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= 024057
         (273 letters)

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

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



>pdb|3R2D|A Chain A, Crystal Structure Of Antitermination Factors Nusb And Nuse
           In Complex With Dsrna
 pdb|3R2D|B Chain B, Crystal Structure Of Antitermination Factors Nusb And Nuse
           In Complex With Dsrna
          Length = 149

 Score = 28.1 bits (61), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 3/44 (6%)

Query: 97  RAARELALLVVYAACLEGSDPIRLFEKRL---NSRREPGYEFDK 137
           + AR+ A LV+Y   L G +P  LF++ +   N + +  YE+ K
Sbjct: 6   KGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAK 49


>pdb|2JR0|A Chain A, Solution Structure Of Nusb From Aquifex Aeolicus
 pdb|3R2C|A Chain A, Crystal Structure Of Antitermination Factors Nusb And Nuse
           In Complex With Boxa Rna
 pdb|3R2C|B Chain B, Crystal Structure Of Antitermination Factors Nusb And Nuse
           In Complex With Boxa Rna
 pdb|4EYA|A Chain A, Crystal Structure Of A Plectonemic Rna Supercoil
 pdb|4EYA|B Chain B, Crystal Structure Of A Plectonemic Rna Supercoil
 pdb|4EYA|C Chain C, Crystal Structure Of A Plectonemic Rna Supercoil
 pdb|4EYA|D Chain D, Crystal Structure Of A Plectonemic Rna Supercoil
 pdb|4EYA|E Chain E, Crystal Structure Of A Plectonemic Rna Supercoil
 pdb|4EYA|F Chain F, Crystal Structure Of A Plectonemic Rna Supercoil
 pdb|4EYA|G Chain G, Crystal Structure Of A Plectonemic Rna Supercoil
 pdb|4EYA|H Chain H, Crystal Structure Of A Plectonemic Rna Supercoil
          Length = 148

 Score = 28.1 bits (61), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 3/44 (6%)

Query: 97  RAARELALLVVYAACLEGSDPIRLFEKRL---NSRREPGYEFDK 137
           + AR+ A LV+Y   L G +P  LF++ +   N + +  YE+ K
Sbjct: 5   KGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAK 48


  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    0.130    0.375 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,166,833
Number of Sequences: 62578
Number of extensions: 256228
Number of successful extensions: 591
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 591
Number of HSP's gapped (non-prelim): 2
length of query: 273
length of database: 14,973,337
effective HSP length: 97
effective length of query: 176
effective length of database: 8,903,271
effective search space: 1566975696
effective search space used: 1566975696
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: 51 (24.3 bits)