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= 024758
         (263 letters)

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

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



>pdb|2CJQ|A Chain A, Bovine Viral Diarrhea Virus Cp7-R12 Rna-Dependent Rna
           Polymerase
          Length = 720

 Score = 30.4 bits (67), Expect = 0.91,   Method: Compositional matrix adjust.
 Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 1/39 (2%)

Query: 88  LTVEGILENWLKIKPVIMEEWSENREALIELSGKVRDEW 126
           L +  ++ NW+K +PV++  + E +  L  +  KVR EW
Sbjct: 296 LAITKVMYNWVKQQPVVIPGY-EGKTPLFNIFNKVRKEW 333


>pdb|1S4F|A Chain A, Crystal Structure Of Rna-Dependent Rna Polymerase
           Construct 2 From Bovine Viral Diarrhea Virus (Bvdv)
 pdb|1S4F|B Chain B, Crystal Structure Of Rna-Dependent Rna Polymerase
           Construct 2 From Bovine Viral Diarrhea Virus (Bvdv)
 pdb|1S4F|C Chain C, Crystal Structure Of Rna-Dependent Rna Polymerase
           Construct 2 From Bovine Viral Diarrhea Virus (Bvdv)
 pdb|1S4F|D Chain D, Crystal Structure Of Rna-Dependent Rna Polymerase
           Construct 2 From Bovine Viral Diarrhea Virus (Bvdv)
          Length = 601

 Score = 29.6 bits (65), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 1/39 (2%)

Query: 88  LTVEGILENWLKIKPVIMEEWSENREALIELSGKVRDEW 126
           L +  ++ NW+K +PV++  + E +  L  +  KVR EW
Sbjct: 218 LAITKVMYNWVKQQPVVIPGY-EGKTPLFNIFDKVRKEW 255


>pdb|2NN6|C Chain C, Structure Of The Human Rna Exosome Composed Of Rrp41,
           Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
          Length = 278

 Score = 27.7 bits (60), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 2/43 (4%)

Query: 3   DLYALDFDGVICDSCEETALSAVKAARVRWPSLFDGVDSALED 45
           DL  LD+DG I D+C    L+A+K   V+ P +    ++AL +
Sbjct: 140 DLICLDYDGNILDACTFALLAALK--NVQLPEVTINEETALAE 180


  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
   0.319    0.137    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,269,705
Number of Sequences: 62578
Number of extensions: 273647
Number of successful extensions: 767
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 766
Number of HSP's gapped (non-prelim): 4
length of query: 263
length of database: 14,973,337
effective HSP length: 97
effective length of query: 166
effective length of database: 8,903,271
effective search space: 1477942986
effective search space used: 1477942986
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)