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= psy9718
         (70 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 = 36.2 bits (82), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 43/72 (59%), Gaps = 15/72 (20%)

Query: 1  MEKRRRARINNCLNELKTLI--LDAMKKDPARHSKLEKADILEMTVKHLENMQRQQLALS 58
          +EKRRR ++N+ ++EL +L+   +AM +      KL+K  +L M V+H++ ++       
Sbjct: 20 IEKRRRDKMNSFIDELASLVPTCNAMSR------KLDKLTVLRMAVQHMKTLR------- 66

Query: 59 AATDPHVLKSFK 70
           AT+P+   ++K
Sbjct: 67 GATNPYTEANYK 78


>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 = 0.096,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 36/57 (63%), Gaps = 8/57 (14%)

Query: 1  MEKRRRARINNCLNELKTLI--LDAMKKDPARHSKLEKADILEMTVKHLENMQRQQL 55
          +EKRRR ++N+ ++EL +L+   +AM +      KL+K  +L M V+H++ ++   L
Sbjct: 16 IEKRRRDKMNSFIDELASLVPTCNAMSR------KLDKLTVLRMAVQHMKTLRGAWL 66


>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 = 31.6 bits (70), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 4/54 (7%)

Query: 1  MEKRRRARINNCLNELKTLILDAMKKDPARHSKLEKADILEMTVKHLENMQRQQ 54
          +E+RRR  IN+ + EL TLI  +   DP    +  K  IL+ +V ++  +QR+Q
Sbjct: 34 IERRRRFNINDRIKELGTLIPKS--NDP--DMRWNKGTILKASVDYIRKLQREQ 83


>pdb|1AM9|A Chain A, Human Srebp-1a Bound To Ldl Receptor Promoter
 pdb|1AM9|B Chain B, Human Srebp-1a Bound To Ldl Receptor Promoter
 pdb|1AM9|C Chain C, Human Srebp-1a Bound To Ldl Receptor Promoter
 pdb|1AM9|D Chain D, Human Srebp-1a Bound To Ldl Receptor Promoter
          Length = 82

 Score = 26.9 bits (58), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 12/75 (16%)

Query: 1  MEKRRRARINNCLNELKTLILDAMKKDPARHSKLEKADILEMTVKHL-----ENMQRQQL 55
          +EKR R+ IN+ + ELK L++          +KL K+ +L   + ++      N + +Q 
Sbjct: 13 IEKRYRSSINDKIIELKDLVVGT-------EAKLNKSAVLRKAIDYIRFLQHSNQKLKQE 65

Query: 56 ALSAATDPHVLKSFK 70
           LS  T  H  KS K
Sbjct: 66 NLSLRTAVHKSKSLK 80


>pdb|1NLW|A Chain A, Crystal Structure Of Mad-Max Recognizing Dna
 pdb|1NLW|D Chain D, Crystal Structure Of Mad-Max Recognizing Dna
          Length = 80

 Score = 26.2 bits (56), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 1  MEKRRRARINNCLNELKTLILDAMKKDPARHSKLEKADILEMTVKHLENMQRQ 53
          MEK RRA +   L +LK L+   +  D +RH+ L      ++ +K LE+  R+
Sbjct: 8  MEKNRRAHLRLSLEKLKGLV--PLGPDSSRHTTLSLLTKAKLHIKKLEDSDRK 58


>pdb|3CT4|A Chain A, Structure Of Dha-Kinase Subunit Dhak From L. Lactis
 pdb|3CT4|B Chain B, Structure Of Dha-Kinase Subunit Dhak From L. Lactis
 pdb|3CT4|C Chain C, Structure Of Dha-Kinase Subunit Dhak From L. Lactis
          Length = 332

 Score = 25.4 bits (54), Expect = 8.4,   Method: Composition-based stats.
 Identities = 15/39 (38%), Positives = 23/39 (58%)

Query: 29  ARHSKLEKADILEMTVKHLENMQRQQLALSAATDPHVLK 67
           A H +    +I ++  K ++N++   LALSAAT P V K
Sbjct: 165 AAHQEASLDEIKDLADKVVKNIKTIGLALSAATVPEVGK 203


>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 = 25.4 bits (54), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 10/23 (43%), Positives = 17/23 (73%)

Query: 1  MEKRRRARINNCLNELKTLILDA 23
          +E+RRR +INN + +L  +I D+
Sbjct: 12 VERRRRDKINNWIVQLSKIIPDS 34


  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
   0.318    0.129    0.348 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,623,611
Number of Sequences: 62578
Number of extensions: 43322
Number of successful extensions: 174
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: 171
Number of HSP's gapped (non-prelim): 9
length of query: 70
length of database: 14,973,337
effective HSP length: 40
effective length of query: 30
effective length of database: 12,470,217
effective search space: 374106510
effective search space used: 374106510
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)