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= 013033
         (451 letters)

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

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



>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 = 40.4 bits (93), Expect = 0.002,   Method: Composition-based stats.
 Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 8/66 (12%)

Query: 289 CRYYMNTGTCKYGADCKFHHPKERIAQSAASNIGPLGLPSRPGQAICSNYSMYGICKFGP 348
           CR +  +GTCKYG  C+F H            +  L    +    +C  +   G C +GP
Sbjct: 9   CRPFEESGTCKYGEKCQFAH--------GFHELRSLTRHPKYKTELCRTFHTIGFCPYGP 60

Query: 349 TCRFDH 354
            C F H
Sbjct: 61  RCHFIH 66



 Score = 32.7 bits (73), Expect = 0.47,   Method: Composition-based stats.
 Identities = 19/69 (27%), Positives = 28/69 (40%), Gaps = 12/69 (17%)

Query: 53  CLFYRRTGLCGYGSNCRFNHPAYAAQG----AQYREELPERNGQPDCGYYLKTGTCKYGS 108
           C  +  +G C YG  C+F H  +  +      +Y+ EL        C  +   G C YG 
Sbjct: 9   CRPFEESGTCKYGEKCQFAHGFHELRSLTRHPKYKTEL--------CRTFHTIGFCPYGP 60

Query: 109 TCKYHHPKD 117
            C + H  D
Sbjct: 61  RCHFIHNAD 69



 Score = 30.8 bits (68), Expect = 1.8,   Method: Composition-based stats.
 Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 7/65 (10%)

Query: 95  CGYYLKTGTCKYGSTCKYHHPKDRNGAGPVSFNILGLPMRQDEKSCPYYMRTGSCKFGVA 154
           C  + ++GTCKYG  C++ H       G      L    +   + C  +   G C +G  
Sbjct: 9   CRPFEESGTCKYGEKCQFAH-------GFHELRSLTRHPKYKTELCRTFHTIGFCPYGPR 61

Query: 155 CKFHH 159
           C F H
Sbjct: 62  CHFIH 66


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

 Score = 38.1 bits (87), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 8/66 (12%)

Query: 289 CRYYMNTGTCKYGADCKFHHPKERIAQSAASNIGPLGLPSRPGQAICSNYSMYGICKFGP 348
           CR Y  +G C+YGA C+F H    + +   +N  P     +    +C  + + G C +G 
Sbjct: 15  CRTYSESGRCRYGAKCQFAHG---LGELRQANRHP-----KYKTELCHKFKLQGRCPYGS 66

Query: 349 TCRFDH 354
            C F H
Sbjct: 67  RCHFIH 72



 Score = 29.6 bits (65), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 12/66 (18%)

Query: 53  CLFYRRTGLCGYGSNCRFNHPAYAAQGA----QYREELPERNGQPDCGYYLKTGTCKYGS 108
           C  Y  +G C YG+ C+F H     + A    +Y+ EL        C  +   G C YGS
Sbjct: 15  CRTYSESGRCRYGAKCQFAHGLGELRQANRHPKYKTEL--------CHKFKLQGRCPYGS 66

Query: 109 TCKYHH 114
            C + H
Sbjct: 67  RCHFIH 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 = 35.8 bits (81), Expect = 0.047,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 97  YYLKTGTCKYGSTCKYHHPKDRNGAGPVSFNILGLPMRQDEKSCPYYMRTGSCKFGVACK 156
           YY   GT +Y +       +  +G+  V    L  P  +  K CP+++  G C+F   C+
Sbjct: 37  YYSSWGTLEYHNAMVVGTEEAEDGSAGVRVLYL-YPTHKSLKPCPFFLE-GKCRFKENCR 94

Query: 157 FHHPQPSSLGTALPL 171
           F H Q  SL    P 
Sbjct: 95  FSHGQVVSLDELRPF 109


>pdb|2FC6|A Chain A, Solution Structure Of The Zf-Ccch Domain Of Target Of
           Egr1, Member 1 (Nuclear)
          Length = 50

 Score = 29.3 bits (64), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 12/26 (46%), Positives = 15/26 (57%)

Query: 333 AICSNYSMYGICKFGPTCRFDHPYAG 358
           +IC N+S YG C  GP C   H  +G
Sbjct: 21  SICDNFSAYGWCPLGPQCPQSHDISG 46


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

 Score = 29.3 bits (64), Expect = 5.3,   Method: Composition-based stats.
 Identities = 13/34 (38%), Positives = 16/34 (47%)

Query: 275 ASSQNLPERPDQPDCRYYMNTGTCKYGADCKFHH 308
           A ++N P       C+ Y  TG C  G DC F H
Sbjct: 25  ARAENCPYMHGDFPCKLYHTTGNCINGDDCMFSH 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
   0.314    0.132    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,099,824
Number of Sequences: 62578
Number of extensions: 644936
Number of successful extensions: 797
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 765
Number of HSP's gapped (non-prelim): 26
length of query: 451
length of database: 14,973,337
effective HSP length: 102
effective length of query: 349
effective length of database: 8,590,381
effective search space: 2998042969
effective search space used: 2998042969
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (25.0 bits)