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= 011776
         (477 letters)

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

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



>pdb|1M9O|A Chain A, Nmr Structure Of The First Zinc Binding Domain Of
           Nup475TTPTIS11
          Length = 77

 Score = 35.0 bits (79), Expect = 0.082,   Method: Compositional matrix adjust.
 Identities = 14/39 (35%), Positives = 23/39 (58%)

Query: 336 SPLGLPLRPGAQPCTFYLQNGRCKFGATCKFDHPMGAMR 374
           S +    R   + C  Y ++GRC++GA C+F H +G +R
Sbjct: 2   SHMTTSSRYKTELCRTYSESGRCRYGAKCQFAHGLGELR 40



 Score = 28.5 bits (62), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 14/69 (20%)

Query: 303 CQYFLKTGDCKFGSSCRFHHPRDRVVPRTNCALSPLGLPLRP---GAQPCTFYLQNGRCK 359
           C+ + ++G C++G+ C+F H            L  L    R      + C  +   GRC 
Sbjct: 15  CRTYSESGRCRYGAKCQFAH-----------GLGELRQANRHPKYKTELCHKFKLQGRCP 63

Query: 360 FGATCKFDH 368
           +G+ C F H
Sbjct: 64  YGSRCHFIH 72


>pdb|4II1|A Chain A, Crystal Structure Of The Zinc Finger Of Zgpat
 pdb|4II1|B Chain B, Crystal Structure Of The Zinc Finger Of Zgpat
 pdb|4II1|C Chain C, Crystal Structure Of The Zinc Finger Of Zgpat
 pdb|4II1|D Chain D, Crystal Structure Of The Zinc Finger Of Zgpat
          Length = 167

 Score = 31.2 bits (69), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 25/105 (23%), Positives = 43/105 (40%), Gaps = 7/105 (6%)

Query: 134 IYGYPLRPGEKECSYYLKTGQCKFGITCKFHHPQPAGTS--LPASAPQFYPPVQSPTVPM 191
           +Y YP     K C ++L+ G+C+F   C+F H Q        P   P     +Q+ +  +
Sbjct: 67  LYLYPTHKSLKPCPFFLE-GKCRFKENCRFSHGQVVSLDELRPFQDPDL-SSLQAGSACL 124

Query: 192 AEQYGGASTSLRVARPPLLASSYVQGAYGPVLFSPGVVPFSGWNP 236
           A+   G   + R+     + + Y    +  +L    VV   G  P
Sbjct: 125 AKHQDGLWHAARITD---VDNGYYTVKFDSLLLREAVVEGDGILP 166



 Score = 30.4 bits (67), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 1/28 (3%)

Query: 341 PLRPGAQPCTFYLQNGRCKFGATCKFDH 368
           P     +PC F+L+ G+C+F   C+F H
Sbjct: 71  PTHKSLKPCPFFLE-GKCRFKENCRFSH 97


>pdb|1RGO|A Chain A, Structural Basis For Recognition Of The Mrna Class Ii Au-
           Rich Element By The Tandem Zinc Finger Domain Of Tis11d
          Length = 70

 Score = 29.6 bits (65), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 8/72 (11%)

Query: 94  RPGEPICQFYLKTGTCKFGASCKFHHPKHSGGSMSHVPLNIYGYPLRPGEKECSYYLKTG 153
           R    +C+ + ++GTCK+G  C+F H  H   S++  P        +   + C  +   G
Sbjct: 3   RYKTELCRPFEESGTCKYGEKCQFAHGFHELRSLTRHP--------KYKTELCRTFHTIG 54

Query: 154 QCKFGITCKFHH 165
            C +G  C F H
Sbjct: 55  FCPYGPRCHFIH 66


>pdb|2RHK|C Chain C, Crystal Structure Of Influenza A Ns1a Protein In Complex
           With F2f3 Fragment Of Human Cellular Factor Cpsf30,
           Northeast Structural Genomics Targets Or8c And Hr6309a
 pdb|2RHK|D Chain D, Crystal Structure Of Influenza A Ns1a Protein In Complex
           With F2f3 Fragment Of Human Cellular Factor Cpsf30,
           Northeast Structural Genomics Targets Or8c And Hr6309a
          Length = 72

 Score = 28.5 bits (62), Expect = 8.2,   Method: Composition-based stats.
 Identities = 21/70 (30%), Positives = 30/70 (42%), Gaps = 19/70 (27%)

Query: 99  ICQFYLKTGTCKFGASCKFHHPKHSGGSMSHVPLNIYGYPLRPGEKECSYYLKTGQCKFG 158
           +C+ +L+ G CK G  C+F H ++    MS                EC +Y K G+C   
Sbjct: 18  VCKHWLR-GLCKKGDQCEFLH-EYDMTKMS----------------ECYFYSKFGECS-N 58

Query: 159 ITCKFHHPQP 168
             C F H  P
Sbjct: 59  KECPFLHIDP 68


>pdb|2CQE|A Chain A, Solution Structure Of The Zinc-Finger Domain In Kiaa1064
          Protein
          Length = 98

 Score = 28.1 bits (61), Expect = 9.8,   Method: Composition-based stats.
 Identities = 13/31 (41%), Positives = 16/31 (51%)

Query: 44 ESYPQRHGVPDCVFYMRTGVCGYGDRCRYNH 74
          E+ P  HG   C  Y  TG C  GD C ++H
Sbjct: 28 ENCPYMHGDFPCKLYHTTGNCINGDDCMFSH 58


  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    0.136    0.439 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,195,588
Number of Sequences: 62578
Number of extensions: 578936
Number of successful extensions: 851
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 820
Number of HSP's gapped (non-prelim): 33
length of query: 477
length of database: 14,973,337
effective HSP length: 102
effective length of query: 375
effective length of database: 8,590,381
effective search space: 3221392875
effective search space used: 3221392875
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)