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= 041528
         (527 letters)

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

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



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

 Score = 31.6 bits (70), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 12/25 (48%), Positives = 16/25 (64%)

Query: 9  KLFVCKYCNKRYPCGKSLGGHIRTH 33
          K+F C+YCNK +    SL  H+R H
Sbjct: 8  KIFTCEYCNKVFKFKHSLQAHLRIH 32


>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 = 31.6 bits (70), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 13/25 (52%), Positives = 16/25 (64%)

Query: 459 KGHECPFCFRVFKSGQALGGHKRSH 483
           + + C FC R F+S QALGGH   H
Sbjct: 5   RSYTCSFCKREFRSAQALGGHMNVH 29


>pdb|3SLG|A Chain A, Crystal Structure Of Pbgp3 Protein From Burkholderia
           Pseudomallei
 pdb|3SLG|B Chain B, Crystal Structure Of Pbgp3 Protein From Burkholderia
           Pseudomallei
 pdb|3SLG|C Chain C, Crystal Structure Of Pbgp3 Protein From Burkholderia
           Pseudomallei
 pdb|3SLG|D Chain D, Crystal Structure Of Pbgp3 Protein From Burkholderia
           Pseudomallei
 pdb|3SLG|E Chain E, Crystal Structure Of Pbgp3 Protein From Burkholderia
           Pseudomallei
 pdb|3SLG|F Chain F, Crystal Structure Of Pbgp3 Protein From Burkholderia
           Pseudomallei
          Length = 372

 Score = 30.4 bits (67), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 5/47 (10%)

Query: 311 GPGFEEFDAKFEKSSNKRTEFGKHLTKEEDFALVDRASTKHGSRKRA 357
           GPG +      E SS   T+F  H+ + E+ +LVD      GS+KRA
Sbjct: 203 GPGLDSIYTPKEGSSRVVTQFLGHIVRGENISLVD-----GGSQKRA 244


>pdb|2I13|A Chain A, Aart, A Six Finger Zinc Finger Designed To Recognize Ann
           Triplets
 pdb|2I13|B Chain B, Aart, A Six Finger Zinc Finger Designed To Recognize Ann
           Triplets
          Length = 190

 Score = 29.3 bits (64), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 31/118 (26%), Positives = 40/118 (33%), Gaps = 10/118 (8%)

Query: 8   KKLFVCKYCNKRYPCGKSLGGHIRTHMXXXXXXXXXXXXXVKLNIDKIFSGRNI---KKD 64
           +K + C  C K +     L  H RTH                   D     R     K  
Sbjct: 19  EKPYACPECGKSFSRSDHLAEHQRTHTGEKPYKCPECGKSFSDKKDLTRHQRTHTGEKPY 78

Query: 65  SCFEAGGQSGYVLRANPKRTRRFVDSNTLTSQQEMVCKECGKVFQSLKALCGHMACHS 122
            C E G    +  RAN +  +R     T T ++   C ECGK F  L  L  H   H+
Sbjct: 79  KCPECG--KSFSQRANLRAHQR-----THTGEKPYACPECGKSFSQLAHLRAHQRTHT 129


>pdb|2EOY|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
          557- 589) Of Human Zinc Finger Protein 473
          Length = 46

 Score = 28.5 bits (62), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 17/32 (53%)

Query: 3  AANQKKKLFVCKYCNKRYPCGKSLGGHIRTHM 34
          ++ QK+K F C  C K + C K L  H R H 
Sbjct: 5  SSGQKEKCFKCNKCEKTFSCSKYLTQHERIHT 36


  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
   0.315    0.130    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,041,219
Number of Sequences: 62578
Number of extensions: 531291
Number of successful extensions: 1493
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1423
Number of HSP's gapped (non-prelim): 69
length of query: 527
length of database: 14,973,337
effective HSP length: 103
effective length of query: 424
effective length of database: 8,527,803
effective search space: 3615788472
effective search space used: 3615788472
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: 54 (25.4 bits)