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= 027444
         (223 letters)

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

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



>pdb|1RPU|A Chain A, Crystal Structure Of Cirv P19 Bound To Sirna
 pdb|1RPU|B Chain B, Crystal Structure Of Cirv P19 Bound To Sirna
          Length = 172

 Score = 31.6 bits (70), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 23/87 (26%), Positives = 36/87 (41%), Gaps = 13/87 (14%)

Query: 92  DQKVGAFAPPQRVPHLEIAAAEGCTDARLVNGRGSSERGNPLGFFDSHLHGKIV------ 145
           D   G    P ++P      +   T+ RL N   +S + NPLGF +S   GK+V      
Sbjct: 20  DGGSGGITSPFKLPD----ESPSWTEWRLYNDETNSNQDNPLGFKESWGFGKVVFKRYLR 75

Query: 146 ---VAVDVDEVLGNFVSALNRFIADRY 169
                  +  VLG++      + A R+
Sbjct: 76  YDRTEASLHRVLGSWTGDSVNYAASRF 102


>pdb|1R9F|A Chain A, Crystal Structure Of P19 Complexed With 19-Bp Small
           Interfering Rna
          Length = 136

 Score = 29.3 bits (64), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 9/63 (14%)

Query: 116 TDARLVNGRGSSERGNPLGFFDSHLHGKIV---------VAVDVDEVLGNFVSALNRFIA 166
           T+ RL N   +S + NPLGF +S   GK+V             +  VLG++      + A
Sbjct: 18  TEWRLHNDETNSNQDNPLGFKESWGFGKVVFKRYLRYDRTEASLHRVLGSWTGDSVNYAA 77

Query: 167 DRY 169
            R+
Sbjct: 78  SRF 80


>pdb|4ADB|A Chain A, Structural And Functional Study Of Succinyl-ornithine
           Transaminase From E. Coli
 pdb|4ADB|B Chain B, Structural And Functional Study Of Succinyl-ornithine
           Transaminase From E. Coli
 pdb|4ADB|C Chain C, Structural And Functional Study Of Succinyl-ornithine
           Transaminase From E. Coli
 pdb|4ADB|D Chain D, Structural And Functional Study Of Succinyl-ornithine
           Transaminase From E. Coli
 pdb|4ADC|A Chain A, Structural And Functional Study Of Succinyl-ornithine
           Transaminase From E. Coli
 pdb|4ADC|B Chain B, Structural And Functional Study Of Succinyl-ornithine
           Transaminase From E. Coli
 pdb|4ADC|C Chain C, Structural And Functional Study Of Succinyl-ornithine
           Transaminase From E. Coli
 pdb|4ADC|D Chain D, Structural And Functional Study Of Succinyl-ornithine
           Transaminase From E. Coli
 pdb|4ADD|A Chain A, Structural And Functional Study Of Succinyl-ornithine
           Transaminase From E. Coli
 pdb|4ADD|B Chain B, Structural And Functional Study Of Succinyl-ornithine
           Transaminase From E. Coli
 pdb|4ADD|C Chain C, Structural And Functional Study Of Succinyl-ornithine
           Transaminase From E. Coli
 pdb|4ADD|D Chain D, Structural And Functional Study Of Succinyl-ornithine
           Transaminase From E. Coli
 pdb|4ADE|A Chain A, Structural And Functional Study Of Succinyl-ornithine
           Transaminase From E. Coli
 pdb|4ADE|B Chain B, Structural And Functional Study Of Succinyl-ornithine
           Transaminase From E. Coli
          Length = 406

 Score = 27.7 bits (60), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 111 AAEGCTDARLVNGRGSSERGNPLGFFDSHLHGKIVVAVDVDEVLGNFVSALNRFIADRYS 170
           A E C     V   G++  GNPL    S + GK++  ++  E+L       + F+    +
Sbjct: 265 ATEECARVMTVGTHGTTYGGNPLA---SAVAGKVLELINTPEMLNGVKQRHDWFVERLNT 321

Query: 171 LNH 173
           +NH
Sbjct: 322 INH 324


>pdb|2COZ|A Chain A, Solution Structure Of The Cap-Gly Domain In Human
           Centrosome-Associated Protein Cap350
          Length = 122

 Score = 27.3 bits (59), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 10/56 (17%)

Query: 62  GFLRFKGKVNNGSLILRGC-FDSTNRVNAGA---------DQKVGAFAPPQRVPHL 107
           G LRFKG+ +       G   D     N G           +K G FAPPQ++ H+
Sbjct: 46  GILRFKGETSFAKGFWAGVELDKPEGNNNGTYDGIAYFECKEKHGIFAPPQKISHI 101


  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
   0.325    0.141    0.428 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,670,616
Number of Sequences: 62578
Number of extensions: 213816
Number of successful extensions: 418
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 416
Number of HSP's gapped (non-prelim): 4
length of query: 223
length of database: 14,973,337
effective HSP length: 95
effective length of query: 128
effective length of database: 9,028,427
effective search space: 1155638656
effective search space used: 1155638656
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)