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= 012166
         (469 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 = 60.8 bits (146), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 26/68 (38%), Positives = 45/68 (66%), Gaps = 1/68 (1%)

Query: 339 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR-ASYAHQK 397
           +R ++++EV  L++ +   G G+W D+K   F ++ HRT +DL+DKW+ L+  AS A Q+
Sbjct: 4   RRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQ 63

Query: 398 NKGEVDPK 405
            +GE  P+
Sbjct: 64  RRGEPVPQ 71


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

 Score = 60.8 bits (146), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 26/67 (38%), Positives = 44/67 (65%), Gaps = 1/67 (1%)

Query: 340 RMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR-ASYAHQKN 398
           R ++++EV  L++ +   G G+W D+K   F ++ HRT +DL+DKW+ L+  AS A Q+ 
Sbjct: 1   RPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQR 60

Query: 399 KGEVDPK 405
           +GE  P+
Sbjct: 61  RGEPVPQ 67


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

 Score = 59.7 bits (143), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 26/68 (38%), Positives = 45/68 (66%), Gaps = 1/68 (1%)

Query: 339 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR-ASYAHQK 397
           +R ++++EV  L++ +   G G+W D+K   F ++ HRT +DL+DKW+ L+  AS A Q+
Sbjct: 17  RRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQ 76

Query: 398 NKGEVDPK 405
            +GE  P+
Sbjct: 77  RRGEPVPQ 84


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

 Score = 57.4 bits (137), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 26/71 (36%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

Query: 339 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR-ASYAHQK 397
           +R +T++EV  L++ +   G G+W D+K   F +  HRT +DL+DKW+ L+  AS A Q+
Sbjct: 31  RRPFTVAEVELLVEAVEHLGTGRWRDVKFRAFENVHHRTYVDLKDKWKTLVHTASIAPQQ 90

Query: 398 NKGEVDPKHAM 408
            +G   P+  +
Sbjct: 91  RRGAPVPQELL 101


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

 Score = 57.4 bits (137), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 24/71 (33%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

Query: 339 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR-ASYAHQK 397
           +R ++++EV  L+  + + G G+W D+K   F  + HRT +DL+DKW+ L+  A  + Q+
Sbjct: 13  RRPFSVAEVEALVQAVEKLGTGRWRDVKLCAFEDADHRTYVDLKDKWKTLVHTAKISPQQ 72

Query: 398 NKGEVDPKHAM 408
            +GE  P+  +
Sbjct: 73  RRGEPVPQELL 83


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

 Score = 34.7 bits (78), Expect = 0.10,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 339 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNL 388
           ++ W   E   L  G+ ++G G W+ I  LL    ++RT + L+D+WR +
Sbjct: 3   RQAWLWEEDKNLRSGVRKYGEGNWSKI--LLHYKFNNRTSVMLKDRWRTM 50


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

 Score = 34.3 bits (77), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 2/47 (4%)

Query: 342 WTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNL 388
           W   E   L  G+ ++G G W+ I  LL    ++RT + L+D+WR +
Sbjct: 13  WLWEEDKNLRSGVRKYGEGNWSKI--LLHYKFNNRTSVMLKDRWRTM 57


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

 Score = 34.3 bits (77), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 2/47 (4%)

Query: 342 WTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNL 388
           W   E   L  G+ ++G G W+ I  LL    ++RT + L+D+WR +
Sbjct: 14  WLWEEDKNLRSGVRKYGEGNWSKI--LLHYKFNNRTSVMLKDRWRTM 58


>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 = 33.5 bits (75), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 2/47 (4%)

Query: 342 WTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNL 388
           W   E   L  G+ ++G G W+ I  LL    ++RT + L+D+WR +
Sbjct: 5   WLWEEDKNLRSGVRKYGEGNWSKI--LLHYKFNNRTSVMLKDRWRTM 49


>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 = 32.0 bits (71), Expect = 0.68,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 2/52 (3%)

Query: 339 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR 390
           ++ WT+ E   +  G+ ++G G W  I +       +RT + ++D+WR + R
Sbjct: 11  KQKWTVEESEWVKAGVQKYGEGNWAAISKNY--PFVNRTAVMIKDRWRTMKR 60


>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 = 32.0 bits (71), Expect = 0.72,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 2/52 (3%)

Query: 339 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR 390
           ++ WT+ E   +  G+ ++G G W  I +       +RT + ++D+WR + R
Sbjct: 2   KQKWTVEESEWVKAGVQKYGEGNWAAISKNY--PFVNRTAVMIKDRWRTMKR 51


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

 Score = 31.6 bits (70), Expect = 0.88,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 2/52 (3%)

Query: 339 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR 390
           ++ WT+ E   +  G+ ++G G W  I +       +RT + ++D+WR + R
Sbjct: 11  KQKWTVEESEWVKAGVQKYGEGNWAAISKNY--PFVNRTAVMIKDRWRTMKR 60


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

 Score = 31.6 bits (70), Expect = 0.96,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 2/52 (3%)

Query: 339 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR 390
           ++ WT+ E   +  G+ ++G G W  I +       +RT + ++D+WR + R
Sbjct: 10  KQKWTVEESEWVKAGVQKYGEGNWAAISKNY--PFVNRTAVMIKDRWRTMKR 59


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

 Score = 31.6 bits (70), Expect = 0.96,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 2/52 (3%)

Query: 339 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR 390
           ++ WT+ E   +  G+ ++G G W  I +       +RT + ++D+WR + R
Sbjct: 14  KQKWTVEESEWVKAGVQKYGEGNWAAISKNY--PFVNRTAVMIKDRWRTMKR 63


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

 Score = 30.4 bits (67), Expect = 2.4,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 4/52 (7%)

Query: 338 NQRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLL 389
           N+  WT  E  ++I+ + ++G  +W+DI + L      R     R++W N L
Sbjct: 26  NKGPWTKEEDQRVIEHVQKYGPKRWSDIAKHL----KGRIGKQCRERWHNHL 73


>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 = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/25 (44%), Positives = 16/25 (64%)

Query: 342 WTLSEVMKLIDGISQFGVGKWTDIK 366
           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 = 2.9,   Method: Compositional matrix adjust.
 Identities = 11/25 (44%), Positives = 16/25 (64%)

Query: 342 WTLSEVMKLIDGISQFGVGKWTDIK 366
           WT  E  KL+ G+ ++G G WT I+
Sbjct: 171 WTKEEDEKLLIGVFKYGYGSWTQIR 195


  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    0.132    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,959,636
Number of Sequences: 62578
Number of extensions: 428040
Number of successful extensions: 784
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 768
Number of HSP's gapped (non-prelim): 18
length of query: 469
length of database: 14,973,337
effective HSP length: 102
effective length of query: 367
effective length of database: 8,590,381
effective search space: 3152669827
effective search space used: 3152669827
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: 53 (25.0 bits)