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= 032222
         (145 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 = 34.3 bits (77), Expect = 0.025,   Method: Composition-based stats.
 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 = 33.9 bits (76), Expect = 0.037,   Method: Composition-based stats.
 Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 73  EIRMPSIRKSSVSEGLTVEGILENWSKIKPVIMEDWSENRDALVDLFGKVRDEW 126
           E R   I+       L +  ++ NW K +PV++  + E +  L ++F KVR EW
Sbjct: 203 EKRPRVIQYPEAKTRLAITKVMYNWVKQQPVVIPGY-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 = 32.3 bits (72), Expect = 0.091,   Method: Composition-based stats.
 Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 73  EIRMPSIRKSSVSEGLTVEGILENWSKIKPVIMEDWSENRDALVDLFGKVRDEW 126
           E R   I+       L +  +  NW K +PV++  + E +  L ++F KVR EW
Sbjct: 211 EKRPRVIQYPEAKTRLAITKVXYNWVKQQPVVIPGY-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 = 29.6 bits (65), Expect = 0.59,   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 = 29.6 bits (65), Expect = 0.62,   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|3L7Z|A Chain A, Crystal Structure Of The S. Solfataricus Archaeal Exosome
 pdb|3L7Z|D Chain D, Crystal Structure Of The S. Solfataricus Archaeal Exosome
 pdb|3L7Z|G Chain G, Crystal Structure Of The S. Solfataricus Archaeal Exosome
          Length = 271

 Score = 27.3 bits (59), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/28 (39%), Positives = 19/28 (67%)

Query: 3   DLYALDFDGVLCDSCGESSLSAVKAAKV 30
           D+Y LD+ G + D+C  +S++A+   KV
Sbjct: 143 DVYVLDYGGNVLDACTLASVAALYNTKV 170


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

 Score = 27.3 bits (59), Expect = 3.1,   Method: Composition-based stats.
 Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 2/35 (5%)

Query: 105 MEDWSENRDALVDLFGKVRDEWMDKDLTTWIGANR 139
           ++ W++ + A  D +G   DEW  KD+T +I  +R
Sbjct: 351 LDGWNQPKAA--DDYGNYFDEWWQKDMTDFIKRDR 383


>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 = 25.8 bits (55), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 2/32 (6%)

Query: 2   ADLYALDFDGVLCDSCGESSLSAVKAAKVRWP 33
            DL  LD+DG + D+C  + L+A+K   V+ P
Sbjct: 139 CDLICLDYDGNILDACTFALLAALK--NVQLP 168


  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    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,289,501
Number of Sequences: 62578
Number of extensions: 157159
Number of successful extensions: 432
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 425
Number of HSP's gapped (non-prelim): 20
length of query: 145
length of database: 14,973,337
effective HSP length: 89
effective length of query: 56
effective length of database: 9,403,895
effective search space: 526618120
effective search space used: 526618120
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: 47 (22.7 bits)