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= 023740
         (278 letters)

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

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



>pdb|1VF9|A Chain A, Solution Structure Of Human Trf2
          Length = 64

 Score = 36.6 bits (83), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 4/53 (7%)

Query: 4  QKQKWTXXXXXXXXXGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNL 56
          +KQKWT         GV K+G G W  I ++  F      R+ + +KD+WR +
Sbjct: 10 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFV----NRTAVMIKDRWRTM 58


>pdb|1VFC|A Chain A, Solution Structure Of The Dna Complex Of Human Trf2
          Length = 63

 Score = 36.6 bits (83), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 4/53 (7%)

Query: 4  QKQKWTXXXXXXXXXGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNL 56
          +KQKWT         GV K+G G W  I ++  F      R+ + +KD+WR +
Sbjct: 9  KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFV----NRTAVMIKDRWRTM 57


>pdb|1XG1|A Chain A, Solution Structure Of Myb-Domain Of Human Trf2
          Length = 67

 Score = 36.6 bits (83), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 4/53 (7%)

Query: 4  QKQKWTXXXXXXXXXGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNL 56
          +KQKWT         GV K+G G W  I ++  F      R+ + +KD+WR +
Sbjct: 13 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFV----NRTAVMIKDRWRTM 61


>pdb|3SJM|A Chain A, Crystal Structure Analysis Of Trf2-Dbd-Dna Complex
 pdb|3SJM|B Chain B, Crystal Structure Analysis Of Trf2-Dbd-Dna Complex
          Length = 64

 Score = 36.2 bits (82), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 4/53 (7%)

Query: 4  QKQKWTXXXXXXXXXGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNL 56
          +KQKWT         GV K+G G W  I ++  F      R+ + +KD+WR +
Sbjct: 10 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFV----NRTAVMIKDRWRTM 58


>pdb|1W0U|A Chain A, Htrf2 Dna-Binding Domain In Complex With Telomeric Dna.
 pdb|1W0U|B Chain B, Htrf2 Dna-Binding Domain In Complex With Telomeric Dna
          Length = 55

 Score = 35.8 bits (81), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 4/53 (7%)

Query: 4  QKQKWTXXXXXXXXXGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNL 56
          +KQKWT         GV K+G G W  I ++  F      R+ + +KD+WR +
Sbjct: 1  KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPF----VNRTAVMIKDRWRTM 49


>pdb|1BA5|A Chain A, Dna-Binding Domain Of Human Telomeric Protein, Htrf1,
          Nmr, 18 Structures
          Length = 53

 Score = 35.0 bits (79), Expect = 0.040,   Method: Composition-based stats.
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 4/53 (7%)

Query: 4  QKQKWTXXXXXXXXXGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNL 56
          ++Q W          GV K+G G W  IL   +F      R+++ LKD+WR +
Sbjct: 2  KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKF----NNRTSVMLKDRWRTM 50


>pdb|1W0T|A Chain A, Htrf1 Dna-Binding Domain In Complex With Telomeric Dna.
 pdb|1W0T|B Chain B, Htrf1 Dna-Binding Domain In Complex With Telomeric Dna
          Length = 53

 Score = 35.0 bits (79), Expect = 0.044,   Method: Composition-based stats.
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 4/53 (7%)

Query: 4  QKQKWTXXXXXXXXXGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNL 56
          ++Q W          GV K+G G W  IL   +F      R+++ LKD+WR +
Sbjct: 1  KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKF----NNRTSVMLKDRWRTM 49


>pdb|1IV6|A Chain A, Solution Structure Of The Dna Complex Of Human Trf1
          Length = 70

 Score = 34.3 bits (77), Expect = 0.082,   Method: Compositional matrix adjust.
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 4/53 (7%)

Query: 4  QKQKWTXXXXXXXXXGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNL 56
          ++Q W          GV K+G G W  IL   +F      R+++ LKD+WR +
Sbjct: 10 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKF----NNRTSVMLKDRWRTM 58


>pdb|1ITY|A Chain A, Solution Structure Of The Dna Binding Domain Of Human
          Trf1
          Length = 69

 Score = 33.9 bits (76), Expect = 0.096,   Method: Compositional matrix adjust.
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 4/53 (7%)

Query: 4  QKQKWTXXXXXXXXXGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNL 56
          ++Q W          GV K+G G W  IL   +F      R+++ LKD+WR +
Sbjct: 9  KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKF----NNRTSVMLKDRWRTM 57


>pdb|3TR4|A Chain A, Structure Of An Inorganic Pyrophosphatase (Ppa) From
           Coxiella Burnetii
 pdb|3TR4|B Chain B, Structure Of An Inorganic Pyrophosphatase (Ppa) From
           Coxiella Burnetii
 pdb|3TR4|C Chain C, Structure Of An Inorganic Pyrophosphatase (Ppa) From
           Coxiella Burnetii
 pdb|3TR4|D Chain D, Structure Of An Inorganic Pyrophosphatase (Ppa) From
           Coxiella Burnetii
 pdb|3TR4|E Chain E, Structure Of An Inorganic Pyrophosphatase (Ppa) From
           Coxiella Burnetii
 pdb|3TR4|F Chain F, Structure Of An Inorganic Pyrophosphatase (Ppa) From
           Coxiella Burnetii
          Length = 178

 Score = 28.9 bits (63), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 20/31 (64%)

Query: 125 FEAISTLKDANGSDISAIANFIEERQEAPPN 155
           +EAI +LKD +   + AI++F E  ++  PN
Sbjct: 119 YEAIQSLKDISSLLLDAISHFFERYKDLEPN 149


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

 Score = 28.5 bits (62), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 6/40 (15%)

Query: 19 GVAKHGPGKWKNILRDPQF--APSLTQRSNIDLKDKWRNL 56
           V   G G+W    RD +F    ++  R+ +DLKDKW+ L
Sbjct: 45 AVEHLGTGRW----RDVKFRAFENVHHRTYVDLKDKWKTL 80


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

 Score = 28.1 bits (61), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 14/38 (36%), Positives = 23/38 (60%), Gaps = 2/38 (5%)

Query: 19 GVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNL 56
           V K G G+W+++ +   F  +   R+ +DLKDKW+ L
Sbjct: 27 AVEKLGTGRWRDV-KLCAFEDA-DHRTYVDLKDKWKTL 62


  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
   0.310    0.125    0.347 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,174,926
Number of Sequences: 62578
Number of extensions: 248513
Number of successful extensions: 502
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 491
Number of HSP's gapped (non-prelim): 20
length of query: 278
length of database: 14,973,337
effective HSP length: 98
effective length of query: 180
effective length of database: 8,840,693
effective search space: 1591324740
effective search space used: 1591324740
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 51 (24.3 bits)