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= 024003
         (274 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 = 30.8 bits (68), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 1/39 (2%)

Query: 94  LTVEGILENWLKIKPVIMEEWSENREALIELSGKVRDEW 132
           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 = 1.8,   Method: Compositional matrix adjust.
 Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 1/39 (2%)

Query: 94  LTVEGILENWLKIKPVIMEEWSENREALIELSGKVRDEW 132
           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 = 28.1 bits (61), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 4/64 (6%)

Query: 3   DLYALDFDGVICDSCEETALSAVKAARVRWPSLFDGVDSALEDWIVDQMHTCFILLQLRP 62
           DL  LD+DG I D+C    L+A+K   V+ P +    ++AL +  V+     ++ ++  P
Sbjct: 140 DLICLDYDGNILDACTFALLAALK--NVQLPEVTINEETALAE--VNLKKKSYLNIRTHP 195

Query: 63  VVET 66
           V  +
Sbjct: 196 VATS 199


  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    0.136    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,821,675
Number of Sequences: 62578
Number of extensions: 299159
Number of successful extensions: 836
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 835
Number of HSP's gapped (non-prelim): 5
length of query: 274
length of database: 14,973,337
effective HSP length: 97
effective length of query: 177
effective length of database: 8,903,271
effective search space: 1575878967
effective search space used: 1575878967
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)