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= 022048
         (303 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 = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/52 (48%), Positives = 31/52 (59%), Gaps = 4/52 (7%)

Query: 5  KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
          KQKWT EE   +KAGV K+G G W  I K+  F      R+ V +KD+WR M
Sbjct: 11 KQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVN----RTAVMIKDRWRTM 58


>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 = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/52 (48%), Positives = 31/52 (59%), Gaps = 4/52 (7%)

Query: 5  KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
          KQKWT EE   +KAGV K+G G W  I K+  F      R+ V +KD+WR M
Sbjct: 11 KQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVN----RTAVMIKDRWRTM 58


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

 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/52 (48%), Positives = 31/52 (59%), Gaps = 4/52 (7%)

Query: 5  KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
          KQKWT EE   +KAGV K+G G W  I K+  F      R+ V +KD+WR M
Sbjct: 10 KQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVN----RTAVMIKDRWRTM 57


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

 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/52 (48%), Positives = 31/52 (59%), Gaps = 4/52 (7%)

Query: 5  KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
          KQKWT EE   +KAGV K+G G W  I K+  F      R+ V +KD+WR M
Sbjct: 14 KQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVN----RTAVMIKDRWRTM 61


>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 = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/52 (48%), Positives = 31/52 (59%), Gaps = 4/52 (7%)

Query: 5  KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
          KQKWT EE   +KAGV K+G G W  I K+  F      R+ V +KD+WR M
Sbjct: 2  KQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVN----RTAVMIKDRWRTM 49


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

 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/53 (41%), Positives = 32/53 (60%), Gaps = 4/53 (7%)

Query: 4  PKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
           +Q W  EE+  L++GV K+G G W  IL   +F+     R++V LKD+WR M
Sbjct: 2  KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNN----RTSVMLKDRWRTM 50


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

 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 32/52 (61%), Gaps = 4/52 (7%)

Query: 5  KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
          +Q W  EE+  L++GV K+G G W  IL   +F+     R++V LKD+WR M
Sbjct: 11 RQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNN----RTSVMLKDRWRTM 58


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

 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 32/52 (61%), Gaps = 4/52 (7%)

Query: 5  KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
          +Q W  EE+  L++GV K+G G W  IL   +F+     R++V LKD+WR M
Sbjct: 10 RQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNN----RTSVMLKDRWRTM 57


>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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/53 (41%), Positives = 32/53 (60%), Gaps = 4/53 (7%)

Query: 4  PKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
           +Q W  EE+  L++GV K+G G W  IL   +F+     R++V LKD+WR M
Sbjct: 1  KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNN----RTSVMLKDRWRTM 49


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

 Score = 36.2 bits (82), Expect = 0.025,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 20/33 (60%), Gaps = 1/33 (3%)

Query: 8   WTQEEEAALKAGVIKHGAGKWRTILKDPEFSGV 40
           WT+EE+  L  GV K+G G W  I  DP F G+
Sbjct: 172 WTKEEDEKLLIGVFKYGYGSWTQIRDDP-FLGI 203


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

 Score = 35.8 bits (81), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 20/33 (60%), Gaps = 1/33 (3%)

Query: 8   WTQEEEAALKAGVIKHGAGKWRTILKDPEFSGV 40
           WT+EE+  L  GV K+G G W  I  DP F G+
Sbjct: 171 WTKEEDEKLLIGVFKYGYGSWTQIRDDP-FLGI 202


>pdb|4B4C|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Human Chd1
          Length = 211

 Score = 31.2 bits (69), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 11/31 (35%), Positives = 19/31 (61%)

Query: 8   WTQEEEAALKAGVIKHGAGKWRTILKDPEFS 38
           W +E+++ L  G+ ++G G W  I  DP+ S
Sbjct: 137 WGKEDDSNLLIGIYEYGYGSWEMIKMDPDLS 167


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

 Score = 31.2 bits (69), Expect = 0.70,   Method: Compositional matrix adjust.
 Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 3/45 (6%)

Query: 13 EAALKAGVIKH-GAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
          E  L    ++H G G+WR + K   F  V + R+ VDLKDKW+ +
Sbjct: 38 EVELLVEAVEHLGTGRWRDV-KFRAFENVHH-RTYVDLKDKWKTL 80


>pdb|3OSF|A Chain A, The Structure Of Protozoan Parasite Trichomonas
          Vaginalis Myb2 In Complex With Mre-2f-13 Dna
 pdb|3OSF|D Chain D, The Structure Of Protozoan Parasite Trichomonas
          Vaginalis Myb2 In Complex With Mre-2f-13 Dna
 pdb|3OSG|A Chain A, The Structure Of Protozoan Parasite Trichomonas
          Vaginalis Myb2 In Complex With Mre-1-12 Dna
 pdb|3OSG|D Chain D, The Structure Of Protozoan Parasite Trichomonas
          Vaginalis Myb2 In Complex With Mre-1-12 Dna
          Length = 126

 Score = 30.8 bits (68), Expect = 0.85,   Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 10/76 (13%)

Query: 2  GAPKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM---SV 58
           A KQK+T EE+  LK  V +HG+  W+ I      +     R+    +D+W+N    S+
Sbjct: 8  AAKKQKFTPEEDEMLKRAVAQHGSD-WKMI------AATFPNRNARQCRDRWKNYLAPSI 60

Query: 59 MSNGWGSRDKSRLAVK 74
              W + + + L  K
Sbjct: 61 SHTPWTAEEDALLVQK 76


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

 Score = 30.4 bits (67), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 19/45 (42%), Positives = 25/45 (55%), Gaps = 2/45 (4%)

Query: 12 EEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
          E  AL   V K G G+WR + K   F    + R+ VDLKDKW+ +
Sbjct: 20 EVEALVQAVEKLGTGRWRDV-KLCAFEDADH-RTYVDLKDKWKTL 62


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

 Score = 28.9 bits (63), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 2/45 (4%)

Query: 12 EEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
          E  AL   V   G G+WR + K   F    + R+ VDLKDKW+ +
Sbjct: 24 EVEALVEAVEHLGTGRWRDV-KMRAFDNADH-RTYVDLKDKWKTL 66


>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 = 28.9 bits (63), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 2/45 (4%)

Query: 12 EEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
          E  AL   V   G G+WR + K   F    + R+ VDLKDKW+ +
Sbjct: 11 EVEALVEAVEHLGTGRWRDV-KMRAFDNADH-RTYVDLKDKWKTL 53


>pdb|1UST|A Chain A, Yeast Histone H1 Globular Domain I, Hho1p Gi, Solution Nmr
           Structures
          Length = 93

 Score = 28.1 bits (61), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 12/28 (42%), Positives = 19/28 (67%)

Query: 130 LIMEAITTLKEPGGSNKTTIAAYIEEKY 157
           LI+E +T LKE  GS++  +  +I+E Y
Sbjct: 13  LIIEGLTALKERKGSSRPALKKFIKENY 40


>pdb|1MBE|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 1
 pdb|1MBF|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 1
          Length = 53

 Score = 28.1 bits (61), Expect = 6.9,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 6/52 (11%)

Query: 5  KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
          K +WT+EE+  LK  V ++G   W+ I      +  L  R++V  + +W+ +
Sbjct: 3  KTRWTREEDEKLKKLVEQNGTDDWKVI------ANYLPNRTDVQCQHRWQKV 48


>pdb|1GUU|A Chain A, Crystal Structure Of C-Myb R1
          Length = 52

 Score = 28.1 bits (61), Expect = 6.9,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 6/52 (11%)

Query: 5  KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
          K +WT+EE+  LK  V ++G   W+ I      +  L  R++V  + +W+ +
Sbjct: 3  KTRWTREEDEKLKKLVEQNGTDDWKVI------ANYLPNRTDVQCQHRWQKV 48


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

 Score = 27.7 bits (60), Expect = 7.3,   Method: Composition-based stats.
 Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 2/45 (4%)

Query: 12 EEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56
          E  AL   V   G G+WR + K   F    + R+ VDLKDKW+ +
Sbjct: 7  EVEALVEAVEHLGTGRWRDV-KMRAFDNADH-RTYVDLKDKWKTL 49


>pdb|1UHM|A Chain A, Solution Structure Of The Globular Domain Of Linker
           Histone Homolog Hho1p From S. Cerevisiae
          Length = 78

 Score = 27.7 bits (60), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 12/28 (42%), Positives = 19/28 (67%)

Query: 130 LIMEAITTLKEPGGSNKTTIAAYIEEKY 157
           LI+E +T LKE  GS++  +  +I+E Y
Sbjct: 10  LIIEGLTALKERKGSSRPALKKFIKENY 37


  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
   0.314    0.130    0.366 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,160,291
Number of Sequences: 62578
Number of extensions: 265262
Number of successful extensions: 656
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 627
Number of HSP's gapped (non-prelim): 31
length of query: 303
length of database: 14,973,337
effective HSP length: 98
effective length of query: 205
effective length of database: 8,840,693
effective search space: 1812342065
effective search space used: 1812342065
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: 51 (24.3 bits)