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= 017626
         (368 letters)

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

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



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

 Score = 30.4 bits (67), Expect = 1.9,   Method: Composition-based stats.
 Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 4/60 (6%)

Query: 141 SGSETDVSNHGIVGSD--SFDKIKDAWKSVVDGVSYTGQKAKDELSPQ--IEQLLDAHPY 196
           +G   DV       +D  ++  +KD WK++V   S   Q+ + E  PQ  ++++L AH Y
Sbjct: 37  TGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQRRGEPVPQDLLDRVLAAHAY 96


>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 = 30.0 bits (66), Expect = 2.0,   Method: Composition-based stats.
 Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 4/60 (6%)

Query: 141 SGSETDVSNHGIVGSD--SFDKIKDAWKSVVDGVSYTGQKAKDELSPQ--IEQLLDAHPY 196
           +G   DV       +D  ++  +KD WK++V   S   Q+ + E  PQ  ++++L AH Y
Sbjct: 24  TGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQRRGEPVPQDLLDRVLAAHAY 83


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

 Score = 30.0 bits (66), Expect = 2.1,   Method: Composition-based stats.
 Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 4/60 (6%)

Query: 141 SGSETDVSNHGIVGSD--SFDKIKDAWKSVVDGVSYTGQKAKDELSPQ--IEQLLDAHPY 196
           +G   DV       +D  ++  +KD WK++V   S   Q+ + E  PQ  ++++L AH Y
Sbjct: 20  TGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQRRGEPVPQDLLDRVLAAHAY 79


>pdb|4F0R|A Chain A, Crystal Structure Of An Adenosine Deaminase Homolog From
           Chromobacterium Violaceum (Target Nysgrc-019589) Bound
           Zn And 5'- Methylthioadenosine (Unproductive Complex)
 pdb|4F0S|A Chain A, Crystal Structure Of An Adenosine Deaminase Homolog From
           Chromobacterium Violaceum (Target Nysgrc-019589) With
           Bound Inosine
          Length = 447

 Score = 29.6 bits (65), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 10/56 (17%)

Query: 28  TSNSYFKLARYAEQKHVKLSCAVVNNNYDNSRLHSALNSINNQLKVHGFAPIGKTQ 83
           + +++ K+   AEQ+   + C           +H   + +NN +K HG  P+ + Q
Sbjct: 198 SDDTFRKVVTLAEQEDXLIHC----------HIHETADEVNNSVKEHGQRPLARLQ 243


>pdb|3KJO|A Chain A, Crystal Structure Of Hpot1v2-Dtrud(Agggttag)
 pdb|3KJP|A Chain A, Crystal Structure Of Hpot1v2-Ggttagggttag
          Length = 299

 Score = 29.3 bits (64), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 12/36 (33%), Positives = 19/36 (52%)

Query: 21 FKPRLLHTSNSYFKLARYAEQKHVKLSCAVVNNNYD 56
          FKP  L     Y  +    +Q +VKL+C + + NY+
Sbjct: 32 FKPPYLSKGTDYCSVVTIVDQTNVKLTCLLFSGNYE 67


>pdb|1XJV|A Chain A, Crystal Structure Of Human Pot1 Bound To Telomeric
          Single- Stranded Dna (Ttagggttag)
          Length = 294

 Score = 29.3 bits (64), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 12/36 (33%), Positives = 19/36 (52%)

Query: 21 FKPRLLHTSNSYFKLARYAEQKHVKLSCAVVNNNYD 56
          FKP  L     Y  +    +Q +VKL+C + + NY+
Sbjct: 27 FKPPYLSKGTDYCSVVTIVDQTNVKLTCLLFSGNYE 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
   0.321    0.134    0.402 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,151,198
Number of Sequences: 62578
Number of extensions: 391991
Number of successful extensions: 947
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 945
Number of HSP's gapped (non-prelim): 6
length of query: 368
length of database: 14,973,337
effective HSP length: 100
effective length of query: 268
effective length of database: 8,715,537
effective search space: 2335763916
effective search space used: 2335763916
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)