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= 029068
         (199 letters)

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

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



>pdb|1GCC|A Chain A, Solution Nmr Structure Of The Complex Of Gcc-Box Binding
          Domain Of Aterf1 And Gcc-Box Dna, Minimized Average
          Structure
          Length = 63

 Score = 68.6 bits (166), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 32/58 (55%), Positives = 43/58 (74%), Gaps = 1/58 (1%)

Query: 17 YKGVRKRKWGKYVSEIRLP-NSRARIWLGSYDTAEKAARAFDAALFCLRGRSAKFNFP 73
          Y+GVR+R WGK+ +EIR P  + AR+WLG+++TAE AA A+D A F +RG  A  NFP
Sbjct: 3  YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 60


>pdb|2GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
          Minimized Mean Structure
 pdb|3GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
          46 Structures
          Length = 70

 Score = 66.6 bits (161), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 43/58 (74%), Gaps = 1/58 (1%)

Query: 17 YKGVRKRKWGKYVSEIRLP-NSRARIWLGSYDTAEKAARAFDAALFCLRGRSAKFNFP 73
          Y+GVR+R WGK+ +EIR P  + AR+WLG+++TAE AA A+D A F +RG  A  NFP
Sbjct: 6  YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 63


>pdb|4HPF|A Chain A, Structure Of The Human Slo3 Gating Ring
 pdb|4HPF|B Chain B, Structure Of The Human Slo3 Gating Ring
          Length = 722

 Score = 29.6 bits (65), Expect = 1.2,   Method: Composition-based stats.
 Identities = 19/76 (25%), Positives = 30/76 (39%), Gaps = 26/76 (34%)

Query: 62  CLRGRSAKFNFPDNPPDISGGRSLKPSEIQAVAAQFANSEPLRSQSPEQSVSELQTEYLS 121
           CL+G S++ +  D+PP +S   S                          S+S   T  L 
Sbjct: 312 CLKGISSRISGQDSPPRVSASTS--------------------------SISNFTTRTLQ 345

Query: 122 PSISEATVQLDSDGVF 137
             + + + QLDS G+F
Sbjct: 346 HDVEQDSDQLDSSGMF 361


  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    0.132    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,070,691
Number of Sequences: 62578
Number of extensions: 237517
Number of successful extensions: 608
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 603
Number of HSP's gapped (non-prelim): 5
length of query: 199
length of database: 14,973,337
effective HSP length: 94
effective length of query: 105
effective length of database: 9,091,005
effective search space: 954555525
effective search space used: 954555525
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 49 (23.5 bits)