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= 019419
         (341 letters)

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

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



>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
 pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
 pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
 pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
           P21 Space Group
 pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
           P21 Space Group
 pdb|4AYB|A Chain A, Rnap At 3.2ang
 pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
 pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
          Length = 880

 Score = 32.0 bits (71), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 24  RLRANSKTRESPKQEAGINGVSLSPELKARAKSVPADVKTNNISKSRRALILNKPKSAEG 83
           R+  +S+T  SP     I+ V + PE+ AR  +VP  +   NI K R+  ++N P    G
Sbjct: 317 RVDFSSRTVISPDPNISIDEVGV-PEIIARTLTVPERITPWNIEKLRQ-FVINGPDKWPG 374

Query: 84  A 84
           A
Sbjct: 375 A 375


>pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine
           Synthase Rlud From Escherichia Coli
 pdb|2IST|A Chain A, Crystal Structure Of Rlud From E. Coli
          Length = 325

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 24  RLRANSKTRESPKQEA-GINGVSLSPELKARAKSVPADVKTNNISKSRRALILNKPKS 80
           R+  N K  + PK++  G   V+++ E++  A+  P D+  + + +    +I+NKP+ 
Sbjct: 43  RVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRD 100


>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 pdb|2PMZ|Q Chain Q, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 pdb|3HKZ|A Chain A, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
 pdb|3HKZ|I Chain I, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
          Length = 880

 Score = 30.4 bits (67), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 24  RLRANSKTRESPKQEAGINGVSLSPELKARAKSVPADVKTNNISKSRRALILNKPKSAEG 83
           R+  +S+T  SP     I+ V + PE+ A+  +VP  +   NI K R+  ++N P    G
Sbjct: 317 RVDFSSRTVISPDPNISIDEVGV-PEIIAKTLTVPERITPWNIEKLRQ-FVINGPDKWPG 374

Query: 84  A 84
           A
Sbjct: 375 A 375


>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
           Pseudouridine Synthase Rlud
          Length = 349

 Score = 29.6 bits (65), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 24  RLRANSKTRESPKQEA-GINGVSLSPELKARAKSVPADVKTNNISKSRRALILNKPKS 80
           R+  N K  + PK++  G   V+++ E++  A+  P D+  + + +    +I+NKP+ 
Sbjct: 67  RVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRD 124


  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
   0.309    0.124    0.326 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,496,156
Number of Sequences: 62578
Number of extensions: 245834
Number of successful extensions: 601
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 598
Number of HSP's gapped (non-prelim): 10
length of query: 341
length of database: 14,973,337
effective HSP length: 100
effective length of query: 241
effective length of database: 8,715,537
effective search space: 2100444417
effective search space used: 2100444417
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)