (63), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 7/63 (11%)

Query: 59  SHKEAERRRRQRINSHLSTLRTLLPNT----IKTDKASLLAEVVHHVKELRSQ---ATDV 111
           +H   ERRRR  IN  +  L TL+P +    ++ +K ++L   V ++++L+ +   A D+
Sbjct: 30  NHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDL 89

Query: 112 AER 114
             R
Sbjct: 90  ENR 92


  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    0.130    0.376 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,945,440
Number of Sequences: 62578
Number of extensions: 170766
Number of successful extensions: 408
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 402
Number of HSP's gapped (non-prelim): 10
length of query: 260
length of database: 14,973,337
effective HSP length: 97
effective length of query: 163
effective length of database: 8,903,271
effective search space: 1451233173
effective search space used: 1451233173
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: 50 (23.9 bits)