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= 046229
         (501 letters)

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

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



>pdb|3VMA|A Chain A, Crystal Structure Of The Full-Length Transglycosylase
           Pbp1b From Escherichia Coli
          Length = 768

 Score = 32.0 bits (71), Expect = 0.88,   Method: Compositional matrix adjust.
 Identities = 26/94 (27%), Positives = 47/94 (50%), Gaps = 8/94 (8%)

Query: 275 NVLAADSVVGNRVTTLKLVKALFFTA----WKEIVFTAVLALIYTLANYVGPYLIDSFVK 330
           N+ A  +V G    T +LVK LF ++    W++    A +ALI   A Y    +++ ++ 
Sbjct: 219 NLTAGRTVQGASTLTQQLVKNLFLSSERSYWRK-ANEAYMALIMD-ARYSKDRILELYMN 276

Query: 331 --YLNGEQEFKHKGYVMVSTFFAAKLVESLSFTQ 362
             YL    + + +G+ + S ++  + VE LS  Q
Sbjct: 277 EVYLGQSGDNEIRGFPLASLYYFGRPVEELSLDQ 310


>pdb|3H3D|X Chain X, Drosophila Pumilio Rna Binding Domain (Puf Domain)
 pdb|3H3D|Y Chain Y, Drosophila Pumilio Rna Binding Domain (Puf Domain)
          Length = 323

 Score = 31.6 bits (70), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 29/91 (31%), Positives = 44/91 (48%), Gaps = 13/91 (14%)

Query: 284 GNRVTTLKLVKALFFTAWKEIVFTAVLALIYTLANYV-GPYLIDSFVKYLNGEQE----F 338
           G+R    KL +A    A K++VF+ +LA  Y+L   V G Y+I  F ++   EQ+     
Sbjct: 37  GSRFIQQKLERAT--AAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGM 94

Query: 339 KHKGYV------MVSTFFAAKLVESLSFTQW 363
           + KG+V      M       K +ES+S  Q 
Sbjct: 95  QVKGHVLQLALQMYGCRVIQKALESISPEQQ 125


>pdb|3FWL|A Chain A, Crystal Structure Of The Full-Length Transglycosylase
           Pbp1b From Escherichia Coli
          Length = 751

 Score = 29.6 bits (65), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 8/94 (8%)

Query: 275 NVLAADSVVGNRVTTLKLVKALFFTA----WKEIVFTAVLALIYTLANYVGPYLIDSFVK 330
           N+ A  +V G    T +LVK LF ++    W++    A  ALI   A Y    +++ +  
Sbjct: 202 NLTAGRTVQGASTLTQQLVKNLFLSSERSYWRK-ANEAYXALIXD-ARYSKDRILELYXN 259

Query: 331 --YLNGEQEFKHKGYVMVSTFFAAKLVESLSFTQ 362
             YL    + + +G+ + S ++  + VE LS  Q
Sbjct: 260 EVYLGQSGDNEIRGFPLASLYYFGRPVEELSLDQ 293


  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    0.138    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,009,235
Number of Sequences: 62578
Number of extensions: 477699
Number of successful extensions: 916
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 916
Number of HSP's gapped (non-prelim): 4
length of query: 501
length of database: 14,973,337
effective HSP length: 103
effective length of query: 398
effective length of database: 8,527,803
effective search space: 3394065594
effective search space used: 3394065594
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)