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= 046476
         (376 letters)

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

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



>pdb|2WSS|U Chain U, The Structure Of The Membrane Extrinsic Region Of Bovine
           Atp Synthase
          Length = 118

 Score = 31.6 bits (70), Expect = 0.69,   Method: Composition-based stats.
 Identities = 15/42 (35%), Positives = 26/42 (61%)

Query: 235 EEKFDIVKLPDEVRKHHDLIQAEEKLGVLDCDDFRSKNKIRV 276
           E+KF+ +K+P    K+   + AEEK  V  C +F +++K R+
Sbjct: 70  EKKFNALKVPIPEDKYTAQVDAEEKEDVKSCAEFLTQSKTRI 111


>pdb|4B2Q|U Chain U, Model Of The Yeast F1fo-Atp Synthase Dimer Based On
           Subtomogram Average
 pdb|4B2Q|UU Chain u, Model Of The Yeast F1fo-Atp Synthase Dimer Based On
           Subtomogram Average
          Length = 120

 Score = 31.6 bits (70), Expect = 0.79,   Method: Composition-based stats.
 Identities = 15/42 (35%), Positives = 26/42 (61%)

Query: 235 EEKFDIVKLPDEVRKHHDLIQAEEKLGVLDCDDFRSKNKIRV 276
           E+KF+ +K+P    K+   + AEEK  V  C +F +++K R+
Sbjct: 67  EKKFNALKVPIPEDKYTAQVDAEEKEDVKSCAEFLTQSKTRI 108


>pdb|2BYE|A Chain A, Nmr Solution Structure Of Phospholipase C Epsilon Ra 1
           Domain
          Length = 110

 Score = 31.2 bits (69), Expect = 1.0,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 15/75 (20%)

Query: 176 HGTPECEIFTLGTTSWRKIDAPPSRIHFRRQGLCANGFIHWIITNPRKTKPVLAVFDVKE 235
           HG P  E FT+ T +                G  A   +  I+TN +  KPV   + + E
Sbjct: 15  HGVPGPEPFTVFTIN---------------GGTKAKQLLQQILTNEQDIKPVTTDYFLME 59

Query: 236 EKFDIVKLPDEVRKH 250
           EK+ I K  +E RK 
Sbjct: 60  EKYFISKEKNECRKQ 74


>pdb|2CLY|B Chain B, Subcomplex Of The Stator Of Bovine Mitochondrial Atp
           Synthase
 pdb|2CLY|E Chain E, Subcomplex Of The Stator Of Bovine Mitochondrial Atp
           Synthase
          Length = 160

 Score = 30.8 bits (68), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 26/42 (61%)

Query: 235 EEKFDIVKLPDEVRKHHDLIQAEEKLGVLDCDDFRSKNKIRV 276
           E+KF+ +K+P    K+   + AEEK  V  C +F +++K R+
Sbjct: 70  EKKFNALKVPIPEDKYTAQVDAEEKEDVKSCAEFLTQSKTRI 111


>pdb|3TC9|A Chain A, Crystal Structure Of A Hypothetical Hydrolase (Bt_3476)
           From Bacteroides Thetaiotaomicron Vpi-5482 At 2.23 A
           Resolution
 pdb|3TC9|B Chain B, Crystal Structure Of A Hypothetical Hydrolase (Bt_3476)
           From Bacteroides Thetaiotaomicron Vpi-5482 At 2.23 A
           Resolution
          Length = 430

 Score = 30.8 bits (68), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 38/149 (25%), Positives = 57/149 (38%), Gaps = 31/149 (20%)

Query: 72  SHLLTVPSDFKLHRVTQL-------------INGFICFYNIVGFEILMRNVVTQEIIDLP 118
           +++LT  S FK+  +T+L             ING + F +    ++   +  TQE   L 
Sbjct: 207 NYILTRESGFKV--ITELTKGQNCNGAETHPINGELYFNSWNAGQVFRYDFTTQETTPL- 263

Query: 119 KSTFVVSDDDEDFSGPMISYFREYFLGFDPSSRDYKVLNISNKHTTNSSSYAWMIDNHGT 178
              F + D     SG       E+ + F PS  +Y  + + N+H    S Y W      T
Sbjct: 264 ---FTIQD-----SG------WEFHIQFHPSG-NYAYIVVVNQHYILRSDYDWKTKRLTT 308

Query: 179 PECEIFTLGTTSWRKIDAPPSRIHFRRQG 207
           P       G   W       +R H  RQG
Sbjct: 309 PYIVCGQQGAKDWVDGVGKKARXHAPRQG 337


>pdb|3AAD|A Chain A, Structure Of The Histone Chaperone Cia/asf1-double
           Bromodomain Complex Linking Histone Modifications And
           Site-specific Histone Eviction
          Length = 292

 Score = 29.6 bits (65), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 3/78 (3%)

Query: 45  LPLIVSFTNSSFSQQHFLTIEHQS--DEASHLLTVPSDFKLHRVTQLINGFICFYNIVGF 102
           L LIV  + +    +H LT   QS  D     L    D KL R+ + IN  +   + V F
Sbjct: 112 LELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKED-KLARLEKAINPLLDDDDQVAF 170

Query: 103 EILMRNVVTQEIIDLPKS 120
             ++ N+VTQ+++ +P S
Sbjct: 171 SFILDNIVTQKMMAVPDS 188


>pdb|3UV5|A Chain A, Crystal Structure Of The Tandem Bromodomains Of Human
           Transcription Initiation Factor Tfiid Subunit 1 (Taf1)
          Length = 265

 Score = 29.6 bits (65), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 3/78 (3%)

Query: 45  LPLIVSFTNSSFSQQHFLTIEHQS--DEASHLLTVPSDFKLHRVTQLINGFICFYNIVGF 102
           L LIV  + +    +H LT   QS  D     L    D KL R+ + IN  +   + V F
Sbjct: 79  LELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKED-KLARLEKAINPLLDDDDQVAF 137

Query: 103 EILMRNVVTQEIIDLPKS 120
             ++ N+VTQ+++ +P S
Sbjct: 138 SFILDNIVTQKMMAVPDS 155


>pdb|1EQF|A Chain A, Crystal Structure Of The Double Bromodomain Module From
           Human Tafii250
          Length = 280

 Score = 29.6 bits (65), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 3/78 (3%)

Query: 45  LPLIVSFTNSSFSQQHFLTIEHQS--DEASHLLTVPSDFKLHRVTQLINGFICFYNIVGF 102
           L LIV  + +    +H LT   QS  D     L    D KL R+ + IN  +   + V F
Sbjct: 91  LELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKED-KLARLEKAINPLLDDDDQVAF 149

Query: 103 EILMRNVVTQEIIDLPKS 120
             ++ N+VTQ+++ +P S
Sbjct: 150 SFILDNIVTQKMMAVPDS 167


>pdb|4DGW|A Chain A, Crystal Structure Of The Sf3a Splicing Factor Complex Of
           U2 Snrnp
          Length = 402

 Score = 28.1 bits (61), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 38  SSIKGTILPLIVS-FTNSSFSQQHFLTIEHQSDEASHLLTVPSDFKLHRVTQLIN 91
           S  KG   P     F  SS  + H +   H+ +E+     V S++KLHR  + +N
Sbjct: 288 SEAKGIYCPFCSRWFKTSSVFESHLVGKIHKKNESKRRNFVYSEYKLHRYLKYLN 342


  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
   0.323    0.138    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,592,150
Number of Sequences: 62578
Number of extensions: 495513
Number of successful extensions: 989
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 983
Number of HSP's gapped (non-prelim): 14
length of query: 376
length of database: 14,973,337
effective HSP length: 100
effective length of query: 276
effective length of database: 8,715,537
effective search space: 2405488212
effective search space used: 2405488212
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)