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= 027821
         (218 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 = 33.5 bits (75), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 38  LTVEGILENWSKIKPVIMEDWSENRDALVDLFGKVRDEW 76
           L +  ++ NW K +PV++  + E +  L ++F 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 = 32.3 bits (72), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 38  LTVEGILENWSKIKPVIMEDWSENRDALVDLFGKVRDEW 76
           L +  ++ NW K +PV++  + E +  L ++F KVR EW
Sbjct: 218 LAITKVMYNWVKQQPVVIPGY-EGKTPLFNIFDKVRKEW 255


>pdb|1S48|A Chain A, Crystal Structure Of Rna-Dependent Rna Polymerase
           Construct 1 (Residues 71-679) From Bvdv
 pdb|1S49|A Chain A, Crystal Structure Of Rna-Dependent Rna Polymerase
           Construct 1 (Residues 71-679) From Bovine Viral Diarrhea
           Virus Complexed With Gtp
          Length = 609

 Score = 31.2 bits (69), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 1/39 (2%)

Query: 38  LTVEGILENWSKIKPVIMEDWSENRDALVDLFGKVRDEW 76
           L +  +  NW K +PV++  + E +  L ++F KVR EW
Sbjct: 226 LAITKVXYNWVKQQPVVIPGY-EGKTPLFNIFDKVRKEW 263


>pdb|3BVG|A Chain A, Manipulating The Coupled Folding And Binding Process
           Drives Affinity Maturation In A Protein-Protein Complex
          Length = 237

 Score = 30.4 bits (67), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 5/56 (8%)

Query: 44  LENWSKIKPVIM-EDWSEN-RDALVDLFGK---VRDEWMDKDLTTWIGANRFYPGI 94
           L+N+ K+K  ++ ED ++  +D +VD++G    V   +  KD +TW G    Y GI
Sbjct: 58  LKNYDKVKTELLNEDLAKKYKDEVVDVYGSNYYVNCYFSSKDASTWHGKTCMYGGI 113


>pdb|3GM8|A Chain A, Crystal Structure Of A Beta-glycosidase From Bacteroides
           Vulgatus
          Length = 801

 Score = 30.0 bits (66), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 2/40 (5%)

Query: 55  MEDWSENRDALVDLFGKVRDEWMDKDLTTWIGANRFYPGI 94
           ++ W++ + A  D +G   DEW  KD+T +I  +R +P I
Sbjct: 351 LDGWNQPKAA--DDYGNYFDEWWQKDMTDFIKRDRNHPSI 388


>pdb|3TQI|A Chain A, Structure Of The Gmp Synthase (Guaa) From Coxiella
           Burnetii
 pdb|3TQI|B Chain B, Structure Of The Gmp Synthase (Guaa) From Coxiella
           Burnetii
 pdb|3TQI|C Chain C, Structure Of The Gmp Synthase (Guaa) From Coxiella
           Burnetii
 pdb|3TQI|D Chain D, Structure Of The Gmp Synthase (Guaa) From Coxiella
           Burnetii
          Length = 527

 Score = 26.9 bits (58), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 14/59 (23%), Positives = 27/59 (45%)

Query: 55  MEDWSENRDALVDLFGKVRDEWMDKDLTTWIGANRFYPGIPDALKFASSRIYIVTTKQS 113
           + D  E R    + F +V +E   K    W+G    YP + ++ K  + + +I+ T  +
Sbjct: 304 ISDPEEKRKIAGEQFIRVFEEQAKKLNVKWLGQGTIYPDVIESAKTKTGKGHIIKTHHN 362


  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
   0.318    0.137    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,442,045
Number of Sequences: 62578
Number of extensions: 266019
Number of successful extensions: 718
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 716
Number of HSP's gapped (non-prelim): 9
length of query: 218
length of database: 14,973,337
effective HSP length: 95
effective length of query: 123
effective length of database: 9,028,427
effective search space: 1110496521
effective search space used: 1110496521
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)