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= 036154
         (193 letters)

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

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



>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 = 85.1 bits (209), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 39/60 (65%), Positives = 49/60 (81%), Gaps = 1/60 (1%)

Query: 118 GKKFRGVRQRPWGKWAAEIRDPLRR-VRLWLGTYDTAEEAAMVYDNAAIQLRGPDALTNF 176
           GK +RGVRQRPWGK+AAEIRDP +   R+WLGT++TAE+AA+ YD AA ++RG  AL NF
Sbjct: 3   GKHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 62


>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 = 82.4 bits (202), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/59 (64%), Positives = 48/59 (81%), Gaps = 1/59 (1%)

Query: 119 KKFRGVRQRPWGKWAAEIRDPLRR-VRLWLGTYDTAEEAAMVYDNAAIQLRGPDALTNF 176
           K +RGVRQRPWGK+AAEIRDP +   R+WLGT++TAE+AA+ YD AA ++RG  AL NF
Sbjct: 1   KHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 59


>pdb|4A18|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 1
 pdb|4A1B|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 3.
 pdb|4A1D|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 4.
 pdb|4A19|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 2
          Length = 89

 Score = 30.0 bits (66), Expect = 0.82,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 8/65 (12%)

Query: 135 EIRDPLRRVRLWLGTYDT-----AEEAAMVYDNAAI---QLRGPDALTNFATPPPKFPSQ 186
           EI D  + ++LW    DT     A++   V  N  I   +LRG   L  F T  PK    
Sbjct: 4   EITDIKKFMKLWQNNKDTPATAGAKKVVYVKTNKRITKFKLRGKKYLYTFKTADPKIAKG 63

Query: 187 IKQSL 191
           IK ++
Sbjct: 64  IKDAI 68


>pdb|3MWY|W Chain W, Crystal Structure Of The Chromodomain-atpase Portion Of
           The Yeast Chd1 Chromatin Remodeler
          Length = 800

 Score = 27.7 bits (60), Expect = 3.7,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 23/32 (71%)

Query: 12  VKYTEHRKHTKLMTPFSTNGQEMKPRVVRISV 43
           VK+ ++R+++K++  +S+N    +PR  ++SV
Sbjct: 196 VKHFQNRENSKILPQYSSNYTSQRPRFEKLSV 227


>pdb|1WH8|A Chain A, Solution Structure Of The Third Cut Domain Of Human
           Homeobox Protein Cux-2
          Length = 111

 Score = 26.6 bits (57), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 10/23 (43%), Positives = 16/23 (69%)

Query: 125 RQRPWGKWAAEIRDPLRRVRLWL 147
           R +PW K + + R+P  R++LWL
Sbjct: 68  RPKPWHKLSLKGREPFVRMQLWL 90


  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
   0.316    0.131    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,884,971
Number of Sequences: 62578
Number of extensions: 155435
Number of successful extensions: 280
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 273
Number of HSP's gapped (non-prelim): 6
length of query: 193
length of database: 14,973,337
effective HSP length: 93
effective length of query: 100
effective length of database: 9,153,583
effective search space: 915358300
effective search space used: 915358300
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: 49 (23.5 bits)