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= psy6276
         (271 letters)

Database: pdbaa 
           65,211 sequences; 15,674,573 total letters

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



>pdb|2NN6|I Chain I, Structure Of The Human Rna Exosome Composed Of Rrp41,
           Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
          Length = 209

 Score =  133 bits (334), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 68/163 (41%), Positives = 106/163 (65%), Gaps = 8/163 (4%)

Query: 4   PPI--CIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSY 61
           PP+  CIPG+R+C L+     G GTY R GY++S+LAG +  +    +N  + V+ V   
Sbjct: 17  PPVRYCIPGERLCNLEEG-SPGSGTYTRHGYIFSSLAGCLMKS---SENGALPVVSVVRE 72

Query: 62  KKEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEM 121
            +  ++P  G +VT ++ ++     K H++ VG+  L  +FR  +R+E+VRATE D++E+
Sbjct: 73  TESQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEI 132

Query: 122 YKCYRPGDIILAR-LPLKELHS-YQLSTAENELGVVIALSEAA 162
           YK +RPGDI+LA+ + L +  S Y L+TAENELGVV+A SE+ 
Sbjct: 133 YKSFRPGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESG 175


>pdb|4IFD|I Chain I, Crystal Structure Of An 11-subunit Eukaryotic Exosome
           Complex Bound To Rna
          Length = 301

 Score = 65.9 bits (159), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 50/68 (73%), Gaps = 1/68 (1%)

Query: 91  ISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLSTAE 149
           +S  ++ L  TFR ++R ++VR+T+ DR+++ +C++PGDI+ A+ L L +  +Y L+TA 
Sbjct: 199 VSQASSDLGETFRGIIRSQDVRSTDRDRVKVIECFKPGDIVRAQVLSLGDGTNYYLTTAR 258

Query: 150 NELGVVIA 157
           N+LGVV A
Sbjct: 259 NDLGVVFA 266


>pdb|4IFD|H Chain H, Crystal Structure Of An 11-subunit Eukaryotic Exosome
           Complex Bound To Rna
          Length = 361

 Score = 38.9 bits (89), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 41/141 (29%), Positives = 62/141 (43%), Gaps = 24/141 (17%)

Query: 2   SNPPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSY 61
           S+  I  PG+ +   D   + G GTY      YS++AGTVS       N+ +SVI +   
Sbjct: 52  SDSQIVTPGELVTD-DPIWMRGHGTYFLDNMTYSSVAGTVS-----RVNRLLSVIPL--- 102

Query: 62  KKEVIVPTPGDVVTARIMAVQQHLCKAH-------VISVGNTALSRTFRALLRRENVRAT 114
            K    P  GD V  RI  V     K         V+ +G+  L      +LRR+    +
Sbjct: 103 -KGRYAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGSVNLP---GGILRRK----S 154

Query: 115 EIDRIEMYKCYRPGDIILARL 135
           E D ++M    + GD++ A +
Sbjct: 155 ESDELQMRSFLKEGDLLNAEV 175


>pdb|2NN6|H Chain H, Structure Of The Human Rna Exosome Composed Of Rrp41,
           Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
          Length = 308

 Score = 36.2 bits (82), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 44/163 (26%), Positives = 72/163 (44%), Gaps = 18/163 (11%)

Query: 6   ICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVS-INKHVEDNKEVSVIEVSSYKKE 64
           + +PG  I   D+  + G GTY+ +  L +++AG+V  +NK         +I V + K  
Sbjct: 41  LVVPGDTITT-DTGFMRGHGTYMGEEKLIASVAGSVERVNK---------LICVKALKTR 90

Query: 65  VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKC 124
            I    GD+V  RI  VQQ   K    S  ++ L  +   L   E  R +  D + M   
Sbjct: 91  YIGEV-GDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGF 149

Query: 125 YRPGDIILARL------PLKELHSYQLSTAENELGVVIALSEA 161
            + GD+I A +          LH+  L   +   GV++ +S +
Sbjct: 150 LQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPS 192


  Database: pdbaa
    Posted date:  Jul 29, 2013  4:35 PM
  Number of letters in database: 15,674,573
  Number of sequences in database:  65,211
  
Lambda     K      H
   0.314    0.131    0.354 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,690,918
Number of Sequences: 65211
Number of extensions: 230486
Number of successful extensions: 608
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 591
Number of HSP's gapped (non-prelim): 21
length of query: 271
length of database: 15,674,573
effective HSP length: 98
effective length of query: 173
effective length of database: 9,283,895
effective search space: 1606113835
effective search space used: 1606113835
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)