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= 024362
         (268 letters)

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

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



>pdb|1YDO|A Chain A, Crystal Structure Of The Bacillis Subtilis Hmg-Coa Lyase,
           Northeast Structural Genomics Target Sr181.
 pdb|1YDO|B Chain B, Crystal Structure Of The Bacillis Subtilis Hmg-Coa Lyase,
           Northeast Structural Genomics Target Sr181.
 pdb|1YDO|C Chain C, Crystal Structure Of The Bacillis Subtilis Hmg-Coa Lyase,
           Northeast Structural Genomics Target Sr181.
 pdb|1YDO|D Chain D, Crystal Structure Of The Bacillis Subtilis Hmg-Coa Lyase,
           Northeast Structural Genomics Target Sr181
          Length = 307

 Score = 29.3 bits (64), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 22/42 (52%)

Query: 208 ALRDLIDFLKIKKREQGESKAKGVKEERAGEAEIEGKASGTC 249
           ALRD ID  K   RE+G + A  V  +R  E  +EG  +  C
Sbjct: 58  ALRDAIDVAKGIDREKGVTYAALVPNQRGLENALEGGINEAC 99


>pdb|1JLH|A Chain A, Human Glucose-6-Phosphate Isomerase
 pdb|1JLH|B Chain B, Human Glucose-6-Phosphate Isomerase
 pdb|1JLH|C Chain C, Human Glucose-6-Phosphate Isomerase
 pdb|1JLH|D Chain D, Human Glucose-6-Phosphate Isomerase
          Length = 558

 Score = 29.3 bits (64), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 49/224 (21%), Positives = 85/224 (37%), Gaps = 31/224 (13%)

Query: 7   VKKMIMDDLEMFLKRKDFHRRVGRGKSSLIAGM----ANFLNFDVYDLELSALLRGNMEL 62
           VK+  +D   MF    +F   VG G+ SL + +    A  + FD ++  LS     +   
Sbjct: 253 VKEFGIDPQNMF----EFWDWVG-GRYSLWSAIGLSIALHVGFDNFEQLLSGAHWMDQHF 307

Query: 63  RNLLIATENK---SLLVVEDIDC----------SIELQNRHAQALAVNPMVSNMNYTARP 109
           R   +        +LL +  I+C            +  +R A       M SN  Y  + 
Sbjct: 308 RTTPLEKNAPVLLALLGIWYINCFGCETHAMLPYDQYLHRFAAYFQQGDMESNGKYITKS 367

Query: 110 GINQGPQVGSKCWAPTTLESEHPFSLEIEELTEKV---MVTPADVAERLMRSEVPEVALR 166
           G     Q G   W       +H F   I + TE +    + P      + +    ++ L 
Sbjct: 368 GTRVDHQTGPIVWGEPGTNGQHAFYQLIHQGTEMIPCDFLIPVQTQHPIRKGLHHKILLA 427

Query: 167 DLI----DFLKNKKREQEVEELTEKVMVTPADVAERLMRSEVPE 206
           + +      ++ K  E+  +EL +    +P D+ ERL+  +V E
Sbjct: 428 NFLAQTEALMRGKSTEEARKEL-QAAGKSPEDL-ERLLPHKVFE 469


>pdb|1G8S|A Chain A, Methanococcus Jannaschii Fibrillarin Pre-Rrna Processing
           Protein
          Length = 230

 Score = 28.1 bits (61), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 137 IEELTEKVMVTPADVAERLMRSEVPEVALR-DLIDFLKNKKREQEVEELTEKVMVTPADV 195
           + ++ +K +V   + A R+MR  +   A R ++I  L +  + QE   + EKV V   DV
Sbjct: 92  VADIADKGIVYAIEYAPRIMRELLDACAERENIIPILGDANKPQEYANIVEKVDVIYEDV 151

Query: 196 AE 197
           A+
Sbjct: 152 AQ 153


  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
   0.315    0.132    0.362 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,083,930
Number of Sequences: 62578
Number of extensions: 268905
Number of successful extensions: 764
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 758
Number of HSP's gapped (non-prelim): 17
length of query: 268
length of database: 14,973,337
effective HSP length: 97
effective length of query: 171
effective length of database: 8,903,271
effective search space: 1522459341
effective search space used: 1522459341
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)