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= 009521
         (532 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 = 38.5 bits (88), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 4/53 (7%)

Query: 329 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEY 377
           R   A E H+  E+RRRD++N  +  L  L+P CN    K DK ++L  A+++
Sbjct: 9   RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQH 61


>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 = 37.0 bits (84), Expect = 0.027,   Method: Composition-based stats.
 Identities = 19/45 (42%), Positives = 28/45 (62%), Gaps = 4/45 (8%)

Query: 337 HNLSERRRRDRINEKMRALQELIPHCNKTD----KASMLDEAIEY 377
           HNL ERRRR  IN++++ L  LIP  N  D    K ++L  +++Y
Sbjct: 31  HNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDY 75


>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 = 0.039,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 4/49 (8%)

Query: 333 AAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEY 377
           A E H+  E+RRRD++N  +  L  L+P CN    K DK ++L  A+++
Sbjct: 9   AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQH 57


>pdb|1R05|A Chain A, Solution Structure Of Max B-Hlh-Lz
 pdb|1R05|B Chain B, Solution Structure Of Max B-Hlh-Lz
          Length = 87

 Score = 35.0 bits (79), Expect = 0.095,   Method: Composition-based stats.
 Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEY 377
           HN  ER+RRD I +   +L++ +P     K  +A +LD+A EY
Sbjct: 8   HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEY 50


>pdb|1NKP|B Chain B, Crystal Structure Of Myc-Max Recognizing Dna
 pdb|1NKP|E Chain E, Crystal Structure Of Myc-Max Recognizing Dna
          Length = 83

 Score = 35.0 bits (79), Expect = 0.12,   Method: Composition-based stats.
 Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEY 377
           HN  ER+RRD I +   +L++ +P     K  +A +LD+A EY
Sbjct: 6   HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEY 48


>pdb|1NLW|B Chain B, Crystal Structure Of Mad-Max Recognizing Dna
 pdb|1NLW|E Chain E, Crystal Structure Of Mad-Max Recognizing Dna
          Length = 76

 Score = 34.3 bits (77), Expect = 0.18,   Method: Composition-based stats.
 Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEY 377
           HN  ER+RRD I +   +L++ +P     K  +A +LD+A EY
Sbjct: 5   HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEY 47


>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
           BHLHZ DOMAIN
          Length = 86

 Score = 34.3 bits (77), Expect = 0.18,   Method: Composition-based stats.
 Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEY 377
           HN  ER+RRD I +   +L++ +P     K  +A +LD+A EY
Sbjct: 7   HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEY 49


>pdb|1HLO|A Chain A, The Crystal Structure Of An Intact Human Max-Dna Complex:
           New Insights Into Mechanisms Of Transcriptional Control
 pdb|1HLO|B Chain B, The Crystal Structure Of An Intact Human Max-Dna Complex:
           New Insights Into Mechanisms Of Transcriptional Control
          Length = 80

 Score = 34.3 bits (77), Expect = 0.20,   Method: Composition-based stats.
 Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEY 377
           HN  ER+RRD I +   +L++ +P     K  +A +LD+A EY
Sbjct: 16  HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEY 58


>pdb|4H10|B Chain B, Intermolecular Recognition Revealed By The Complex
           Structure Of Human Clock-bmal1 Basic Helix-loop-helix
           Domains With E-box Dna
          Length = 71

 Score = 31.6 bits (70), Expect = 1.1,   Method: Composition-based stats.
 Identities = 14/41 (34%), Positives = 29/41 (70%), Gaps = 1/41 (2%)

Query: 338 NLSERRRRDRINEKMRALQELIP-HCNKTDKASMLDEAIEY 377
           N SE++RRD+ N  ++ L  ++P +  K DK+++L ++I++
Sbjct: 13  NKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDF 53


>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
           Transcriptional Activator Complex
          Length = 361

 Score = 31.6 bits (70), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 14/41 (34%), Positives = 29/41 (70%), Gaps = 1/41 (2%)

Query: 338 NLSERRRRDRINEKMRALQELIP-HCNKTDKASMLDEAIEY 377
           N SE++RRD+ N  ++ L  ++P +  K DK+++L ++I++
Sbjct: 17  NKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDF 57


>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 = 31.2 bits (69), Expect = 1.5,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 330 RSRAAEVHNLSERRRRDRINEKMRALQELIPHCN-KTDKASMLDEAIEY 377
           R      HN  E+R R  IN+K+  L++L+     K +K+++L +AI+Y
Sbjct: 3   RGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDY 51


>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 = 29.3 bits (64), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 17/24 (70%)

Query: 337 HNLSERRRRDRINEKMRALQELIP 360
           HN  ERRRRD+IN  +  L ++IP
Sbjct: 9   HNEVERRRRDKINNWIVQLSKIIP 32


  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
   0.313    0.127    0.376 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,693,754
Number of Sequences: 62578
Number of extensions: 556361
Number of successful extensions: 765
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 757
Number of HSP's gapped (non-prelim): 16
length of query: 532
length of database: 14,973,337
effective HSP length: 103
effective length of query: 429
effective length of database: 8,527,803
effective search space: 3658427487
effective search space used: 3658427487
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (25.4 bits)