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= psy10606
         (128 letters)

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

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



>pdb|1L9U|A Chain A, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 pdb|1L9U|B Chain B, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 pdb|1L9U|J Chain J, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 pdb|1L9U|K Chain K, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 pdb|1L9Z|A Chain A, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
 pdb|1L9Z|B Chain B, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
 pdb|1YNJ|A Chain A, Taq Rna Polymerase-Sorangicin Complex
 pdb|1YNJ|B Chain B, Taq Rna Polymerase-Sorangicin Complex
 pdb|1YNN|A Chain A, Taq Rna Polymerase-rifampicin Complex
 pdb|1YNN|B Chain B, Taq Rna Polymerase-rifampicin Complex
 pdb|2GHO|A Chain A, Recombinant Thermus Aquaticus Rna Polymerase For
           Structural Studies
 pdb|2GHO|B Chain B, Recombinant Thermus Aquaticus Rna Polymerase For
           Structural Studies
          Length = 314

 Score = 30.0 bits (66), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 13/39 (33%), Positives = 19/39 (48%)

Query: 56  KIYSKRRVVRGCGYINEERDDCYRRTGTFDVDSTYCACK 94
           K+Y + RV RG GY+  ER     R     VD+ +   +
Sbjct: 137 KLYMEVRVDRGVGYVPAERHGIKDRINAIPVDAIFSPVR 175


>pdb|1I6V|A Chain A, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
 pdb|1I6V|B Chain B, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
          Length = 314

 Score = 30.0 bits (66), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 13/39 (33%), Positives = 19/39 (48%)

Query: 56  KIYSKRRVVRGCGYINEERDDCYRRTGTFDVDSTYCACK 94
           K+Y + RV RG GY+  ER     R     VD+ +   +
Sbjct: 137 KLYMEVRVDRGVGYVPAERHGIKDRINAIPVDAIFSPVR 175


>pdb|1HQM|A Chain A, Crystal Structure Of Thermus Aquaticus Core Rna
           Polymerase- Includes Complete Structure With Side-Chains
           (Except For Disordered Regions)-Further Refined From
           Original Deposition-Contains Additional Sequence
           Information
 pdb|1HQM|B Chain B, Crystal Structure Of Thermus Aquaticus Core Rna
           Polymerase- Includes Complete Structure With Side-Chains
           (Except For Disordered Regions)-Further Refined From
           Original Deposition-Contains Additional Sequence
           Information
          Length = 313

 Score = 30.0 bits (66), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 13/39 (33%), Positives = 19/39 (48%)

Query: 56  KIYSKRRVVRGCGYINEERDDCYRRTGTFDVDSTYCACK 94
           K+Y + RV RG GY+  ER     R     VD+ +   +
Sbjct: 136 KLYMEVRVDRGVGYVPAERHGIKDRINAIPVDAIFSPVR 174


>pdb|2WNS|A Chain A, Human Orotate Phosphoribosyltransferase (Oprtase) Domain
           Of Uridine 5'-Monophosphate Synthase (Umps) In Complex
           With Its Substrate Orotidine 5'-Monophosphate (Omp)
 pdb|2WNS|B Chain B, Human Orotate Phosphoribosyltransferase (Oprtase) Domain
           Of Uridine 5'-Monophosphate Synthase (Umps) In Complex
           With Its Substrate Orotidine 5'-Monophosphate (Omp)
          Length = 205

 Score = 28.5 bits (62), Expect = 0.93,   Method: Compositional matrix adjust.
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 11/57 (19%)

Query: 11  AYDPRCGDPFDPYSLGTVNCSLLPIPENLLHKEYQTPVICRKIIQKIYSKRRVVRGC 67
           ++D  CG P+    L TV CS             Q P++ R+   K Y  +R+V G 
Sbjct: 62  SFDTVCGVPYTALPLATVICS-----------TNQIPMLIRRKETKDYGTKRLVEGT 107


  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
   0.323    0.142    0.467 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,710,919
Number of Sequences: 62578
Number of extensions: 142427
Number of successful extensions: 230
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 225
Number of HSP's gapped (non-prelim): 7
length of query: 128
length of database: 14,973,337
effective HSP length: 87
effective length of query: 41
effective length of database: 9,529,051
effective search space: 390691091
effective search space used: 390691091
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)