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= psy10139
         (106 letters)

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

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



>pdb|2E5N|A Chain A, Solution Structure Of The Ell_n2 Domain Of Target Of Rna
          Polymerase Ii Elongation Factor Ell2
          Length = 100

 Score = 76.3 bits (186), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 36/79 (45%), Positives = 57/79 (72%), Gaps = 2/79 (2%)

Query: 3  QDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIA--FARDNTYHLQRHVWN 60
          +DR+IHLLA++ YKKPEL A L +DG+  +D+N + AIL  +A   ++D +Y L+ +V+ 
Sbjct: 15 RDRVIHLLALKAYKKPELLARLQKDGVNQKDKNSLGAILQQVANLNSKDLSYTLKDYVFK 74

Query: 61 DVQDDWPFYSQQDKNMLKS 79
          ++Q DWP YS+ D+  L+S
Sbjct: 75 ELQRDWPGYSEIDRRSLES 93


>pdb|2DOA|A Chain A, Solution Structure Of The Helical Domain In Human Eleven-
           Nineteen Lysine-Rich Leukemia Protein Ell
          Length = 104

 Score = 73.9 bits (180), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 38/90 (42%), Positives = 57/90 (63%), Gaps = 3/90 (3%)

Query: 4   DRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIA--FARDNTYHLQRHVWND 61
           DR++HLLA+RPY+K EL   L +DG+   D++ +  +L  +A   A+D T  LQ  ++ D
Sbjct: 15  DRVLHLLALRPYRKAELLLRLQKDGLTQADKDALDGLLQQVANMSAKDGTCTLQDCMYKD 74

Query: 62  VQDDWPFYSQQDKNMLKSRELLQNFSENHS 91
           VQ DWP YS+ D+ +LK R L++  S   S
Sbjct: 75  VQKDWPGYSEGDQQLLK-RVLVRKLSGPSS 103


>pdb|2IQ9|H Chain H, Pfa2 Fab Fragment, Triclinic Apo Form
 pdb|2IQA|H Chain H, Pfa2 Fab Fragment, Monoclinic Apo Form
 pdb|2IQA|B Chain B, Pfa2 Fab Fragment, Monoclinic Apo Form
          Length = 223

 Score = 27.3 bits (59), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 2/56 (3%)

Query: 18  PELYAALTRDGIRDRDRNQMMAILNGIAFARDNTYHLQRHVWNDVQDDWPFYSQQD 73
           P L + LT    +D  RNQ+   +  +  A   TY+  R   N V  DW  Y  Q 
Sbjct: 63  PSLKSQLTIS--KDTSRNQVFLKITSVDTADTATYYCVRRAHNVVLGDWFAYWGQG 116


>pdb|2R0W|H Chain H, Pfa2 Fab Complexed With Abeta1-8
          Length = 223

 Score = 26.9 bits (58), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 2/56 (3%)

Query: 18  PELYAALTRDGIRDRDRNQMMAILNGIAFARDNTYHLQRHVWNDVQDDWPFYSQQD 73
           P L + LT    +D  RNQ+   +  +  A   TY+  R   N V  DW  Y  Q 
Sbjct: 63  PSLKSQLTIS--KDTSRNQVFLKITSVDTADTATYYCVRRAHNVVLGDWFAYWGQG 116


>pdb|2DEP|A Chain A, Crystal Structure Of Xylanase B From Clostridium
           Stercorarium F9
 pdb|2DEP|B Chain B, Crystal Structure Of Xylanase B From Clostridium
           Stercorarium F9
          Length = 356

 Score = 26.2 bits (56), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 12/40 (30%), Positives = 23/40 (57%), Gaps = 2/40 (5%)

Query: 44  IAFARDNTYHLQRH--VWNDVQDDWPFYSQQDKNMLKSRE 81
           + FA++N   L+ H  VW++   DW F  ++ K M++  +
Sbjct: 69  VQFAKENGMELRFHTLVWHNQTPDWFFLDKEGKPMVEETD 108


>pdb|2R0Z|H Chain H, Pfa1 Fab Complexed With Gripi Peptide Fragment
          Length = 223

 Score = 25.4 bits (54), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 17/56 (30%), Positives = 23/56 (41%), Gaps = 2/56 (3%)

Query: 18  PELYAALTRDGIRDRDRNQMMAILNGIAFARDNTYHLQRHVWNDVQDDWPFYSQQD 73
           P L + LT    +D  RNQ+   +  +  A   TY+  R     V  DW  Y  Q 
Sbjct: 63  PSLKSQLTIS--KDTSRNQVFLRITSVDTADTATYYCVRRAHTTVLGDWFAYWGQG 116


  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
   0.323    0.135    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,097,597
Number of Sequences: 62578
Number of extensions: 113648
Number of successful extensions: 244
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 237
Number of HSP's gapped (non-prelim): 10
length of query: 106
length of database: 14,973,337
effective HSP length: 71
effective length of query: 35
effective length of database: 10,530,299
effective search space: 368560465
effective search space used: 368560465
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)