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= psy8033
         (267 letters)

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

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



>pdb|3NR5|A Chain A, Crystal Structure Of Human Maf1
          Length = 164

 Score =  129 bits (323), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 55/82 (67%), Positives = 68/82 (82%)

Query: 176 LYWVMNAIDSNLSTTAGEQYRTLRPHLWAALEDEIVLPECDIYSYNPDLTSDPFSEDGSL 235
           L WV+NA++ +L +   E ++ L+P LW A+++EI L ECDIYSYNPDL SDPF EDGSL
Sbjct: 83  LSWVVNAVNCSLFSAVREDFKDLKPQLWNAVDEEICLAECDIYSYNPDLDSDPFGEDGSL 142

Query: 236 WSFNYFFYNKKLKRIVFFSCRA 257
           WSFNYFFYNK+LKRIVFFSCR+
Sbjct: 143 WSFNYFFYNKRLKRIVFFSCRS 164



 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 17/27 (62%), Positives = 21/27 (77%)

Query: 5  FEALNRALCINVGDSKIVGRIESYSCK 31
          FEA+N  L +  GD+ I+GRIESYSCK
Sbjct: 15 FEAINSQLTVETGDAHIIGRIESYSCK 41


>pdb|3R6U|A Chain A, Crystal Structure Of Choline Binding Protein Opubc From
           Bacillus Subtilis
          Length = 284

 Score = 28.5 bits (62), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 11/22 (50%), Positives = 16/22 (72%)

Query: 23  GRIESYSCKMAGNDKQFYKKFN 44
           GRI+SY  KM  +DKQF+  ++
Sbjct: 201 GRIKSYGLKMLKDDKQFFPPYD 222



 Score = 27.7 bits (60), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 17/81 (20%)

Query: 25  IESYSCKMAGNDKQFYKKFNSEQGTTPQDLQALSPPQSGL---GISPGR--------SHY 73
           +++Y  K+ GN    Y+ F    G T        P Q GL    +  G+        +  
Sbjct: 148 VDNYWMKLKGNG---YQDFTKTYGMT---FGGTYPMQIGLVYDAVKSGKMDIVLAYSTDG 201

Query: 74  RIESYSCKMAGNDKQFYKKFN 94
           RI+SY  KM  +DKQF+  ++
Sbjct: 202 RIKSYGLKMLKDDKQFFPPYD 222


>pdb|1RY2|A Chain A, Crystal Structure Of Yeast Acetyl-Coenzyme A Synthetase In
           Complex With Amp
          Length = 663

 Score = 27.7 bits (60), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 8/84 (9%)

Query: 178 WVMNAIDSNLSTTAGEQYRTLRPHLWAALEDEIVLPECDIYSYNPDLTSDPFS-----ED 232
           W++  +D  ++ +    +R     + AA+ ++ ++ EC +  +N DLT    +     ++
Sbjct: 520 WILGRVDDVVNVSG---HRLSTAEIEAAIIEDPIVAECAVVGFNDDLTGQAVAAFVVLKN 576

Query: 233 GSLWSFNYFFYNKKLKRIVFFSCR 256
            S WS       + +K+ + F+ R
Sbjct: 577 KSSWSTATDDELQDIKKHLVFTVR 600


>pdb|1WOY|A Chain A, Crystal Structure Of Methionyl Trna Synthetase Y225f
           Mutant From Thermus Thermophilus
 pdb|2D5B|A Chain A, Crystal Structure Of Thermus Thermophilus Methionyl Trna
           Synthetase Y225f Mutant Obtained In The Presence Of
           Peg6000
          Length = 500

 Score = 27.3 bits (59), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 15/31 (48%)

Query: 185 SNLSTTAGEQYRTLRPHLWAALEDEIVLPEC 215
           S L    GE YRT  PH W  +  +I+ P  
Sbjct: 236 SALDYPEGEAYRTFWPHAWHLIGKDILKPHA 266


>pdb|1A8H|A Chain A, Methionyl-Trna Synthetase From Thermus Thermophilus
          Length = 500

 Score = 27.3 bits (59), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 15/31 (48%)

Query: 185 SNLSTTAGEQYRTLRPHLWAALEDEIVLPEC 215
           S L    GE YRT  PH W  +  +I+ P  
Sbjct: 236 SALDYPEGEAYRTFWPHAWHLIGKDILKPHA 266


>pdb|2D54|A Chain A, Crystal Structure Of Methionyl Trna Synthetase Y225a
           Mutant From Thermus Thermophilus
          Length = 502

 Score = 27.3 bits (59), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 15/31 (48%)

Query: 185 SNLSTTAGEQYRTLRPHLWAALEDEIVLPEC 215
           S L    GE YRT  PH W  +  +I+ P  
Sbjct: 236 SALDYPEGEAYRTFWPHAWHLIGKDILKPHA 266


  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
   0.316    0.133    0.399 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,628,486
Number of Sequences: 62578
Number of extensions: 373589
Number of successful extensions: 858
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 849
Number of HSP's gapped (non-prelim): 10
length of query: 267
length of database: 14,973,337
effective HSP length: 97
effective length of query: 170
effective length of database: 8,903,271
effective search space: 1513556070
effective search space used: 1513556070
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: 50 (23.9 bits)