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= psy4482
         (133 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 = 74.7 bits (182), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 37/71 (52%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 14 NPRYKTEFCRNIDELGVCRYSLKCQFAHHPGELLPKFTHHPHYRTQLCRAYHKAGYCSFG 73
          + RYKTE CR  +E G C+Y  KCQFAH   EL    T HP Y+T+LCR +H  G+C +G
Sbjct: 1  STRYKTELCRPFEESGTCKYGEKCQFAHGFHELR-SLTRHPKYKTELCRTFHTIGFCPYG 59

Query: 74 ARCIFIHEERE 84
           RC FIH   E
Sbjct: 60 PRCHFIHNADE 70



 Score = 35.8 bits (81), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 9  KAILLNPRYKTEFCRNIDELGVCRYSLKCQFAHHPGE 45
          +++  +P+YKTE CR    +G C Y  +C F H+  E
Sbjct: 34 RSLTRHPKYKTELCRTFHTIGFCPYGPRCHFIHNADE 70



 Score = 32.3 bits (72), Expect = 0.080,   Method: Compositional matrix adjust.
 Identities = 12/30 (40%), Positives = 20/30 (66%)

Query: 56 YRTQLCRAYHKAGYCSFGARCIFIHEEREI 85
          Y+T+LCR + ++G C +G +C F H   E+
Sbjct: 4  YKTELCRPFEESGTCKYGEKCQFAHGFHEL 33


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

 Score = 71.2 bits (173), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/74 (48%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 11 ILLNPRYKTEFCRNIDELGVCRYSLKCQFAHHPGELLPKFTHHPHYRTQLCRAYHKAGYC 70
          +  + RYKTE CR   E G CRY  KCQFAH  GE L +   HP Y+T+LC  +   G C
Sbjct: 4  MTTSSRYKTELCRTYSESGRCRYGAKCQFAHGLGE-LRQANRHPKYKTELCHKFKLQGRC 62

Query: 71 SFGARCIFIHEERE 84
           +G+RC FIH   E
Sbjct: 63 PYGSRCHFIHNPTE 76


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

 Score = 28.9 bits (63), Expect = 0.78,   Method: Compositional matrix adjust.
 Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 1/38 (2%)

Query: 44 GELLPKFTHHPHYRTQLCRAYHKAGYCSFGARCIFIHE 81
          G  LP  TH PH  T +C  +   G+C  G +C   H+
Sbjct: 7  GCCLPPATHRPH-PTSICDNFSAYGWCPLGPQCPQSHD 43


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

 Score = 25.8 bits (55), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 9/21 (42%), Positives = 12/21 (57%)

Query: 61 CRAYHKAGYCSFGARCIFIHE 81
          C+ YH  G C  G  C+F H+
Sbjct: 39 CKLYHTTGNCINGDDCMFSHD 59


>pdb|3D3U|A Chain A, Crystal Structure Of 4-Hydroxybutyrate Coa-Transferase
           (Abft-2) From Porphyromonas Gingivalis. Northeast
           Structural Genomics Consortium Target Pgr26
          Length = 439

 Score = 25.8 bits (55), Expect = 8.0,   Method: Composition-based stats.
 Identities = 9/23 (39%), Positives = 13/23 (56%)

Query: 65  HKAGYCSFGARCIFIHEEREISP 87
           ++ GYCSFG  C +     E +P
Sbjct: 128 NEEGYCSFGVSCDYTKAAAECAP 150


  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
   0.324    0.137    0.449 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,416,952
Number of Sequences: 62578
Number of extensions: 169204
Number of successful extensions: 406
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 392
Number of HSP's gapped (non-prelim): 15
length of query: 133
length of database: 14,973,337
effective HSP length: 88
effective length of query: 45
effective length of database: 9,466,473
effective search space: 425991285
effective search space used: 425991285
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 46 (22.3 bits)