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= 004522
         (747 letters)

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

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



>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
 pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
          Length = 1724

 Score = 30.8 bits (68), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 33/116 (28%), Positives = 53/116 (45%), Gaps = 12/116 (10%)

Query: 36   LSVIDCLKNQVAADHFVSVQRRVEKNRQKLIGVTNHLYRLSLERRNNQTINTHGSVDLLT 95
            ++ ++ L  QV  D +   Q R+ K    L G T+    L L  + N  I+T    D+L+
Sbjct: 978  ITPMEALAEQVYMDWYEKFQDRLNKKVVLLTGETST--DLKLLGKGNIIISTPEKWDILS 1035

Query: 96   KRQREALGVQNGIDVSSGDRDSHISQEDGYASTAV-----YGSSNPTKNIIRPIKL 146
            +R ++   VQN I++   D    I  E+G     +     Y SS     I RPI++
Sbjct: 1036 RRWKQRKNVQN-INLFVVDEVHLIGGENGPVLEVICSRMRYISS----QIERPIRI 1086


>pdb|4F91|B Chain B, Brr2 Helicase Region
          Length = 1724

 Score = 30.4 bits (67), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 33/116 (28%), Positives = 53/116 (45%), Gaps = 12/116 (10%)

Query: 36   LSVIDCLKNQVAADHFVSVQRRVEKNRQKLIGVTNHLYRLSLERRNNQTINTHGSVDLLT 95
            ++ ++ L  QV  D +   Q R+ K    L G T+    L L  + N  I+T    D+L+
Sbjct: 978  ITPMEALAEQVYMDWYEKFQDRLNKKVVLLTGETST--DLKLLGKGNIIISTPEKWDILS 1035

Query: 96   KRQREALGVQNGIDVSSGDRDSHISQEDGYASTAV-----YGSSNPTKNIIRPIKL 146
            +R ++   VQN I++   D    I  E+G     +     Y SS     I RPI++
Sbjct: 1036 RRWKQRKNVQN-INLFVVDEVHLIGGENGPVLEVICSRMRYISS----QIERPIRI 1086


>pdb|1V53|A Chain A, The Crystal Structure Of 3-Isopropylmalate Dehydrogenase
           From Bacillus Coagulans
 pdb|1V53|B Chain B, The Crystal Structure Of 3-Isopropylmalate Dehydrogenase
           From Bacillus Coagulans
          Length = 366

 Score = 30.0 bits (66), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 35/151 (23%), Positives = 61/151 (40%), Gaps = 38/151 (25%)

Query: 415 SPSKSKLVGKVGICKRKSKRVAERALVCKQKKQKKMAAFDLDSVASGGVLPSDMKLRSTS 474
            P ++++V  +   + + +R+ E+A    Q ++KK+A+ D  +V              +S
Sbjct: 150 GPGENEVVDTLAYTREEIERIIEKAFQLAQIRRKKLASVDKANVL------------ESS 197

Query: 475 RKENEDANXXXXXXXXXXXXGKTRKKEMQIQDSRNLMHVRVPLGSSQEIVSNPPAISTND 534
           R   E A              +T KK   ++ S  L+       +S ++++NP       
Sbjct: 198 RMWREIAE-------------ETAKKYPDVELSHMLVD-----STSMQLIANPGQF---- 235

Query: 535 SLRKDEFVAENMCKQELSDEKSWKTIEKGLF 565
               D  V ENM    LSDE S  T   G+ 
Sbjct: 236 ----DVIVTENMFGDILSDEASVITGSLGML 262


>pdb|2AYQ|A Chain A, 3-Isopropylmalate Dehydrogenase From The Moderate
           Facultative Thermophile, Bacillus Coagulans
 pdb|2AYQ|B Chain B, 3-Isopropylmalate Dehydrogenase From The Moderate
           Facultative Thermophile, Bacillus Coagulans
          Length = 366

 Score = 30.0 bits (66), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 35/151 (23%), Positives = 61/151 (40%), Gaps = 38/151 (25%)

Query: 415 SPSKSKLVGKVGICKRKSKRVAERALVCKQKKQKKMAAFDLDSVASGGVLPSDMKLRSTS 474
            P ++++V  +   + + +R+ E+A    Q ++KK+A+ D  +V              +S
Sbjct: 150 GPGENEVVDTLAYTREEIERIIEKAFQLAQIRRKKLASVDKANVL------------ESS 197

Query: 475 RKENEDANXXXXXXXXXXXXGKTRKKEMQIQDSRNLMHVRVPLGSSQEIVSNPPAISTND 534
           R   E A              +T KK   ++ S  L+       +S ++++NP       
Sbjct: 198 RMWREIAE-------------ETAKKYPDVELSHMLVD-----STSMQLIANPGQF---- 235

Query: 535 SLRKDEFVAENMCKQELSDEKSWKTIEKGLF 565
               D  V ENM    LSDE S  T   G+ 
Sbjct: 236 ----DVIVTENMFGDILSDEASVITGSLGML 262


  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
   0.316    0.130    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,335,569
Number of Sequences: 62578
Number of extensions: 778353
Number of successful extensions: 1700
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 1693
Number of HSP's gapped (non-prelim): 29
length of query: 747
length of database: 14,973,337
effective HSP length: 106
effective length of query: 641
effective length of database: 8,340,069
effective search space: 5345984229
effective search space used: 5345984229
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: 55 (25.8 bits)