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= 033906
         (109 letters)

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

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



>pdb|2DIQ|A Chain A, Solution Structure Of The Tudor Domain Of Tudor And Kh
          Domain Containing Protein
          Length = 110

 Score = 29.6 bits (65), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 10/22 (45%), Positives = 19/22 (86%)

Query: 41 LINEINQNHESKIPDNLTRNVG 62
          L+NE+ Q++E+ +P++LT +VG
Sbjct: 15 LVNEMTQHYENSVPEDLTVHVG 36


>pdb|3FDR|A Chain A, Crystal Structure Of Tdrd2
          Length = 94

 Score = 29.3 bits (64), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 10/22 (45%), Positives = 19/22 (86%)

Query: 41 LINEINQNHESKIPDNLTRNVG 62
          L+NE+ Q++E+ +P++LT +VG
Sbjct: 10 LVNEMTQHYENSVPEDLTVHVG 31


>pdb|2KM4|A Chain A, Solution Structure Of Rtt103 Ctd Interacting Domain
 pdb|2L0I|A Chain A, Solution Structure Of Rtt103 Ctd-Interacting Domain Bound
           To A Ser2 Phosphorylated Ctd Peptide
          Length = 142

 Score = 28.5 bits (62), Expect = 0.88,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 9/76 (11%)

Query: 15  QVNGRVMQTFQRSFGQVQDILDQNRLLINEINQNHESKIPDNLTRNVGLIKELNNNIRRV 74
           Q  G+ +  FQ SFG+V         ++  INQ     +   L+R V ++KE N   ++V
Sbjct: 70  QAKGQKIIQFQDSFGKVAA------EVLGRINQEFPRDLKKKLSRVVNILKERNIFSKQV 123

Query: 75  VNLYADLSTSFSRSVE 90
           VN   D+  S + ++E
Sbjct: 124 VN---DIERSLAAALE 136


>pdb|1VLP|A Chain A, Crystal Structure Of A Putative Nicotinate
           Phosphoribosyltransferase (Yor209c, Npt1) From
           Saccharomyces Cerevisiae At 1.75 A Resolution
 pdb|1VLP|B Chain B, Crystal Structure Of A Putative Nicotinate
           Phosphoribosyltransferase (Yor209c, Npt1) From
           Saccharomyces Cerevisiae At 1.75 A Resolution
 pdb|1VLP|C Chain C, Crystal Structure Of A Putative Nicotinate
           Phosphoribosyltransferase (Yor209c, Npt1) From
           Saccharomyces Cerevisiae At 1.75 A Resolution
 pdb|1VLP|D Chain D, Crystal Structure Of A Putative Nicotinate
           Phosphoribosyltransferase (Yor209c, Npt1) From
           Saccharomyces Cerevisiae At 1.75 A Resolution
          Length = 441

 Score = 26.6 bits (57), Expect = 3.4,   Method: Composition-based stats.
 Identities = 11/19 (57%), Positives = 13/19 (68%)

Query: 44  EINQNHESKIPDNLTRNVG 62
           E+N NH  KI DNL +N G
Sbjct: 394 EVNGNHAIKISDNLGKNXG 412


>pdb|3ETU|A Chain A, Crystal Structure Of Yeast Dsl1p
          Length = 365

 Score = 26.2 bits (56), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 8/51 (15%)

Query: 33 DILDQNRLLINEINQNHESKIPDNLTRNVGLIKEL--NNNIRRVVNLYADL 81
          D+L +  +L NE+N      I DNL   + LIKE+  N NI  + N Y  L
Sbjct: 44 DLLQREAILANELN------ILDNLKTFLNLIKEVKTNLNILELENCYYSL 88


  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    0.132    0.352 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,893,798
Number of Sequences: 62578
Number of extensions: 100505
Number of successful extensions: 288
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 276
Number of HSP's gapped (non-prelim): 22
length of query: 109
length of database: 14,973,337
effective HSP length: 73
effective length of query: 36
effective length of database: 10,405,143
effective search space: 374585148
effective search space used: 374585148
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)