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= psy663
         (275 letters)

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

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



>pdb|2IV2|X Chain X, Reinterpretation Of Reduced Form Of Formate Dehydrogenase
           H From E. Coli
 pdb|1AA6|A Chain A, Reduced Form Of Formate Dehydrogenase H From E. Coli
 pdb|1FDI|A Chain A, Oxidized Form Of Formate Dehydrogenase H From E. Coli
           Complexed With The Inhibitor Nitrite
 pdb|1FDO|A Chain A, Oxidized Form Of Formate Dehydrogenase H From E. Coli
          Length = 715

 Score = 28.5 bits (62), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 11/99 (11%)

Query: 144 APPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMV 203
            P   Q  G  + +        QKF+ A+     N+  C       P V G   S+G+  
Sbjct: 99  GPDAIQTTGSSRGTGNETNYVMQKFARAVIG--TNNVDCCARVXHGPSVAGLHQSVGN-- 154

Query: 204 RSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSD 242
              + N IN I + +L+ +F        NP+D   IV++
Sbjct: 155 -GAMSNAINEIDNTDLVFVFGY------NPADSHPIVAN 186


>pdb|1W6S|A Chain A, The High Resolution Structure Of Methanol Dehydrogenase
           From Methylobacterium Extorquens
 pdb|1W6S|C Chain C, The High Resolution Structure Of Methanol Dehydrogenase
           From Methylobacterium Extorquens
          Length = 599

 Score = 27.7 bits (60), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 12/42 (28%), Positives = 26/42 (61%)

Query: 89  AQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEV 130
           A+KLL H D +GI++T+++     +   ++ +  NV +S ++
Sbjct: 322 ARKLLTHPDRNGIVYTLDRTDGALVSANKLDDTVNVFKSVDL 363


>pdb|1H4I|A Chain A, Methylobacterium Extorquens Methanol Dehydrogenase
 pdb|1H4I|C Chain C, Methylobacterium Extorquens Methanol Dehydrogenase
          Length = 599

 Score = 27.7 bits (60), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 12/42 (28%), Positives = 26/42 (61%)

Query: 89  AQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEV 130
           A+KLL H D +GI++T+++     +   ++ +  NV +S ++
Sbjct: 322 ARKLLTHPDRNGIVYTLDRTDGALVSANKLDDTVNVFKSVDL 363


>pdb|1H4J|A Chain A, Methylobacterium Extorquens Methanol Dehydrogenase D303e
           Mutant
 pdb|1H4J|C Chain C, Methylobacterium Extorquens Methanol Dehydrogenase D303e
           Mutant
 pdb|1H4J|E Chain E, Methylobacterium Extorquens Methanol Dehydrogenase D303e
           Mutant
 pdb|1H4J|G Chain G, Methylobacterium Extorquens Methanol Dehydrogenase D303e
           Mutant
          Length = 599

 Score = 27.7 bits (60), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 12/42 (28%), Positives = 26/42 (61%)

Query: 89  AQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEV 130
           A+KLL H D +GI++T+++     +   ++ +  NV +S ++
Sbjct: 322 ARKLLTHPDRNGIVYTLDRTDGALVSANKLDDTVNVFKSVDL 363


  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    0.135    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,533,178
Number of Sequences: 62578
Number of extensions: 275497
Number of successful extensions: 566
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 552
Number of HSP's gapped (non-prelim): 22
length of query: 275
length of database: 14,973,337
effective HSP length: 97
effective length of query: 178
effective length of database: 8,903,271
effective search space: 1584782238
effective search space used: 1584782238
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: 51 (24.3 bits)