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= psy13847
         (91 letters)

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

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



>pdb|1MHD|A Chain A, Crystal Structure Of A Smad Mh1 Domain Bound To Dna
 pdb|1MHD|B Chain B, Crystal Structure Of A Smad Mh1 Domain Bound To Dna
          Length = 132

 Score = 81.6 bits (200), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 41/69 (59%), Positives = 49/69 (71%), Gaps = 3/69 (4%)

Query: 1  MTSLFPFTPPIVKKLLGWKKGDG---EDKYSEKAXXXXXXXXXXXNGLDELEKAITTQDP 57
          M+S+ PFTPPIVK+LLGWKKG+    E+K+ EKA             LDELEKAITTQ+ 
Sbjct: 1  MSSILPFTPPIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNV 60

Query: 58 NTKCVTIPR 66
          NTKC+TIPR
Sbjct: 61 NTKCITIPR 69


>pdb|1OZJ|A Chain A, Crystal Structure Of Smad3-mh1 Bound To Dna At 2.4 A
          Resolution
 pdb|1OZJ|B Chain B, Crystal Structure Of Smad3-mh1 Bound To Dna At 2.4 A
          Resolution
          Length = 144

 Score = 81.3 bits (199), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 41/69 (59%), Positives = 49/69 (71%), Gaps = 3/69 (4%)

Query: 1  MTSLFPFTPPIVKKLLGWKKGDG---EDKYSEKAXXXXXXXXXXXNGLDELEKAITTQDP 57
          M+S+ PFTPPIVK+LLGWKKG+    E+K+ EKA             LDELEKAITTQ+ 
Sbjct: 1  MSSILPFTPPIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNV 60

Query: 58 NTKCVTIPR 66
          NTKC+TIPR
Sbjct: 61 NTKCITIPR 69


>pdb|3KMP|A Chain A, Crystal Structure Of Smad1-Mh1DNA COMPLEX
 pdb|3KMP|B Chain B, Crystal Structure Of Smad1-Mh1DNA COMPLEX
          Length = 124

 Score = 56.2 bits (134), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 29/61 (47%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 7  FTPPIVKKLLGWKKGDGEDKYSEKAXXXXXXXXXXXNG-LDELEKAITTQDPNTKCVTIP 65
          FT P VK+LLGWK+GD E+K++EKA            G ++ELEKA++     + CVTIP
Sbjct: 1  FTSPAVKRLLGWKQGDEEEKWAEKAVDALVKKLKKKKGAMEELEKALSCPGQPSNCVTIP 60

Query: 66 R 66
          R
Sbjct: 61 R 61


  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
   0.313    0.133    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,701,652
Number of Sequences: 62578
Number of extensions: 83850
Number of successful extensions: 94
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 87
Number of HSP's gapped (non-prelim): 4
length of query: 91
length of database: 14,973,337
effective HSP length: 58
effective length of query: 33
effective length of database: 11,343,813
effective search space: 374345829
effective search space used: 374345829
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)