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= 015039
         (414 letters)

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

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



>pdb|2QHB|A Chain A, Crystal Structure Of Ngtrf Complexed With Telomeric Dna
 pdb|2QHB|B Chain B, Crystal Structure Of Ngtrf Complexed With Telomeric Dna
          Length = 86

 Score = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/44 (34%), Positives = 29/44 (65%)

Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLR 399
           +R ++++EV  L++ +   G G+W D+K   F ++ HRT +DL+
Sbjct: 4   RRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLK 47


>pdb|2JUH|A Chain A, Solution Structure Of Dna Binding Domain Of Ngtrf1
          Length = 121

 Score = 42.7 bits (99), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/44 (34%), Positives = 29/44 (65%)

Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLR 399
           +R ++++EV  L++ +   G G+W D+K   F ++ HRT +DL+
Sbjct: 17  RRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLK 60


>pdb|2CKX|A Chain A, Crystal Structure Of Ngtrf1, Double-Stranded Telomeric
           Repeat Binding Factor From Nicotiana Tabacum
          Length = 83

 Score = 42.7 bits (99), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/43 (34%), Positives = 28/43 (65%)

Query: 357 RMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLR 399
           R ++++EV  L++ +   G G+W D+K   F ++ HRT +DL+
Sbjct: 1   RPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLK 43


>pdb|2AJE|A Chain A, Solution Structure Of The Arabidopsis Thaliana Telomeric
           Repeat-Binding Protein Dna Binding Domain
          Length = 105

 Score = 42.4 bits (98), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/44 (34%), Positives = 28/44 (63%)

Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLR 399
           +R ++++EV  L+  + + G G+W D+K   F  + HRT +DL+
Sbjct: 13  RRPFSVAEVEALVQAVEKLGTGRWRDVKLCAFEDADHRTYVDLK 56


>pdb|2ROH|A Chain A, The Dna Binding Domain Of Rtbp1
          Length = 122

 Score = 42.0 bits (97), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 16/44 (36%), Positives = 28/44 (63%)

Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLR 399
           +R +T++EV  L++ +   G G+W D+K   F +  HRT +DL+
Sbjct: 31  RRPFTVAEVELLVEAVEHLGTGRWRDVKFRAFENVHHRTYVDLK 74


>pdb|3TED|A Chain A, Crystal Structure Of The Chd1 Dna-Binding Domain In
           Complex With A Dna Duplex
          Length = 271

 Score = 30.0 bits (66), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 11/25 (44%), Positives = 16/25 (64%)

Query: 359 WTLSEVMKLIDGISQFGVGKWTDIK 383
           WT  E  KL+ G+ ++G G WT I+
Sbjct: 172 WTKEEDEKLLIGVFKYGYGSWTQIR 196


>pdb|2XB0|X Chain X, Dna-Binding Domain From Saccharomyces Cerevisiae
           Chromatin- Remodelling Protein Chd1
          Length = 270

 Score = 30.0 bits (66), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/25 (44%), Positives = 16/25 (64%)

Query: 359 WTLSEVMKLIDGISQFGVGKWTDIK 383
           WT  E  KL+ G+ ++G G WT I+
Sbjct: 171 WTKEEDEKLLIGVFKYGYGSWTQIR 195


>pdb|1H8A|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex3
          Length = 128

 Score = 28.5 bits (62), Expect = 7.7,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 20/32 (62%)

Query: 355 NQRMWTLSEVMKLIDGISQFGVGKWTDIKRLL 386
           N+  WT  E  ++I+ + ++G  +W+DI + L
Sbjct: 26  NKGPWTKEEDQRVIEHVQKYGPKRWSDIAKHL 57


  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
   0.318    0.134    0.394 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,854,703
Number of Sequences: 62578
Number of extensions: 334795
Number of successful extensions: 641
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 633
Number of HSP's gapped (non-prelim): 8
length of query: 414
length of database: 14,973,337
effective HSP length: 101
effective length of query: 313
effective length of database: 8,652,959
effective search space: 2708376167
effective search space used: 2708376167
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: 53 (25.0 bits)