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= 037283
         (136 letters)

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

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



>pdb|2K0A|A Chain A, 1h, 15n And 13c Chemical Shift Assignments For Rds3
           Protein
          Length = 109

 Score =  115 bits (289), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 55/97 (56%), Positives = 72/97 (74%), Gaps = 1/97 (1%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICG-GVGIS 93
           ++C KQPG+  G LCEKCDGKC ICDSYVRP   VRVC+ C++G     C+IC   VG++
Sbjct: 11  IMCLKQPGVQTGLLCEKCDGKCPICDSYVRPKRKVRVCENCSFGKQAKNCIICNLNVGVN 70

Query: 94  DAYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKK 130
           DA+YC EC +  KD+DGCP+I+NLGS + D  +E+KK
Sbjct: 71  DAFYCWECCRLGKDKDGCPRILNLGSNRLDRHFEKKK 107


>pdb|3QQC|E Chain E, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
          CLAMP DOMAIN
          Length = 61

 Score = 25.8 bits (55), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 8/28 (28%), Positives = 17/28 (60%)

Query: 70 RVCDECNYGSFQGRCVICGGVGISDAYY 97
          + C  C+Y + + RC +CG   +S+ ++
Sbjct: 4  KACRHCHYITSEDRCPVCGSRDLSEEWF 31


>pdb|1RYQ|A Chain A, Putative Dna-directed Rna Polymerase, Subunit E'' From
          Pyrococcus Furiosus Pfu-263306-001
          Length = 69

 Score = 25.4 bits (54), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 8/28 (28%), Positives = 17/28 (60%)

Query: 70 RVCDECNYGSFQGRCVICGGVGISDAYY 97
          + C  C+Y + + RC +CG   +S+ ++
Sbjct: 12 KACRHCHYITSEDRCPVCGSRDLSEEWF 39


  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
   0.326    0.141    0.463 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,040,602
Number of Sequences: 62578
Number of extensions: 152929
Number of successful extensions: 277
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 270
Number of HSP's gapped (non-prelim): 11
length of query: 136
length of database: 14,973,337
effective HSP length: 88
effective length of query: 48
effective length of database: 9,466,473
effective search space: 454390704
effective search space used: 454390704
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 46 (22.3 bits)