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= 027175
         (227 letters)

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

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



>pdb|2F15|A Chain A, Glycogen-Binding Domain Of The Amp-Activated Protein
           Kinase Beta2 Subunit
          Length = 96

 Score = 55.1 bits (131), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 42/80 (52%)

Query: 97  AAITWSLGGKQVAVTGSWDNWENVDPLWRLGKDFVIMKMLPSGVYHYRFIVDECLRYAPD 156
             I WS GGK+V ++GS++NW    PL +   DFV +  LP G + Y+F VD    + P 
Sbjct: 12  TVIRWSEGGKEVFISGSFNNWSTKIPLIKSHNDFVAILDLPEGEHQYKFFVDGQWVHDPS 71

Query: 157 VPWECDDSGNAYNVLDLQPA 176
            P      G   N++ ++ +
Sbjct: 72  EPVVTSQLGTINNLIHVKKS 91


>pdb|1Z0M|A Chain A, The Glycogen-Binding Domain Of The Amp-Activated Protein
           Kinase Beta1 Subunit
 pdb|1Z0M|B Chain B, The Glycogen-Binding Domain Of The Amp-Activated Protein
           Kinase Beta1 Subunit
 pdb|1Z0M|C Chain C, The Glycogen-Binding Domain Of The Amp-Activated Protein
           Kinase Beta1 Subunit
          Length = 96

 Score = 50.4 bits (119), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 101 WSLGGKQVAVTGSWDNWENVDPLWRLGKDFVIMKMLPSGVYHYRFIVDECLRYAPDVPWE 160
           W+ GGK+V ++GS++NW  + PL R   +FV +  LP G + Y+F VD    + P  P  
Sbjct: 17  WTGGGKEVYLSGSFNNWSKL-PLTRSQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIV 75

Query: 161 CDDSGNAYNVLDLQ 174
               G   N++ ++
Sbjct: 76  TSQLGTVNNIIQVK 89


>pdb|2QLV|B Chain B, Crystal Structure Of The Heterotrimer Core Of The S.
           Cerevisiae Ampk Homolog Snf1
 pdb|2QLV|E Chain E, Crystal Structure Of The Heterotrimer Core Of The S.
           Cerevisiae Ampk Homolog Snf1
          Length = 252

 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 43/84 (51%), Gaps = 5/84 (5%)

Query: 95  VAAAITWSLGGKQVAVTGSWDNWENVDPLW----RLGKDFVIMKMLPSGVYHYRFIVDEC 150
           V   I W  GG +V VTGS+  W  +  L       G   V +++LP G + +RFIVD  
Sbjct: 4   VPVEIRWQQGGSKVYVTGSFTKWRKMIGLIPDSDNNGSFHVKLRLLP-GTHRFRFIVDNE 62

Query: 151 LRYAPDVPWECDDSGNAYNVLDLQ 174
           LR +  +P   D  GN  N ++++
Sbjct: 63  LRVSDFLPTATDQMGNFVNYIEVR 86


>pdb|1Z0N|A Chain A, The Glycogen-Binding Domain Of The Amp-Activated Protein
           Kinase
 pdb|1Z0N|B Chain B, The Glycogen-Binding Domain Of The Amp-Activated Protein
           Kinase
 pdb|1Z0N|C Chain C, The Glycogen-Binding Domain Of The Amp-Activated Protein
           Kinase
          Length = 96

 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 101 WSLGGKQVAVTGSWDNWENVDPLWRLGKDFVIMKMLPSGVYHYRFIVDECLRYAPDVPWE 160
           W+ GGK+V ++GS++NW  + P  R   +FV +  LP G + Y+F VD    + P  P  
Sbjct: 17  WTGGGKEVYLSGSFNNWSKL-PXTRSQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIV 75

Query: 161 CDDSGNAYNVLDLQ 174
               G   N++ ++
Sbjct: 76  TSQLGTVNNIIQVK 89


>pdb|4I79|A Chain A, Crystal Structure Of Human Nup43
 pdb|4I79|B Chain B, Crystal Structure Of Human Nup43
          Length = 399

 Score = 29.6 bits (65), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 1/29 (3%)

Query: 102 SLGGKQVAVTGSWDNWENVDPLWRLGKDF 130
           SL   +   TGSWDN EN   LW +G DF
Sbjct: 44  SLQTAETFATGSWDNEENYISLWSIG-DF 71


>pdb|4AEF|A Chain A, The Crystal Structure Of Thermostable Amylase From The
           Pyrococcus
 pdb|4AEF|B Chain B, The Crystal Structure Of Thermostable Amylase From The
           Pyrococcus
          Length = 645

 Score = 28.5 bits (62), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 14/32 (43%), Positives = 18/32 (56%)

Query: 127 GKDFVIMKMLPSGVYHYRFIVDECLRYAPDVP 158
           GK++ I   LP GV+HY F +D      PD P
Sbjct: 50  GKNWKIKIALPEGVWHYAFSIDGKFVLDPDNP 81


  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
   0.318    0.137    0.437 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,378,416
Number of Sequences: 62578
Number of extensions: 302361
Number of successful extensions: 556
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 547
Number of HSP's gapped (non-prelim): 6
length of query: 227
length of database: 14,973,337
effective HSP length: 95
effective length of query: 132
effective length of database: 9,028,427
effective search space: 1191752364
effective search space used: 1191752364
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)