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= 025843
         (247 letters)

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

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



>pdb|2O5A|A Chain A, Crystal Structure Of Q9kd89 From Bacillus Halodurans.
           Northeast Structural Genomics Target Bhr21
 pdb|2O5A|B Chain B, Crystal Structure Of Q9kd89 From Bacillus Halodurans.
           Northeast Structural Genomics Target Bhr21
          Length = 125

 Score = 70.9 bits (172), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 38/114 (33%), Positives = 62/114 (54%), Gaps = 4/114 (3%)

Query: 126 DAESLSFAVAMARVVSDVKAADIKVLFVKPLVYWTHFFIIATAFSRPQIDAIGSRIRDLA 185
           + E L  AV     V D KA  +  L  K +     FF+I    S  Q+ AI   ++ +A
Sbjct: 3   NQELLQLAV---NAVDDKKAEQVVALNXKGISLIADFFLICHGNSEKQVQAIAHELKKVA 59

Query: 186 EKEYGKVPSGDSKPNS-WTLLDFGDVVIHIFLPQQRAFYNLEEFYGNATTIELP 238
           +++  ++   +    + W L+D GDVV+H+F   +RA+YNLE+ +G+A T+EL 
Sbjct: 60  QEQGIEIKRLEGYEQARWVLIDLGDVVVHVFHKDERAYYNLEKLWGDAPTVELE 113


>pdb|3UPS|A Chain A, Crystal Structure Of Iojap-Like Protein From Zymomonas
           Mobilis
          Length = 136

 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/70 (37%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 162 FFIIATAFSRPQIDAIGSRIRDLAEKEYGKVPSGDSKPNS-WTLLDFGDVVIHIFLPQQR 220
           + +IA+  S  Q+ A   ++ D  +   G V   +  P + W LLD GD++IH+F P+ R
Sbjct: 52  YXVIASGRSSRQVTAXAQKLADRIKAATGYVSKIEGLPAADWVLLDAGDIIIHLFRPEVR 111

Query: 221 AFYNLEEFYG 230
           +FYNLE  +G
Sbjct: 112 SFYNLERXWG 121


>pdb|2ID1|A Chain A, X-Ray Crystal Structure Of Protein Cv0518 From
           Chromobacterium Violaceum, Northeast Structural Genomics
           Consortium Target Cvr5.
 pdb|2ID1|B Chain B, X-Ray Crystal Structure Of Protein Cv0518 From
           Chromobacterium Violaceum, Northeast Structural Genomics
           Consortium Target Cvr5
          Length = 130

 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/93 (32%), Positives = 46/93 (49%), Gaps = 1/93 (1%)

Query: 140 VSDVKAADIKVLFVKPLVYWTHFFIIATAFSRPQIDAIGSRIR-DLAEKEYGKVPSGDSK 198
           + D+K  DI  L    L       I+AT  S  Q+ A+ + ++  L E     V S   +
Sbjct: 14  LEDIKGKDIIELDTSKLTSLFQRXIVATGDSNRQVKALANSVQVKLKEAGVDIVGSEGHE 73

Query: 199 PNSWTLLDFGDVVIHIFLPQQRAFYNLEEFYGN 231
              W L+D GDVV+H+ LP  R +Y++E  +G 
Sbjct: 74  SGEWVLVDAGDVVVHVXLPAVRDYYDIEALWGG 106


>pdb|3A9R|A Chain A, X-Ray Structures Of Bacillus Pallidus D-Arabinose
           Isomerasecomplex With (4r)-2-Methylpentane-2,4-Diol
 pdb|3A9R|B Chain B, X-Ray Structures Of Bacillus Pallidus D-Arabinose
           Isomerasecomplex With (4r)-2-Methylpentane-2,4-Diol
 pdb|3A9R|C Chain C, X-Ray Structures Of Bacillus Pallidus D-Arabinose
           Isomerasecomplex With (4r)-2-Methylpentane-2,4-Diol
 pdb|3A9S|A Chain A, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
           Complex With Glycerol
 pdb|3A9S|B Chain B, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
           Complex With Glycerol
 pdb|3A9S|C Chain C, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
           Complex With Glycerol
 pdb|3A9T|A Chain A, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
           Complex With L-Fucitol
 pdb|3A9T|B Chain B, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
           Complex With L-Fucitol
 pdb|3A9T|C Chain C, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
           Complex With L-Fucitol
          Length = 595

 Score = 28.5 bits (62), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 11/31 (35%), Positives = 17/31 (54%)

Query: 67  NFKPRDLPLHFAYGKDAEDSSLSNVSEDTDE 97
            +  + LP    YGKD +D+  +N+ ED  E
Sbjct: 132 GYNQKGLPAFGIYGKDVQDAGDTNIPEDVKE 162


  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
   0.321    0.136    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,601,586
Number of Sequences: 62578
Number of extensions: 315198
Number of successful extensions: 739
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 734
Number of HSP's gapped (non-prelim): 4
length of query: 247
length of database: 14,973,337
effective HSP length: 96
effective length of query: 151
effective length of database: 8,965,849
effective search space: 1353843199
effective search space used: 1353843199
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)