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= 026375
         (239 letters)

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

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



>pdb|2EFC|A Chain A, Ara7-GdpATVPS9A
 pdb|2EFC|C Chain C, Ara7-GdpATVPS9A
 pdb|2EFD|A Chain A, Ara7ATVPS9A
 pdb|2EFD|C Chain C, Ara7ATVPS9A
 pdb|2EFE|A Chain A, Ara7-Gdpnh2ATVPS9A
 pdb|2EFE|C Chain C, Ara7-Gdpnh2ATVPS9A
 pdb|4G01|A Chain A, Ara7-gdp-ca2+/vps9a
          Length = 267

 Score = 30.0 bits (66), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 12/82 (14%)

Query: 77  ERVLPSIIHETLKAVVAQYNASQLITQRETVSREIRKILTERAANFNIALDDVSITSLTF 136
           +  LP +I+ T+KA   Q +++ L  QR    R   K++ E A  F         T++  
Sbjct: 187 DEFLPVLIYVTIKANPPQLHSNLLYIQR---YRRESKLVGEAAYFF---------TNILS 234

Query: 137 GKEFTSAIEAKQVAAQEAERAK 158
            + F S I+AK ++  EAE  K
Sbjct: 235 AESFISNIDAKSISLDEAEFEK 256


>pdb|2EFH|A Chain A, Ara7-GdpATVPS9A(D185N)
 pdb|2EFH|C Chain C, Ara7-GdpATVPS9A(D185N)
          Length = 267

 Score = 29.3 bits (64), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 12/79 (15%)

Query: 80  LPSIIHETLKAVVAQYNASQLITQRETVSREIRKILTERAANFNIALDDVSITSLTFGKE 139
           LP +I+ T+KA   Q +++ L  QR    R   K++ E A  F         T++   + 
Sbjct: 190 LPVLIYVTIKANPPQLHSNLLYIQR---YRRESKLVGEAAYFF---------TNILSAES 237

Query: 140 FTSAIEAKQVAAQEAERAK 158
           F S I+AK ++  EAE  K
Sbjct: 238 FISNIDAKSISLDEAEFEK 256


>pdb|3PEA|A Chain A, Crystal Structure Of Enoyl-Coa Hydratase From Bacillus
           Anthracis Str. 'ames Ancestor'
 pdb|3PEA|B Chain B, Crystal Structure Of Enoyl-Coa Hydratase From Bacillus
           Anthracis Str. 'ames Ancestor'
 pdb|3PEA|C Chain C, Crystal Structure Of Enoyl-Coa Hydratase From Bacillus
           Anthracis Str. 'ames Ancestor'
 pdb|3PEA|D Chain D, Crystal Structure Of Enoyl-Coa Hydratase From Bacillus
           Anthracis Str. 'ames Ancestor'
 pdb|3PEA|E Chain E, Crystal Structure Of Enoyl-Coa Hydratase From Bacillus
           Anthracis Str. 'ames Ancestor'
 pdb|3PEA|F Chain F, Crystal Structure Of Enoyl-Coa Hydratase From Bacillus
           Anthracis Str. 'ames Ancestor'
          Length = 261

 Score = 26.9 bits (58), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 26/90 (28%), Positives = 39/90 (43%), Gaps = 10/90 (11%)

Query: 95  YNASQLITQRETVSREIRKILTERAANFNIALDDVSITSLTFGKEFTSAIEAKQVAAQEA 154
           ++ ++LI Q E     IR ++      F  A  D+        KEFTS  EAKQ A + A
Sbjct: 35  HDVTELIDQVEK-DDNIRVVVIHGEGRFFSAGADI--------KEFTSVTEAKQ-ATELA 84

Query: 155 ERAKYIVEKAEQDKRSAIIRAQGEATSAQL 184
           +  +   E+ E+  +  I    G A    L
Sbjct: 85  QLGQVTFERVEKCSKPVIAAIHGAALGGGL 114


>pdb|3E98|A Chain A, Crystal Structure Of A Gaf Domain Containing Protein That
           Belongs To Pfam Duf484 Family (Pa5279) From Pseudomonas
           Aeruginosa At 2.43 A Resolution
 pdb|3E98|B Chain B, Crystal Structure Of A Gaf Domain Containing Protein That
           Belongs To Pfam Duf484 Family (Pa5279) From Pseudomonas
           Aeruginosa At 2.43 A Resolution
          Length = 252

 Score = 26.9 bits (58), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 24/94 (25%), Positives = 45/94 (47%), Gaps = 8/94 (8%)

Query: 138 KEFTSAIEAKQVAAQEAERAKYIVEKAEQDKRSAIIRAQGEATSAQLIGQAIANNPAFIT 197
           +E T+A++A+QVAA  ++  ++ VE  E      I    G+A S       +      + 
Sbjct: 25  QEPTAALDAEQVAAYLSQHPEFFVEHDELIPELRIPHQPGDAVS------LVERQVRLLR 78

Query: 198 LRKIEAAREIAQ--TIAHSANKVFLNSDDLLLNL 229
            R IE    ++Q   +A   +++F  +  L+L+L
Sbjct: 79  ERNIEXRHRLSQLXDVARENDRLFDKTRRLVLDL 112


  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
   0.317    0.131    0.353 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,748,507
Number of Sequences: 62578
Number of extensions: 197484
Number of successful extensions: 664
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 660
Number of HSP's gapped (non-prelim): 12
length of query: 239
length of database: 14,973,337
effective HSP length: 96
effective length of query: 143
effective length of database: 8,965,849
effective search space: 1282116407
effective search space used: 1282116407
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)