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= 017062
         (378 letters)

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

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



>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 = 39.3 bits (90), Expect = 0.003,   Method: Composition-based stats.
 Identities = 22/59 (37%), Positives = 36/59 (61%), Gaps = 7/59 (11%)

Query: 198 MAERRRRKKLNDRLYMLRSVVPKISKMD----RASILGDAIDYLKEL---LQRINDLHN 249
           + ERRRR  +NDR+  L +++PK +  D    + +IL  ++DY+++L    QR  DL N
Sbjct: 33  LIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLEN 91


>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 = 37.7 bits (86), Expect = 0.011,   Method: Composition-based stats.
 Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 2/55 (3%)

Query: 200 ERRRRKKLNDRLYMLRSVVPKIS--KMDRASILGDAIDYLKELLQRINDLHNELE 252
           ER+RR  + D  + LR  VP +   K  RA IL  A +Y++ + ++++ L  +++
Sbjct: 12  ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTLQQDID 66


>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 = 35.8 bits (81), Expect = 0.044,   Method: Composition-based stats.
 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 3/53 (5%)

Query: 200 ERRRRKKLNDRLYMLRSVVPKIS--KMDRASILGDAIDYLKELLQRINDLHNE 250
           ER+RR  + D  + LR  VP +   K  RA IL  A +Y+ + ++R N  H +
Sbjct: 10  ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYI-QYMRRKNHTHQQ 61


>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 = 35.4 bits (80), Expect = 0.055,   Method: Composition-based stats.
 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 3/53 (5%)

Query: 200 ERRRRKKLNDRLYMLRSVVPKIS--KMDRASILGDAIDYLKELLQRINDLHNE 250
           ER+RR  + D  + LR  VP +   K  RA IL  A +Y+ + ++R N  H +
Sbjct: 9   ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYI-QYMRRKNHTHQQ 60


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

 Score = 35.4 bits (80), Expect = 0.060,   Method: Composition-based stats.
 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 3/53 (5%)

Query: 200 ERRRRKKLNDRLYMLRSVVPKIS--KMDRASILGDAIDYLKELLQRINDLHNE 250
           ER+RR  + D  + LR  VP +   K  RA IL  A +Y+ + ++R N  H +
Sbjct: 11  ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYI-QYMRRKNHTHQQ 62


>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 = 35.0 bits (79), Expect = 0.062,   Method: Composition-based stats.
 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 3/53 (5%)

Query: 200 ERRRRKKLNDRLYMLRSVVPKIS--KMDRASILGDAIDYLKELLQRINDLHNE 250
           ER+RR  + D  + LR  VP +   K  RA IL  A +Y+ + ++R N  H +
Sbjct: 20  ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYI-QYMRRKNHTHQQ 71


>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 = 33.5 bits (75), Expect = 0.19,   Method: Composition-based stats.
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 9/64 (14%)

Query: 185 LEGKRKGLPAKNLMAERRRRKKLNDRLYMLRSVVPKISK------MDRASILGDAIDYLK 238
           ++ KR+   A++   ERRRR K+N+ +  L  ++P  S         +  IL  A DY++
Sbjct: 1   MDEKRR---AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQ 57

Query: 239 ELLQ 242
           EL Q
Sbjct: 58  ELRQ 61


>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 = 33.1 bits (74), Expect = 0.27,   Method: Composition-based stats.
 Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 200 ERRRRKKLNDRLYMLRS-VVPKISKMDRASILGDAIDYLKELLQRINDLHNE 250
           E+R R  +ND++  L+  VV   +K++++++L  AIDY++ L      L  E
Sbjct: 14  EKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQE 65


>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 = 31.6 bits (70), Expect = 0.80,   Method: Composition-based stats.
 Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 4/59 (6%)

Query: 186 EGKRKGLPAKNLMAERRRRKKLNDRLYMLRSVVPKIS----KMDRASILGDAIDYLKEL 240
           +G+ K     +   E+RRR K+N  +  L S+VP  +    K+D+ ++L  A+ ++K L
Sbjct: 3   QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTL 61


>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 = 31.2 bits (69), Expect = 0.93,   Method: Composition-based stats.
 Identities = 14/42 (33%), Positives = 29/42 (69%), Gaps = 1/42 (2%)

Query: 199 AERRRRKKLNDRLYMLRSVVP-KISKMDRASILGDAIDYLKE 239
           +E++RR + N  +  L S++P    KMD++++L  +ID+L++
Sbjct: 15  SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRK 56


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

 Score = 31.2 bits (69), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 29/42 (69%), Gaps = 1/42 (2%)

Query: 199 AERRRRKKLNDRLYMLRSVVP-KISKMDRASILGDAIDYLKE 239
           +E++RR + N  +  L S++P    KMD++++L  +ID+L++
Sbjct: 19  SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRK 60


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

 Score = 30.8 bits (68), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 4/59 (6%)

Query: 186 EGKRKGLPAKNLMAERRRRKKLNDRLYMLRSVVPKIS----KMDRASILGDAIDYLKEL 240
           +G+ K     +   E+RRR K+N  +  L S+VP  +    K+D+ ++L  A+ ++K L
Sbjct: 7   QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTL 65


>pdb|1UKL|C Chain C, Crystal Structure Of Importin-Beta And Srebp-2 Complex
 pdb|1UKL|D Chain D, Crystal Structure Of Importin-Beta And Srebp-2 Complex
 pdb|1UKL|E Chain E, Crystal Structure Of Importin-Beta And Srebp-2 Complex
 pdb|1UKL|F Chain F, Crystal Structure Of Importin-Beta And Srebp-2 Complex
          Length = 61

 Score = 28.9 bits (63), Expect = 5.1,   Method: Composition-based stats.
 Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 204 RKKLNDRLYMLRSVVPKI-SKMDRASILGDAIDYLKELLQRINDLHNE 250
           R  +ND++  L+ +V    +K  ++ +L  AIDY+K L Q  + L  E
Sbjct: 1   RSSINDKIIELKDLVXGTDAKXHKSGVLRKAIDYIKYLQQVNHKLRQE 48


>pdb|1NU7|D Chain D, Staphylocoagulase-Thrombin Complex
 pdb|1NU7|H Chain H, Staphylocoagulase-Thrombin Complex
          Length = 282

 Score = 28.1 bits (61), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 3/44 (6%)

Query: 45 EMHVNAVSLSGFKSILDTDWFLNSTLNNPPQDFTNTTGLLETHQ 88
          E  VN  S  G    L +DW+L   L +    F N  G+LET+ 
Sbjct: 10 ESRVNENSKYG---TLISDWYLKGRLTSLESQFINALGILETYH 50


>pdb|1NU9|C Chain C, Staphylocoagulase-prethrombin-2 Complex
 pdb|1NU9|F Chain F, Staphylocoagulase-prethrombin-2 Complex
          Length = 281

 Score = 28.1 bits (61), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 3/44 (6%)

Query: 45 EMHVNAVSLSGFKSILDTDWFLNSTLNNPPQDFTNTTGLLETHQ 88
          E  VN  S  G    L +DW+L   L +    F N  G+LET+ 
Sbjct: 9  ESRVNENSKYG---TLISDWYLKGRLTSLESQFINALGILETYH 49


  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
   0.319    0.135    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,311,920
Number of Sequences: 62578
Number of extensions: 388454
Number of successful extensions: 823
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 821
Number of HSP's gapped (non-prelim): 17
length of query: 378
length of database: 14,973,337
effective HSP length: 100
effective length of query: 278
effective length of database: 8,715,537
effective search space: 2422919286
effective search space used: 2422919286
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)