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= 026151
         (242 letters)

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

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



>pdb|1PH1|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere End-
          Binding Protein Complexed With Noncognate Ssdna
          Ggggttttggggt
 pdb|1PH6|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere End-
          Binding Protein Complexed With Noncognate Ssdna
          Ggggttttgtgg
          Length = 217

 Score = 28.1 bits (61), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 5/41 (12%)

Query: 49 NFLVTEGYVDAAEKFRMESGTE-----PDIDLATITDRMAV 84
          +FLVT+GY   A  F  E+  E     P++++  +TD++ V
Sbjct: 42 HFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIV 82


>pdb|1PA6|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere
          End-Binding Protein Complexed With Noncognate Ssdna
          Ggggttttgagg
 pdb|1PH2|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere End-
          Binding Protein Complexed With Noncognate Ssdna
          Ggggttttg
 pdb|1PH3|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere
          End-Binding Protein Complexed With Noncognate Ssdna
          Ggggttttggtg
 pdb|1PH4|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere
          End-Binding Protein Complexed With Noncognate Ssdna
          Ggggttttggcg
 pdb|1PH5|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere End-
          Binding Protein Complexed With Noncognate Ssdna
          Ggggttttg(3dr)gg
 pdb|1PH7|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere
          End-Binding Protein Complexed With Noncognate Ssdna
          Ggggttttgigg
 pdb|1PH8|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere End-
          Binding Protein Complexed With Noncognate Ssdna
          Ggggttttgcgg
 pdb|1PH9|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere
          End-Binding Protein Complexed With Noncognate Ssdna
          Ggggttttgagg
 pdb|1PHJ|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere End-
          Binding Protein Complexed With Noncognate Ssdna Gg(3dr)
          Gttttgggg
          Length = 216

 Score = 28.1 bits (61), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 5/41 (12%)

Query: 49 NFLVTEGYVDAAEKFRMESGTE-----PDIDLATITDRMAV 84
          +FLVT+GY   A  F  E+  E     P++++  +TD++ V
Sbjct: 41 HFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIV 81


>pdb|1OTC|B Chain B, The O. Nova Telomere End Binding Protein Complexed With
          Single Strand Dna
 pdb|1JB7|B Chain B, Dna G-Quartets In A 1.86 A Resolution Structure Of An
          Oxytricha Nova Telomeric Protein-Dna Complex
          Length = 260

 Score = 28.1 bits (61), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 5/41 (12%)

Query: 49 NFLVTEGYVDAAEKFRMESGTE-----PDIDLATITDRMAV 84
          +FLVT+GY   A  F  E+  E     P++++  +TD++ V
Sbjct: 49 HFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIV 89


>pdb|2I0Q|B Chain B, Crystal Structure Of A Telomere Single-Strand
          Dna-Protein Complex From O. Nova With Full-Length Alpha
          And Beta Telomere Proteins
          Length = 385

 Score = 27.3 bits (59), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 5/41 (12%)

Query: 49 NFLVTEGYVDAAEKFRMESGTE-----PDIDLATITDRMAV 84
          +FLVT+GY   A  F  E+  E     P++++  +TD++ V
Sbjct: 49 HFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIV 89


  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    0.366 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,164,943
Number of Sequences: 62578
Number of extensions: 212281
Number of successful extensions: 584
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 583
Number of HSP's gapped (non-prelim): 6
length of query: 242
length of database: 14,973,337
effective HSP length: 96
effective length of query: 146
effective length of database: 8,965,849
effective search space: 1309013954
effective search space used: 1309013954
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: 50 (23.9 bits)