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= 042538
         (167 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 = 38.1 bits (87), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 27/46 (58%), Gaps = 4/46 (8%)

Query: 1  FAHGKEELRSTLFPTTKNKSEAQICKSF-TTGSCIYGSKCRFIHQV 45
          FAHG  ELRS    T   K + ++C++F T G C YG +C FIH  
Sbjct: 26 FAHGFHELRSL---TRHPKYKTELCRTFHTIGFCPYGPRCHFIHNA 68



 Score = 26.9 bits (58), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 11/34 (32%), Positives = 20/34 (58%), Gaps = 1/34 (2%)

Query: 19 KSEAQICKSFT-TGSCIYGSKCRFIHQVMTDSAL 51
          + + ++C+ F  +G+C YG KC+F H      +L
Sbjct: 3  RYKTELCRPFEESGTCKYGEKCQFAHGFHELRSL 36


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

 Score = 34.7 bits (78), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 24/49 (48%), Gaps = 4/49 (8%)

Query: 1  FAHGKEELRSTLFPTTKNKSEAQICKSFT-TGSCIYGSKCRFIHQVMTD 48
          FAHG  ELR         K + ++C  F   G C YGS+C FIH    D
Sbjct: 32 FAHGLGELRQA---NRHPKYKTELCHKFKLQGRCPYGSRCHFIHNPTED 77



 Score = 30.8 bits (68), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 11/32 (34%), Positives = 24/32 (75%), Gaps = 1/32 (3%)

Query: 15 TTKNKSEAQICKSFT-TGSCIYGSKCRFIHQV 45
          TT ++ + ++C++++ +G C YG+KC+F H +
Sbjct: 5  TTSSRYKTELCRTYSESGRCRYGAKCQFAHGL 36


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

 Score = 28.5 bits (62), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)

Query: 25 CKSF-TTGSCIYGSKCRFIHQVMTDSALVLTIQM 57
          CK + TTG+CI G  C F H  +T+    L  +M
Sbjct: 39 CKLYHTTGNCINGDDCMFSHDPLTEETRELLDKM 72


>pdb|3U1L|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
 pdb|3U1M|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
          Length = 240

 Score = 26.6 bits (57), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 2/32 (6%)

Query: 16 TKNKSEAQI--CKSFTTGSCIYGSKCRFIHQV 45
          T+  ++ Q+  C  F  G C  G KC ++H +
Sbjct: 62 TRGDNDGQLFFCLFFAKGMCCLGPKCEYLHHI 93


>pdb|3TP2|A Chain A, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
 pdb|3TP2|B Chain B, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
          Length = 229

 Score = 26.2 bits (56), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 2/32 (6%)

Query: 16 TKNKSEAQI--CKSFTTGSCIYGSKCRFIHQV 45
          T+  ++ Q+  C  F  G C  G KC ++H +
Sbjct: 64 TRGDNDGQLFFCLFFAKGMCCLGPKCEYLHHI 95


  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    0.130    0.401 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,677,467
Number of Sequences: 62578
Number of extensions: 161917
Number of successful extensions: 314
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 305
Number of HSP's gapped (non-prelim): 10
length of query: 167
length of database: 14,973,337
effective HSP length: 92
effective length of query: 75
effective length of database: 9,216,161
effective search space: 691212075
effective search space used: 691212075
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)