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= 039972
         (169 letters)

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

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



>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 = 0.031,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 40 RQRRHRISDRFKILQSMVPG--GTKMDTASMLDEAINYVKFLKAVIWFHENIIN 91
          R+RR  I D F  L+  VP   G K   A +LD+A  Y+++++     H+  I+
Sbjct: 21 RKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDID 74


>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 = 0.037,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 40 RQRRHRISDRFKILQSMVPG--GTKMDTASMLDEAINYVKFLKAVIWFHENIIN 91
          R+RR  I D F  L+  VP   G K   A +LD+A  Y+++++     H+  I+
Sbjct: 12 RKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDID 65


>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 = 33.9 bits (76), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 40 RQRRHRISDRFKILQSMVPG--GTKMDTASMLDEAINYVKFLKAVIWFHENIIN 91
          R+RR  I D F  L+  VP   G K   A +LD+A  Y+++++     H+  I+
Sbjct: 10 RKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDID 63


>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 = 33.9 bits (76), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 40 RQRRHRISDRFKILQSMVPG--GTKMDTASMLDEAINYVKFLKAVIWFHENIIN 91
          R+RR  I D F  L+  VP   G K   A +LD+A  Y+++++     H+  I+
Sbjct: 11 RKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDID 64


>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 = 32.7 bits (73), Expect = 0.099,   Method: Compositional matrix adjust.
 Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 2/46 (4%)

Query: 40 RQRRHRISDRFKILQSMVPG--GTKMDTASMLDEAINYVKFLKAVI 83
          R+RR  I D F  L+  VP   G K   A +LD+A  Y+++++  +
Sbjct: 13 RKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKV 58


>pdb|3CG3|A Chain A, Crystal Structure Of P. Horikoshii Periplasmic Binding
           Protein ModaWTPA WITH BOUND TUNGSTATE
          Length = 320

 Score = 29.6 bits (65), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 4/55 (7%)

Query: 56  MVPGGTKMDTASMLDEAINYVKFLKAVIWFHENIINFADHHHHEHDPPVAFGQLP 110
           +V G T +  A   + AI +++FL      +E    F D++     PPVAFG +P
Sbjct: 260 IVYGITVLKNAPNRELAIEFLRFLLG----NEGRKIFEDNYQEFLSPPVAFGNVP 310


>pdb|2M2E|A Chain A, Solution Nmr Structure Of The Sant Domain Of Human
          Dnajc2, Northeast Structural Genomics Consortium Target
          Hr8254a
          Length = 73

 Score = 29.3 bits (64), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 3/44 (6%)

Query: 48 DRFKILQSMVPGGTKMDTASMLDEAINYVKFLKAVIWFHENIIN 91
          +R+K +   VPG TK D      E +  VK  KA     E ++N
Sbjct: 27 ERWKKIAEAVPGRTKKDCMKRYKELVEMVKAKKAA---QEQVLN 67


>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 = 1.4,   Method: Compositional matrix adjust.
 Identities = 13/54 (24%), Positives = 30/54 (55%), Gaps = 4/54 (7%)

Query: 31 STDPQSVAARQRRHRISDRFKILQSMVPGGT----KMDTASMLDEAINYVKFLK 80
            D  ++  R+RR  I+DR K L +++P       + +  ++L  +++Y++ L+
Sbjct: 27 KKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQ 80


>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 = 28.9 bits (63), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 30/42 (71%), Gaps = 3/42 (7%)

Query: 41 QRRHR--ISDRFKILQSMVPGG-TKMDTASMLDEAINYVKFL 79
          ++R+R  I+D+   L+ +V G   K++ +++L +AI+Y++FL
Sbjct: 14 EKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFL 55


>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 = 27.3 bits (59), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 15/51 (29%), Positives = 31/51 (60%), Gaps = 2/51 (3%)

Query: 38 AARQRRHRISDRFKILQSMVPG-GTKMDTASMLDEAINYVKFLKAVI-WFH 86
          + ++RR + +   K L SM+PG   KMD +++L ++I++++  K +  W  
Sbjct: 15 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE 65


  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    0.132    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,691,238
Number of Sequences: 62578
Number of extensions: 195456
Number of successful extensions: 7443
Number of sequences better than 100.0: 81
Number of HSP's better than 100.0 without gapping: 26
Number of HSP's successfully gapped in prelim test: 55
Number of HSP's that attempted gapping in prelim test: 7399
Number of HSP's gapped (non-prelim): 91
length of query: 169
length of database: 14,973,337
effective HSP length: 92
effective length of query: 77
effective length of database: 9,216,161
effective search space: 709644397
effective search space used: 709644397
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)