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= 008466
         (564 letters)

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

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



>pdb|2O8B|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
 pdb|2O8C|B Chain B, Human Mutsalpha (msh2/msh6) Bound To Adp And An
           O6-methyl-guanine T Mispair
 pdb|2O8D|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
 pdb|2O8E|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
           ADP BOUND TO Msh2 Only
 pdb|2O8F|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE
           T INSERT
          Length = 1022

 Score = 30.0 bits (66), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 16/37 (43%), Positives = 21/37 (56%)

Query: 503 GREADKLQHQGYGTLLMEEAERIALGEHRSRKMAVIS 539
           GR +D L  +GY    +E+ E   + E R RKMA IS
Sbjct: 129 GRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHIS 165


>pdb|4AP6|A Chain A, Crystal Structure Of Human Pofut2 E54a Mutant In Complex
           With Gdp- Fucose
 pdb|4AP6|B Chain B, Crystal Structure Of Human Pofut2 E54a Mutant In Complex
           With Gdp- Fucose
 pdb|4AP6|C Chain C, Crystal Structure Of Human Pofut2 E54a Mutant In Complex
           With Gdp- Fucose
 pdb|4AP6|D Chain D, Crystal Structure Of Human Pofut2 E54a Mutant In Complex
           With Gdp- Fucose
          Length = 422

 Score = 28.5 bits (62), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 36/128 (28%), Positives = 47/128 (36%), Gaps = 32/128 (25%)

Query: 449 GWETFLSYEDTRQDILVGLLRLRKCGRNVTCPELMGKCSIVRELHVYGT-AVPVHGREAD 507
           GW  F  YE+TR             G NV+C  + G  SIV  L +  T A  V    A+
Sbjct: 170 GW--FWGYEETR-------------GLNVSCLSVQGSASIVAPLLLRNTSARSVMLDRAE 214

Query: 508 KLQHQGYG---------TLLMEEAERIALGEHRSRKMAVISGVGTRHYYR-------KLG 551
            L H  YG         +++     R    E RSR +          +         KLG
Sbjct: 215 NLLHDHYGGKEYWDTRRSMVFARHLREVGDEFRSRHLNSTDDADRIPFQEDWMKMKVKLG 274

Query: 552 YELEGPYM 559
             L GPY+
Sbjct: 275 SALGGPYL 282


  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    0.138    0.415 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,020,930
Number of Sequences: 62578
Number of extensions: 698400
Number of successful extensions: 1370
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1369
Number of HSP's gapped (non-prelim): 3
length of query: 564
length of database: 14,973,337
effective HSP length: 104
effective length of query: 460
effective length of database: 8,465,225
effective search space: 3894003500
effective search space used: 3894003500
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: 54 (25.4 bits)