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= 022958
         (289 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 = 29.6 bits (65), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 12/82 (14%)

Query: 127 ERVLPSIIHETLKAVVAQYNASQLITQRETVSREIRKILTERAANFNIALDDVSITSLTF 186
           +  LP +I+ T+KA   Q +++ L  QR    R   K++ E A  F         T++  
Sbjct: 187 DEFLPVLIYVTIKANPPQLHSNLLYIQR---YRRESKLVGEAAYFF---------TNILS 234

Query: 187 GKEFTSAIEAKQVAAQEAERAK 208
            + 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 = 2.8,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 12/79 (15%)

Query: 130 LPSIIHETLKAVVAQYNASQLITQRETVSREIRKILTERAANFNIALDDVSITSLTFGKE 189
           LP +I+ T+KA   Q +++ L  QR    R   K++ E A  F         T++   + 
Sbjct: 190 LPVLIYVTIKANPPQLHSNLLYIQR---YRRESKLVGEAAYFF---------TNILSAES 237

Query: 190 FTSAIEAKQVAAQEAERAK 208
           F S I+AK ++  EAE  K
Sbjct: 238 FISNIDAKSISLDEAEFEK 256


>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 = 27.7 bits (60), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 24/94 (25%), Positives = 45/94 (47%), Gaps = 8/94 (8%)

Query: 188 KEFTSAIEAKQVAAQEAERAKYIVEKAEQDKRSAIIRAQGEATSAQLIGQAIANNPAFIT 247
           +E T+A++A+QVAA  ++  ++ VE  E      I    G+A S       +      + 
Sbjct: 25  QEPTAALDAEQVAAYLSQHPEFFVEHDELIPELRIPHQPGDAVS------LVERQVRLLR 78

Query: 248 LRKIEAAREIAQ--TIAHSANKVFLNSDDLLLNL 279
            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    0.355 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,126,478
Number of Sequences: 62578
Number of extensions: 254750
Number of successful extensions: 773
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 770
Number of HSP's gapped (non-prelim): 11
length of query: 289
length of database: 14,973,337
effective HSP length: 98
effective length of query: 191
effective length of database: 8,840,693
effective search space: 1688572363
effective search space used: 1688572363
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: 51 (24.3 bits)