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= 003522
         (813 letters)

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

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



>pdb|1UW4|B Chain B, The Structural Basis Of The Interaction Between Nonsense
           Mediated Decay Factors Upf2 And Upf3
 pdb|1UW4|D Chain D, The Structural Basis Of The Interaction Between Nonsense
           Mediated Decay Factors Upf2 And Upf3
          Length = 248

 Score =  142 bits (359), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 69/133 (51%), Positives = 91/133 (68%), Gaps = 2/133 (1%)

Query: 640 RPPLHQYIRKLLFSDLDKSSIEHVLRQLRKLPWSDCE--SYLLKCFMKVHKGKYGQIHLI 697
           RPPL +Y+RKLL+ DL K + E VLRQ+RKLPW D E   Y++ C + +   KY  IH +
Sbjct: 1   RPPLQEYVRKLLYKDLSKVTTEKVLRQMRKLPWQDQEVKDYVICCMINIWNVKYNSIHCV 60

Query: 698 ASLTAGLSRYHDEFAVAVVDEVLEEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSS 757
           A+L AGL  Y ++  + VVD VLE+IRLG+E+N     QRR++  +FLGELYNY  V+S+
Sbjct: 61  ANLLAGLVLYQEDVGIHVVDGVLEDIRLGMEVNQPKFNQRRISSAKFLGELYNYRMVESA 120

Query: 758 VIFDTLYLILVFG 770
           VIF TLY    FG
Sbjct: 121 VIFRTLYSFTSFG 133



 Score = 32.0 bits (71), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 25/124 (20%), Positives = 55/124 (44%), Gaps = 17/124 (13%)

Query: 480 LFNVPRTSLELLPYYSRMVATLSTCMKDVSSMLIQMLEEEFNFLINKKDQMNIETKIRNI 539
           ++NV   S+  +   + ++A L    +DV   ++  + E+    +        + +I + 
Sbjct: 49  IWNVKYNSIHCV---ANLLAGLVLYQEDVGIHVVDGVLEDIRLGMEVNQPKFNQRRISSA 105

Query: 540 RFIGELCKFKIAPAGLVFSCL-------------KACLDDFTH-HNIDVACNLLETCGRF 585
           +F+GEL  +++  + ++F  L              + LD   H   I + C +L+TCG++
Sbjct: 106 KFLGELYNYRMVESAVIFRTLYSFTSFGVNPDGSPSSLDPPEHLFRIRLVCTILDTCGQY 165

Query: 586 LYRS 589
             R 
Sbjct: 166 FDRG 169


>pdb|1HU3|A Chain A, Middle Domain Of Human Eif4gii
          Length = 260

 Score = 35.4 bits (80), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 26/51 (50%)

Query: 536 IRNIRFIGELCKFKIAPAGLVFSCLKACLDDFTHHNIDVACNLLETCGRFL 586
           I NI+FIGEL K K     +   C+   L +    +++  C LL T G+ L
Sbjct: 147 IGNIKFIGELFKLKXLTEAIXHDCVVKLLKNHDEESLECLCRLLTTIGKDL 197


>pdb|3CKM|A Chain A, Crystal Structure Of The Yram (Lpoa) C-Terminal Domain
          Length = 327

 Score = 32.0 bits (71), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 162 RIFLGLPLSGPGQEIYEEFFKGLNITADQKKIFKKAFHTYYNAVQELL-QAEHTSLRQM 219
           +I L LPLSG GQ +      G N       I  + F T  N+VQ+++ QA+   ++ +
Sbjct: 4   QIGLLLPLSGDGQILGTTIQSGFNDAKGNSTIPVQVFDTSXNSVQDIIAQAKQAGIKTL 62


  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
   0.320    0.136    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,251,423
Number of Sequences: 62578
Number of extensions: 769177
Number of successful extensions: 2075
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: 2069
Number of HSP's gapped (non-prelim): 6
length of query: 813
length of database: 14,973,337
effective HSP length: 107
effective length of query: 706
effective length of database: 8,277,491
effective search space: 5843908646
effective search space used: 5843908646
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: 56 (26.2 bits)