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= psy7671
         (115 letters)

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

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



>pdb|2FN9|A Chain A, Thermotoga Maritima Ribose Binding Protein Unliganded Form
 pdb|2FN9|B Chain B, Thermotoga Maritima Ribose Binding Protein Unliganded Form
          Length = 290

 Score = 27.7 bits (60), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 2/36 (5%)

Query: 75  LGLISVYDLYERGQGFRSLVSLSEE--MIVQQALKF 108
           LG++S    ++R  GF S+V    E  M+ QQ+ +F
Sbjct: 138 LGILSAQPTWDRSNGFHSVVDQYPEFKMVAQQSAEF 173


>pdb|2FN8|A Chain A, Thermotoga Maritima Ribose Binding Protein Ribose Bound
           Form
          Length = 303

 Score = 27.7 bits (60), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 2/36 (5%)

Query: 75  LGLISVYDLYERGQGFRSLVSLSEE--MIVQQALKF 108
           LG++S    ++R  GF S+V    E  M+ QQ+ +F
Sbjct: 138 LGILSAQPTWDRSNGFHSVVDQYPEFKMVAQQSAEF 173


>pdb|3GDB|A Chain A, Crystal Structure Of Spr0440 Glycoside Hydrolase Domain,
           Endo-D From Streptococcus Pneumoniae R6
          Length = 937

 Score = 26.9 bits (58), Expect = 2.9,   Method: Composition-based stats.
 Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 8/44 (18%)

Query: 2   IVVFMGGTDGNLYEIKYQRDA-SWFSASCSKVCLTSSSLTYILP 44
           +V F G  D + YE+ Y++D  SW      K+   SSS T  LP
Sbjct: 713 VVQFKGNKDADFYEV-YEKDGDSW------KLLTGSSSTTIYLP 749


>pdb|2W91|A Chain A, Structure Of A Streptococcus Pneumoniae Family 85
           Glycoside Hydrolase, Endo-D.
 pdb|2W92|A Chain A, Structure Of A Streptococcus Pneumoniae Family 85
           Glycoside Hydrolase, Endo-D, In Complex With
           Nag-Thiazoline
          Length = 653

 Score = 26.9 bits (58), Expect = 2.9,   Method: Composition-based stats.
 Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 8/44 (18%)

Query: 2   IVVFMGGTDGNLYEIKYQRDA-SWFSASCSKVCLTSSSLTYILP 44
           +V F G  D + YE+ Y++D  SW      K+   SSS T  LP
Sbjct: 562 VVQFKGNKDADFYEV-YEKDGDSW------KLLTGSSSTTIYLP 598


>pdb|3LWJ|A Chain A, Crystal Structure Of Putative Tetr-family
          Transcriptional Regulator (yp_752756.1) From
          Syntrophomonas Wolfei Str. Goettingen At 2.07 A
          Resolution
          Length = 202

 Score = 26.6 bits (57), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 45 TFINALITQEDSLAQICIDNSRNVLYTRSELGLISVYDLYER 86
          TF N  + +ED L  +  D ++ ++ + SE  L+   DLYER
Sbjct: 48 TFYNYFVDKEDILKNLLEDFAKQIISSISEYYLVE-KDLYER 88


>pdb|3DWL|A Chain A, Crystal Structure Of Fission Yeast Arp2/3 Complex Lacking
           The Arp2 Subunit
 pdb|3DWL|B Chain B, Crystal Structure Of Fission Yeast Arp2/3 Complex Lacking
           The Arp2 Subunit
          Length = 427

 Score = 26.2 bits (56), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 11/22 (50%), Positives = 13/22 (59%)

Query: 7   GGTDGNLYEIKYQRDASWFSAS 28
           GG D N+   K QR+A WF  S
Sbjct: 370 GGVDVNVISHKRQRNAVWFGGS 391


>pdb|2OVP|B Chain B, Structure Of The Skp1-Fbw7 Complex
 pdb|2OVQ|B Chain B, Structure Of The Skp1-Fbw7-Cyclinedegc Complex
 pdb|2OVR|B Chain B, Structure Of The Skp1-Fbw7-Cyclinedegn Complex
          Length = 445

 Score = 26.2 bits (56), Expect = 4.9,   Method: Composition-based stats.
 Identities = 13/39 (33%), Positives = 25/39 (64%), Gaps = 1/39 (2%)

Query: 58  AQICIDNSRNVLYTRSELGLISVYDLYERGQGFRSLVSL 96
           A  C+  ++N + T S+ G + ++DL + G+  R+LV+L
Sbjct: 364 AVTCLQFNKNFVITSSDDGTVKLWDL-KTGEFIRNLVTL 401


  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    0.136    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,082,994
Number of Sequences: 62578
Number of extensions: 96165
Number of successful extensions: 199
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 198
Number of HSP's gapped (non-prelim): 7
length of query: 115
length of database: 14,973,337
effective HSP length: 78
effective length of query: 37
effective length of database: 10,092,253
effective search space: 373413361
effective search space used: 373413361
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)