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= 002380
         (929 letters)

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

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



>pdb|1YA0|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Smg7
 pdb|1YA0|B Chain B, Crystal Structure Of The N-Terminal Domain Of Human Smg7
          Length = 497

 Score =  116 bits (291), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 139/522 (26%), Positives = 216/522 (41%), Gaps = 121/522 (23%)

Query: 1   MRENYEAIILEDHAFSEQHNVEYALWQLHYRRIEELRAHYSAAVSSAGSNTSQATKVPLR 60
           +++ Y+ +++ D  ++    VE  LW           A  +   +  G   ++A   P R
Sbjct: 36  LQDLYQKMLVTDLEYALDKKVEQDLWN---------HAFKNQITTLQGQAKNRAN--PNR 84

Query: 61  SDRVTKIRQQFKTFLSEATGFYHELILKIRAKYGLPLGNFSEDSENRIIMDKDGKKSSEV 120
           S+    ++     FL  A+GFY +L+ ++   + + L    + S+  II +K    S+ V
Sbjct: 85  SE----VQANLSLFLEAASGFYTQLLQELCTVFNVDLPCRVKSSQLGIISNKQTHTSAIV 140

Query: 121 KKGLVSC----HRCLIYLGDLARYKGLYGEGDSKSREXXXXXXXXXXXXXXWPSSGNPHH 176
           K    SC      CL++LGD+ARY+    + +S  R                PS+G P++
Sbjct: 141 KPQSSSCSYICQHCLVHLGDIARYRNQTSQAESYYRHAAQLV----------PSNGQPYN 190

Query: 177 QLAILASYSSDELVAVYRYFRSLAVDSPFSTARDNLIVAFEKNRQSYSQMSGDVKSSTAK 236
           QLAILAS   D L  ++ Y RS+AV  PF  A  NL  A  K  +S              
Sbjct: 191 QLAILASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSKALES-------------- 236

Query: 237 EAGRLTGKGRGKVEVKLASKDADMETSAVKESVSGVQEKLKAFCTRFVRLNGILFTRTSL 296
                    R +V+ K                  GV + +KA    F++ +G ++   SL
Sbjct: 237 ---------RDEVKTKW-----------------GVSDFIKA----FIKFHGHVYLSKSL 266

Query: 297 ETFAEVLALVSSGLCELLSSGPEEELNFGSDANENALFIVRLVSILIFTVHNLK---KEN 353
           E  + +   +     ELL         F    N   L  V +  I +F +H+L+    E 
Sbjct: 267 EKLSPLREKLEEQFKELL---------FQKAFNSQQL--VHVTVINLFQLHHLRDFSNET 315

Query: 354 ENQTYAEIVQRAVLLQNAFTAVFELMGHIIERCMQLSDPS-----SSYLLPGVLVFVEWL 408
           E  TY++  Q   L      A+F     I+ +C  L + S     ++Y LP V V ++WL
Sbjct: 316 EQHTYSQDEQ---LCWTQLLALFMSFLGILCKC-PLQNESQEESYNAYPLPAVKVSMDWL 371

Query: 409 ACYPDIASGSDADERQATVRSNFWNQCISFLNKILSLGPMSVADDEDLTCFFNMSRYDEA 468
              P +   +  DERQ       W   IS LN   S  P     +EDL+           
Sbjct: 372 RLRPRVFQEAVVDERQY-----IWPWLISLLN---SFHP----HEEDLSSI--------- 410

Query: 469 ETENRLALWEDIELRGFLPLLPAQTILDFSRKISFGGDGNKE 510
              +   L E+ EL+GFL L P+   LDFS+    G  G+KE
Sbjct: 411 ---SATPLPEEFELQGFLALRPSFRNLDFSKGHQ-GITGDKE 448


  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
   0.315    0.132    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,766,496
Number of Sequences: 62578
Number of extensions: 1097571
Number of successful extensions: 2544
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 2539
Number of HSP's gapped (non-prelim): 10
length of query: 929
length of database: 14,973,337
effective HSP length: 108
effective length of query: 821
effective length of database: 8,214,913
effective search space: 6744443573
effective search space used: 6744443573
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (26.2 bits)