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= 028156
         (213 letters)

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

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



>pdb|1DE5|A Chain A, L-Rhamnose Isomerase
 pdb|1DE5|B Chain B, L-Rhamnose Isomerase
 pdb|1DE5|C Chain C, L-Rhamnose Isomerase
 pdb|1DE5|D Chain D, L-Rhamnose Isomerase
 pdb|1DE6|A Chain A, L-Rhamnose Isomerase
 pdb|1DE6|B Chain B, L-Rhamnose Isomerase
 pdb|1DE6|C Chain C, L-Rhamnose Isomerase
 pdb|1DE6|D Chain D, L-Rhamnose Isomerase
          Length = 426

 Score = 30.8 bits (68), Expect = 0.63,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 8/73 (10%)

Query: 138 HSRNFLQLPKP--VGVDFRASCFCHKNTIDMGYICSVCLSI---YCKHLKKCSTCGSVFG 192
           H +N+++  K   +G+DF  SCF H  + D   +     SI   +  H K      + FG
Sbjct: 121 HFKNWVEWAKANQLGLDFNPSCFSHPLSADGFTLSHADDSIRQFWIDHCKASRRVSAYFG 180

Query: 193 QAQTQSDEPSATN 205
           +   Q   PS  N
Sbjct: 181 E---QLGTPSVMN 190


>pdb|1D8W|A Chain A, L-Rhamnose Isomerase
 pdb|1D8W|B Chain B, L-Rhamnose Isomerase
 pdb|1D8W|C Chain C, L-Rhamnose Isomerase
 pdb|1D8W|D Chain D, L-Rhamnose Isomerase
          Length = 426

 Score = 30.4 bits (67), Expect = 0.66,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 8/73 (10%)

Query: 138 HSRNFLQLPKP--VGVDFRASCFCHKNTIDMGYICSVCLSI---YCKHLKKCSTCGSVFG 192
           H +N+++  K   +G+DF  SCF H  + D   +     SI   +  H K      + FG
Sbjct: 121 HFKNWVEWAKANQLGLDFNPSCFSHPLSADGFTLSHADDSIRQFWIDHCKASRRVSAYFG 180

Query: 193 QAQTQSDEPSATN 205
           +   Q   PS  N
Sbjct: 181 E---QLGTPSVXN 190


>pdb|2CW7|A Chain A, Crystal Structure Of Intein Homing Endonuclease Ii
          Length = 537

 Score = 27.3 bits (59), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 12/42 (28%), Positives = 21/42 (50%)

Query: 109 SYITGGVHHKPQQLDGLFQYLLTIFGTDLHSRNFLQLPKPVG 150
           SY     +  P+ LD + +     FG     RN++++PK +G
Sbjct: 302 SYSVKLYNEDPEVLDDMERLASRFFGKVRRGRNYVEIPKKIG 343


  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
   0.323    0.136    0.419 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,235,721
Number of Sequences: 62578
Number of extensions: 246163
Number of successful extensions: 417
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 416
Number of HSP's gapped (non-prelim): 4
length of query: 213
length of database: 14,973,337
effective HSP length: 95
effective length of query: 118
effective length of database: 9,028,427
effective search space: 1065354386
effective search space used: 1065354386
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)