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= 024415
         (268 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 = 33.9 bits (76), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 88  LTVEGILENWSKIKPVIMEDWSENRDALVDLFGKVRDEW 126
           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 = 32.7 bits (73), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 88  LTVEGILENWSKIKPVIMEDWSENRDALVDLFGKVRDEW 126
           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 = 31.6 bits (70), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 1/39 (2%)

Query: 88  LTVEGILENWSKIKPVIMEDWSENRDALVDLFGKVRDEW 126
           L +  +  NW K +PV++  + E +  L ++F KVR EW
Sbjct: 226 LAITKVXYNWVKQQPVVIPGY-EGKTPLFNIFDKVRKEW 263


>pdb|2JE6|A Chain A, Structure Of A 9-Subunit Archaeal Exosome
 pdb|2JEA|A Chain A, Structure Of A 9-Subunit Archaeal Exosome Bound To Rna
 pdb|2JEB|A Chain A, Structure Of A 9-Subunit Archaeal Exosome Bound To Mn Ions
 pdb|4BA1|A Chain A, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
           Inorganic Phosphate
 pdb|4BA2|A Chain A, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
           Inorganic Phosphate
          Length = 277

 Score = 30.0 bits (66), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 3   DLYALDFDGVLCDSCGESSLSAVKAAKVRWPGLFDGVDSVIEDWIVDQMHILRPVV 58
           D+Y LD+ G + D+C  +S++A+   KV          SV ++ +V ++ +  PVV
Sbjct: 145 DVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVV 200


>pdb|2BR2|A Chain A, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|C Chain C, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|E Chain E, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|G Chain G, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|I Chain I, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|K Chain K, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|M Chain M, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|O Chain O, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|S Chain S, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|U Chain U, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|W Chain W, Rnase Ph Core Of The Archaeal Exosome
 pdb|2C37|A Chain A, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|C Chain C, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|E Chain E, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|G Chain G, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|I Chain I, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|K Chain K, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|M Chain M, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|O Chain O, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|S Chain S, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|U Chain U, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|W Chain W, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C38|A Chain A, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|E Chain E, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|G Chain G, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|I Chain I, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|K Chain K, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|M Chain M, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|O Chain O, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|S Chain S, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|U Chain U, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C39|A Chain A, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|C Chain C, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|E Chain E, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|G Chain G, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|I Chain I, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|K Chain K, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|M Chain M, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|O Chain O, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|S Chain S, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|U Chain U, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|W Chain W, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C38|C Chain C, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|W Chain W, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
          Length = 275

 Score = 30.0 bits (66), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 3   DLYALDFDGVLCDSCGESSLSAVKAAKVRWPGLFDGVDSVIEDWIVDQMHILRPVV 58
           D+Y LD+ G + D+C  +S++A+   KV          SV ++ +V ++ +  PVV
Sbjct: 143 DVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVV 198


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

 Score = 29.6 bits (65), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 2/40 (5%)

Query: 105 MEDWSENRDALVDLFGKVRDEWMDKDLTTWIGANRFYPGI 144
           ++ W++ + A  D +G   DEW  KD+T +I  +R +P I
Sbjct: 351 LDGWNQPKAA--DDYGNYFDEWWQKDMTDFIKRDRNHPSI 388


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

 Score = 29.6 bits (65), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 5/56 (8%)

Query: 94  LENWSKIKPVIM-EDWSEN-RDALVDLFGK---VRDEWMDKDLTTWIGANRFYPGI 144
           L+N+ K+K  ++ ED ++  +D +VD++G    V   +  KD +TW G    Y GI
Sbjct: 58  LKNYDKVKTELLNEDLAKKYKDEVVDVYGSNYYVNCYFSSKDASTWHGKTCMYGGI 113


  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    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,950,992
Number of Sequences: 62578
Number of extensions: 325564
Number of successful extensions: 853
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 852
Number of HSP's gapped (non-prelim): 11
length of query: 268
length of database: 14,973,337
effective HSP length: 97
effective length of query: 171
effective length of database: 8,903,271
effective search space: 1522459341
effective search space used: 1522459341
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: 50 (23.9 bits)