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= 028346
         (210 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 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 =  112 bits (281), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 66/158 (41%), Positives = 94/158 (59%), Gaps = 7/158 (4%)

Query: 13  PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
           PGE L    E   G G Y    +G +++SL G L   S         P V V        
Sbjct: 24  PGERLCNLEEGSPGSGTYT--RHGYIFSSLAGCLMKSS----ENGALPVVSVVRETESQL 77

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
           +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR++DVRATE DKV+++ SFR
Sbjct: 78  LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFR 137

Query: 133 PGDIVRASVLSLGDARA-YFLSTAKNDLGVVSAESTAG 169
           PGDIV A V+SLGDA++ Y L+TA+N+LGVV A S +G
Sbjct: 138 PGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESG 175


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

 Score = 86.3 bits (212), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 55/157 (35%), Positives = 79/157 (50%), Gaps = 36/157 (22%)

Query: 53  PDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAK---------- 102
           P +   R T +   +     +P+ G +V+ RVT++  + A+ +I+ V  K          
Sbjct: 121 PGTEKGRKTNKYANNDFANNLPKEGDIVLTRVTRLSLQRANVEILAVEDKPSPIDSGIGS 180

Query: 103 ------------------------SVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVR 138
                                    + E F GIIR QDVR+T+ D+V +   F+PGDIVR
Sbjct: 181 NGSGIVAAGGGSGAATFSVSQASSDLGETFRGIIRSQDVRSTDRDRVKVIECFKPGDIVR 240

Query: 139 ASVLSLGDARAYFLSTAKNDLGVV--SAESTAGKLVY 173
           A VLSLGD   Y+L+TA+NDLGVV   A + AG L+Y
Sbjct: 241 AQVLSLGDGTNYYLTTARNDLGVVFARAANGAGGLMY 277


>pdb|1DDG|A Chain A, Crystal Structure Of Sir-Fp60
 pdb|1DDG|B Chain B, Crystal Structure Of Sir-Fp60
 pdb|1DDI|A Chain A, Crystal Structure Of Sir-Fp60
          Length = 374

 Score = 35.0 bits (79), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 27/49 (55%)

Query: 87  VMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGD 135
           + T   S D   V + SV +K +G   ++DVR  EID  D  L ++PGD
Sbjct: 1   IHTSPYSKDAPLVASLSVNQKITGRNSEKDVRHIEIDLGDSGLRYQPGD 49


>pdb|2Z0S|A Chain A, Crystal Structure Of Putative Exosome Complex Rna-Binding
           Protein
          Length = 235

 Score = 29.3 bits (64), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 37/153 (24%), Positives = 59/153 (38%), Gaps = 21/153 (13%)

Query: 10  LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
           +V PGE L +  E       YV  + G+  A++ GLLR      +  D      V   + 
Sbjct: 11  IVVPGEPLPEEVEASP---PYVIDYKGVKRATVVGLLR------EKGDGGGRAFVKLKEI 61

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKV--DM 127
           +  VP+ G VVI  +  V       DI           +  ++  QD      +    DM
Sbjct: 62  Y--VPQAGDVVIGLIQSVGIMNWFVDI--------NSPYVAVLSVQDFLGRPFNPAVDDM 111

Query: 128 HLSFRPGDIVRASVLSLGDARAYFLSTAKNDLG 160
               + GD ++A V++    R+  L+     LG
Sbjct: 112 QSLLKVGDYIKAKVVAFDKTRSPLLTVQGEGLG 144


>pdb|1B9B|A Chain A, Triosephosphate Isomerase Of Thermotoga Maritima
 pdb|1B9B|B Chain B, Triosephosphate Isomerase Of Thermotoga Maritima
          Length = 255

 Score = 27.3 bits (59), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 32/133 (24%), Positives = 50/133 (37%), Gaps = 21/133 (15%)

Query: 3   VKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTV 62
           VKE E+V+  P   L +  E+ +G+   +   N + Y         +SP      Q   V
Sbjct: 34  VKEFEIVVCPPFTALSEVGEILSGRNIKLGAQN-VFYEDQGAFTGEISPLML---QEIGV 89

Query: 63  E--VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGA---------------KSVR 105
           E  + GH     + +     I R  K +       I+CVG                K VR
Sbjct: 90  EYVIVGHSERRRIFKEDDEFINRKVKAVLEKGMTPILCVGETLEEREKGLTFCVVEKQVR 149

Query: 106 EKFSGIIRQQDVR 118
           E F G+ +++  R
Sbjct: 150 EGFYGLDKEEAKR 162


  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    0.136    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,701,615
Number of Sequences: 62578
Number of extensions: 209820
Number of successful extensions: 537
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 532
Number of HSP's gapped (non-prelim): 10
length of query: 210
length of database: 14,973,337
effective HSP length: 95
effective length of query: 115
effective length of database: 9,028,427
effective search space: 1038269105
effective search space used: 1038269105
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: 49 (23.5 bits)