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= 041639
         (137 letters)

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

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



>pdb|3TTS|A Chain A, Crystal Structure Of Beta-Galactosidase From Bacillus
           Circulans Sp. Alkalophilus
 pdb|3TTS|B Chain B, Crystal Structure Of Beta-Galactosidase From Bacillus
           Circulans Sp. Alkalophilus
 pdb|3TTS|C Chain C, Crystal Structure Of Beta-Galactosidase From Bacillus
           Circulans Sp. Alkalophilus
 pdb|3TTS|D Chain D, Crystal Structure Of Beta-Galactosidase From Bacillus
           Circulans Sp. Alkalophilus
 pdb|3TTS|E Chain E, Crystal Structure Of Beta-Galactosidase From Bacillus
           Circulans Sp. Alkalophilus
 pdb|3TTS|F Chain F, Crystal Structure Of Beta-Galactosidase From Bacillus
           Circulans Sp. Alkalophilus
 pdb|3TTY|A Chain A, Crystal Structure Of Beta-Galactosidase From Bacillus
           Circulans Sp. Alkalophilus In Complex With Galactose
 pdb|3TTY|B Chain B, Crystal Structure Of Beta-Galactosidase From Bacillus
           Circulans Sp. Alkalophilus In Complex With Galactose
 pdb|3TTY|C Chain C, Crystal Structure Of Beta-Galactosidase From Bacillus
           Circulans Sp. Alkalophilus In Complex With Galactose
 pdb|3TTY|D Chain D, Crystal Structure Of Beta-Galactosidase From Bacillus
           Circulans Sp. Alkalophilus In Complex With Galactose
 pdb|3TTY|E Chain E, Crystal Structure Of Beta-Galactosidase From Bacillus
           Circulans Sp. Alkalophilus In Complex With Galactose
 pdb|3TTY|F Chain F, Crystal Structure Of Beta-Galactosidase From Bacillus
           Circulans Sp. Alkalophilus In Complex With Galactose
          Length = 675

 Score = 30.0 bits (66), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 27/113 (23%), Positives = 46/113 (40%), Gaps = 11/113 (9%)

Query: 5   HVFFILARTCLANIANATSMNDRLNNKIKLGYDLAIRLEASGGLTECWNTLM-EMKSCSN 63
           H F+        N  +     +R N +   G  L  R   S  L EC+     E+K  + 
Sbjct: 189 HTFYDWDEIVAPNALSEEWSGNRTNFQ---GISLDYRRFQSDSLLECFKMERDELKRWTP 245

Query: 64  EIVIF-----FLDSQDDIGLDCCRAIDIITRNCWPAMLTSLGFTAEEGNILRG 111
           +I +      F    D       + +D+++ + +P+M T   FTA   N++RG
Sbjct: 246 DIPVTTNLMGFYPELD--YFKWAKEMDVVSWDNYPSMDTPFSFTAMAHNLMRG 296


>pdb|4F2G|A Chain A, The Crystal Structure Of Ornithine Carbamoyltransferase
           From Burkholderia Thailandensis E264
          Length = 309

 Score = 28.9 bits (63), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 4/36 (11%)

Query: 79  DCCRAIDIITRNCWPAMLTSLGFTAEEGNILRGYCD 114
           + C+  D++T + W    TS+GF AE     R + D
Sbjct: 212 EACKGADLVTTDVW----TSMGFEAENEARKRAFAD 243


>pdb|3I9W|A Chain A, Crystal Structure Of The E. Coli Histidine Kinase Sensor
           Tors Sensor Domain
          Length = 290

 Score = 28.1 bits (61), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 15/54 (27%), Positives = 28/54 (51%)

Query: 20  NATSMNDRLNNKIKLGYDLAIRLEASGGLTECWNTLMEMKSCSNEIVIFFLDSQ 73
           NA ++  +LNN +K+     IR+E  G   +   TL  +   S+ + ++  DS+
Sbjct: 198 NAPTLEKQLNNAVKILQRRQIRIEDPGVRAQVATTLTTVSQYSDLLALYQQDSE 251


>pdb|2VSV|A Chain A, Crystal Structure Of The Pdz Domain Of Human Rhophilin-2
 pdb|2VSV|B Chain B, Crystal Structure Of The Pdz Domain Of Human Rhophilin-2
          Length = 109

 Score = 26.6 bits (57), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 15/60 (25%)

Query: 83  AIDIITRNCW-PAMLTSLGFTAEEGNI---LRG-----------YCDASFAPSLGGFVVI 127
            +D+ T N +  +M  S+ FTAEEG++   LRG           YC AS A +  G  ++
Sbjct: 10  GVDLGTENLYFQSMPRSIRFTAEEGDLGFTLRGNAPVQVHFLDPYCSASVAGAREGDYIV 69


  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
   0.326    0.139    0.431 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,550,511
Number of Sequences: 62578
Number of extensions: 125029
Number of successful extensions: 357
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 355
Number of HSP's gapped (non-prelim): 4
length of query: 137
length of database: 14,973,337
effective HSP length: 89
effective length of query: 48
effective length of database: 9,403,895
effective search space: 451386960
effective search space used: 451386960
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 46 (22.3 bits)