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= psy7862
         (101 letters)

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

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



>pdb|1Y2Y|A Chain A, Structural Characterization Of Nop10p Using Nuclear
          Magnetic Resonance Spectroscopy
 pdb|3U28|B Chain B, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex From
          Saccharomyces Cerevisiae
 pdb|3UAI|B Chain B, Structure Of The Shq1-Cbf5-Nop10-Gar1 Complex From
          Saccharomyces Cerevisiae
          Length = 58

 Score = 85.5 bits (210), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 39/55 (70%), Positives = 47/55 (85%)

Query: 38 MYLMYYLGEDGKRVYTLKKVDPAGNPTVSAHPARFSPDDKYSRERITILRRFGLL 92
          M+LMY LG DGKR+YTLKKV  +G  T SAHPARFSPDDKYSR+R+T+ +RFGL+
Sbjct: 1  MHLMYTLGPDGKRIYTLKKVTESGEITKSAHPARFSPDDKYSRQRVTLKKRFGLV 55


>pdb|2AQA|A Chain A, Nmr Structural Analysis Of Nop10p From Saccharomyces
          Cerevisiae
          Length = 63

 Score = 83.2 bits (204), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 38/54 (70%), Positives = 46/54 (85%)

Query: 39 YLMYYLGEDGKRVYTLKKVDPAGNPTVSAHPARFSPDDKYSRERITILRRFGLL 92
          +LMY LG DGKR+YTLKKV  +G  T SAHPARFSPDDKYSR+R+T+ +RFGL+
Sbjct: 1  HLMYTLGPDGKRIYTLKKVTESGEITKSAHPARFSPDDKYSRQRVTLKKRFGLV 54


>pdb|2EY4|E Chain E, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
 pdb|2EY4|F Chain F, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
          Length = 55

 Score = 34.3 bits (77), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 17/29 (58%), Positives = 19/29 (65%), Gaps = 1/29 (3%)

Query: 52 YTLKKVDP-AGNPTVSAHPARFSPDDKYS 79
          YTLK+V P  G  T  AHP RFSP+D Y 
Sbjct: 14 YTLKEVCPVCGEKTKVAHPPRFSPEDPYG 42


>pdb|3LWO|B Chain B, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA
          CONTAINING 5BRU
 pdb|3LWP|B Chain B, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA
          CONTAINING 5BRDU
 pdb|3LWQ|B Chain B, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA
          CONTAINING 3MU
 pdb|3LWR|B Chain B, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA
          CONTAINING 4SU
 pdb|3LWV|B Chain B, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA
          CONTAINING 2'- Deoxyuridine
          Length = 60

 Score = 34.3 bits (77), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 17/29 (58%), Positives = 19/29 (65%), Gaps = 1/29 (3%)

Query: 52 YTLKKVDP-AGNPTVSAHPARFSPDDKYS 79
          YTLK+V P  G  T  AHP RFSP+D Y 
Sbjct: 14 YTLKEVCPVCGEKTKVAHPPRFSPEDPYG 42


>pdb|2HVY|C Chain C, Crystal Structure Of An HACA BOX RNP FROM PYROCOCCUS
          FURIOSUS
 pdb|3HAX|C Chain C, Crystal Structure Of A Substrate-Bound Gar1-Minus HACA
          RNP FROM Pyrococcus Furiosus
 pdb|3HAY|C Chain C, Crystal Structure Of A Substrate-Bound Full HACA RNP
          FROM Pyrococcus Furiosus
          Length = 60

 Score = 34.3 bits (77), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 26/47 (55%), Gaps = 2/47 (4%)

Query: 52 YTLKKVDP-AGNPTVSAHPARFSPDDKYSRERITILRR-FGLLRTQQ 96
          YTLK+V P  G  T  AHP RFSP+D Y   R    R   G+ R ++
Sbjct: 14 YTLKEVCPVCGEKTKVAHPPRFSPEDPYGEYRRRWKREVLGIGRKEK 60


>pdb|2RFK|B Chain B, Substrate Rna Positioning In The Archaeal HACA
          Ribonucleoprotein Complex
 pdb|3HJW|B Chain B, Structure Of A Functional Ribonucleoprotein
          Pseudouridine Synthase Bound To A Substrate Rna
 pdb|3HJY|B Chain B, Structure Of A Functional Ribonucleoprotein
          Pseudouridine Synthase Bound To A Substrate Rna
          Length = 53

 Score = 34.3 bits (77), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 17/29 (58%), Positives = 19/29 (65%), Gaps = 1/29 (3%)

Query: 52 YTLKKVDP-AGNPTVSAHPARFSPDDKYS 79
          YTLK+V P  G  T  AHP RFSP+D Y 
Sbjct: 12 YTLKEVCPVCGEKTKVAHPPRFSPEDPYG 40


>pdb|3MQK|B Chain B, Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna
          Containing Aca Trinucleotide
          Length = 52

 Score = 34.3 bits (77), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 17/29 (58%), Positives = 19/29 (65%), Gaps = 1/29 (3%)

Query: 52 YTLKKVDP-AGNPTVSAHPARFSPDDKYS 79
          YTLK+V P  G  T  AHP RFSP+D Y 
Sbjct: 11 YTLKEVCPVCGEKTKVAHPPRFSPEDPYG 39


>pdb|2AUS|D Chain D, Crystal Structure Of The Archaeal Box HACA SRNP
          NOP10-Cbf5 Complex
 pdb|2AUS|B Chain B, Crystal Structure Of The Archaeal Box HACA SRNP
          NOP10-Cbf5 Complex
          Length = 60

 Score = 33.5 bits (75), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 26/47 (55%), Gaps = 2/47 (4%)

Query: 52 YTLKKVDP-AGNPTVSAHPARFSPDDKYSRERITILRR-FGLLRTQQ 96
          YTLK+  P  G  T  AHP RFSP+D Y   R  + R   G+ R ++
Sbjct: 14 YTLKETCPVCGEKTKVAHPPRFSPEDPYGEYRRRLKRELLGIGRKEK 60


>pdb|3ME9|A Chain A, Crystal Structure Of Sgf29 In Complex With H3k4me3 Peptide
 pdb|3ME9|B Chain B, Crystal Structure Of Sgf29 In Complex With H3k4me3 Peptide
 pdb|3MET|A Chain A, Crystal Structure Of Sgf29 In Complex With H3k4me2
 pdb|3MET|B Chain B, Crystal Structure Of Sgf29 In Complex With H3k4me2
 pdb|3MEU|A Chain A, Crystal Structure Of Sgf29 In Complex With H3r2me2sk4me3
 pdb|3MEU|B Chain B, Crystal Structure Of Sgf29 In Complex With H3r2me2sk4me3
 pdb|3MEV|A Chain A, Crystal Structure Of Sgf29 In Complex With R2ak4me3
 pdb|3MEV|B Chain B, Crystal Structure Of Sgf29 In Complex With R2ak4me3
          Length = 180

 Score = 25.0 bits (53), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 12  AHQVDLTGGSDQVYLIEYFPYFPLITMYLMYYLGEDGKRVYTLKKVDPAGNPTVSAHPAR 71
           A +V    G +Q  L E   Y      Y +  + E+GK  +TL +      P   A+P  
Sbjct: 50  AARVKAVDGDEQWILAEVVSYSHATNKYEVDDIDEEGKERHTLSRRRVIPLPQWKANP-E 108

Query: 72  FSPDDKYSRERITI 85
             P+  + +E++ +
Sbjct: 109 TDPEALFQKEQLVL 122


  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
   0.322    0.140    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,387,594
Number of Sequences: 62578
Number of extensions: 135358
Number of successful extensions: 214
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 206
Number of HSP's gapped (non-prelim): 13
length of query: 101
length of database: 14,973,337
effective HSP length: 67
effective length of query: 34
effective length of database: 10,780,611
effective search space: 366540774
effective search space used: 366540774
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: 45 (21.9 bits)