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= 013627
         (439 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 = 31.6 bits (70), Expect = 0.87,   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|4AT7|B Chain B, Crystal Structure Of The Nf90-Nf45 Dimerisation Domain
           Complex
 pdb|4AT8|B Chain B, Crystal Structure Of The Nf90-Nf45 Dimerisation Domain
           Complex With Atp
 pdb|4AT8|D Chain D, Crystal Structure Of The Nf90-Nf45 Dimerisation Domain
           Complex With Atp
 pdb|4AT9|B Chain B, Crystal Structure Of The Nf90-Nf45 Dimerisation Domain
           Complex With Utp
 pdb|4ATB|B Chain B, Crystal Structure Of The Nf90-Nf45 Dimerisation Domain
           Complex With Ctp
 pdb|4ATB|D Chain D, Crystal Structure Of The Nf90-Nf45 Dimerisation Domain
           Complex With Ctp
          Length = 383

 Score = 30.8 bits (68), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 5/69 (7%)

Query: 350 IQKVLAAAYTNIEDLLEFVDWLDKELSSLADERAVLKHFKWPEKKADAMREAAVEYRDLK 409
           ++KVLA    ++ D  + +D   K L++LA     L+H KW + +A+ ++   +  R L+
Sbjct: 182 MEKVLAGETLSVNDPPDVLD-RQKCLAALAS----LRHAKWFQARANGLKSCVIVIRVLR 236

Query: 410 QLENEISSY 418
            L   + ++
Sbjct: 237 DLCTRVPTW 245


>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 = 29.6 bits (65), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 15/57 (26%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 24 RLRANSKTRESPKQEA-GINGVSLSPELKARAKSVPADVKTNNISKSRRALILNKPK 79
          R+  N K  + PK++  G   V+++ E++  A+  P D+  + + +    +I+NKP+
Sbjct: 43 RVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPR 99


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

 Score = 29.3 bits (64), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 15/57 (26%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 24  RLRANSKTRESPKQEA-GINGVSLSPELKARAKSVPADVKTNNISKSRRALILNKPK 79
           R+  N K  + PK++  G   V+++ E++  A+  P D+  + + +    +I+NKP+
Sbjct: 67  RVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPR 123


  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
   0.310    0.126    0.334 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,235,731
Number of Sequences: 62578
Number of extensions: 361743
Number of successful extensions: 924
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 921
Number of HSP's gapped (non-prelim): 9
length of query: 439
length of database: 14,973,337
effective HSP length: 102
effective length of query: 337
effective length of database: 8,590,381
effective search space: 2894958397
effective search space used: 2894958397
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (25.0 bits)