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= 046965
         (286 letters)

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

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



>pdb|2L1O|A Chain A, Zinc To Cadmium Replacement In The A. Thaliana Superman
           Cys2his2 Zinc Finger Induces Structural Rearrangements
           Of Typical Dna Base Determinant Positions
 pdb|1NJQ|A Chain A, Nmr Structure Of The Single Qalggh Zinc Finger Domain From
           Arabidopsis Thaliana Superman Protein
          Length = 39

 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 15/25 (60%), Positives = 21/25 (84%)

Query: 107 RVFSCNYCKREFSTSQALGGHQNAH 131
           R ++C++CKREF ++QALGGH N H
Sbjct: 5   RSYTCSFCKREFRSAQALGGHMNVH 29


>pdb|2EN9|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
           415- 447) Of Human Zinc Finger Protein 28 Homolog
          Length = 46

 Score = 30.8 bits (68), Expect = 0.92,   Method: Composition-based stats.
 Identities = 12/29 (41%), Positives = 18/29 (62%)

Query: 107 RVFSCNYCKREFSTSQALGGHQNAHKQER 135
           ++F CN CK+ F+ S +L  HQ  H  E+
Sbjct: 11  KLFKCNECKKTFTQSSSLTVHQRIHTGEK 39


>pdb|2ELS|A Chain A, Solution Structure Of The 2nd C2h2 Zinc Finger Of Human
           Zinc Finger Protein 406
          Length = 36

 Score = 29.3 bits (64), Expect = 2.5,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 16/32 (50%)

Query: 104 SEARVFSCNYCKREFSTSQALGGHQNAHKQER 135
           S  ++F+C YC + F    +L  H   H  E+
Sbjct: 5   SSGKIFTCEYCNKVFKFKHSLQAHLRIHTNEK 36


>pdb|2EM6|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
           199- 231) Of Human Zinc Finger Protein 224
          Length = 46

 Score = 28.1 bits (61), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 11/29 (37%), Positives = 16/29 (55%)

Query: 107 RVFSCNYCKREFSTSQALGGHQNAHKQER 135
           + + C+ C +EFS S  L  HQ  H  E+
Sbjct: 11  KCYKCDVCGKEFSQSSHLQTHQRVHTGEK 39


>pdb|2EMX|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
           273- 303) Of Human Zinc Finger Protein 268
          Length = 44

 Score = 27.7 bits (60), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 19/33 (57%)

Query: 103 SSEARVFSCNYCKREFSTSQALGGHQNAHKQER 135
           SS  + F C+ C++ FS+   L  HQ  H +E+
Sbjct: 5   SSGEKPFGCSCCEKAFSSKSYLLVHQQTHAEEK 37


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

 Score = 27.3 bits (59), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 14/41 (34%), Positives = 19/41 (46%)

Query: 104 SEARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGV 144
           SEA+   C +C R F TS     H      ++  +KRR  V
Sbjct: 288 SEAKGIYCPFCSRWFKTSSVFESHLVGKIHKKNESKRRNFV 328


  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
   0.317    0.131    0.394 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,299,379
Number of Sequences: 62578
Number of extensions: 200826
Number of successful extensions: 457
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 31
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 422
Number of HSP's gapped (non-prelim): 35
length of query: 286
length of database: 14,973,337
effective HSP length: 98
effective length of query: 188
effective length of database: 8,840,693
effective search space: 1662050284
effective search space used: 1662050284
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: 51 (24.3 bits)