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= 020338
         (327 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 = 92.0 bits (227), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 38/67 (56%), Positives = 46/67 (68%)

Query: 245 FKTELCNKWQETGACPYGDHCQFAHGIEELRPVIRHPRYKTEVCRMVLAGDVCPYGHRCH 304
           +KTELC  ++E+G C YG+ CQFAHG  ELR + RHP+YKTE+CR       CPYG RCH
Sbjct: 4   YKTELCRPFEESGTCKYGEKCQFAHGFHELRSLTRHPKYKTELCRTFHTIGFCPYGPRCH 63

Query: 305 FRHALTE 311
           F H   E
Sbjct: 64  FIHNADE 70



 Score = 37.0 bits (84), Expect = 0.017,   Method: Composition-based stats.
 Identities = 15/37 (40%), Positives = 17/37 (45%)

Query: 282 RYKTEVCRMVLAGDVCPYGHRCHFRHALTEQERFMGH 318
           RYKTE+CR       C YG +C F H   E      H
Sbjct: 3   RYKTELCRPFEESGTCKYGEKCQFAHGFHELRSLTRH 39


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

 Score = 84.7 bits (208), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 38/67 (56%), Positives = 44/67 (65%)

Query: 245 FKTELCNKWQETGACPYGDHCQFAHGIEELRPVIRHPRYKTEVCRMVLAGDVCPYGHRCH 304
           +KTELC  + E+G C YG  CQFAHG+ ELR   RHP+YKTE+C        CPYG RCH
Sbjct: 10  YKTELCRTYSESGRCRYGAKCQFAHGLGELRQANRHPKYKTELCHKFKLQGRCPYGSRCH 69

Query: 305 FRHALTE 311
           F H  TE
Sbjct: 70  FIHNPTE 76



 Score = 34.3 bits (77), Expect = 0.085,   Method: Compositional matrix adjust.
 Identities = 15/30 (50%), Positives = 17/30 (56%)

Query: 282 RYKTEVCRMVLAGDVCPYGHRCHFRHALTE 311
           RYKTE+CR       C YG +C F H L E
Sbjct: 9   RYKTELCRTYSESGRCRYGAKCQFAHGLGE 38


>pdb|2D9M|A Chain A, Solution Structure Of Ccch Type Zinc-Finger Domain 3 In
           Zinc Finger Ccch-Type Domain Containing 7a
          Length = 69

 Score = 29.3 bits (64), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 12/26 (46%), Positives = 18/26 (69%), Gaps = 1/26 (3%)

Query: 249 LCNKWQETGACPYGDHCQFAHGIEEL 274
           +C+++   G CP G+ C+FAHG  EL
Sbjct: 22  ICDRYM-NGTCPEGNSCKFAHGNAEL 46


>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 = 27.7 bits (60), Expect = 9.5,   Method: Composition-based stats.
 Identities = 11/24 (45%), Positives = 13/24 (54%), Gaps = 1/24 (4%)

Query: 246 KTELCNKWQETGACPYGDHCQFAH 269
           KT +C  W   G C  GD C+F H
Sbjct: 15  KTVVCKHWLR-GLCKKGDQCEFLH 37


  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
   0.316    0.131    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,663,095
Number of Sequences: 62578
Number of extensions: 245873
Number of successful extensions: 610
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 599
Number of HSP's gapped (non-prelim): 14
length of query: 327
length of database: 14,973,337
effective HSP length: 99
effective length of query: 228
effective length of database: 8,778,115
effective search space: 2001410220
effective search space used: 2001410220
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)