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= psy5385
         (180 letters)

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

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



>pdb|4DVJ|A Chain A, Crystal Structure Of A Putative Zinc-Dependent Alcohol
           Dehydrogenase Protein From Rhizobium Etli Cfn 42
 pdb|4DVJ|B Chain B, Crystal Structure Of A Putative Zinc-Dependent Alcohol
           Dehydrogenase Protein From Rhizobium Etli Cfn 42
          Length = 363

 Score = 29.6 bits (65), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 31/72 (43%), Gaps = 15/72 (20%)

Query: 112 SYLFTRSPQPTCRCGDILTTVKHILTCPLDIQLRSSLPNPPSLTD-ETTGVDAK------ 164
           S L    P+P     DIL  VK +   P+D ++R S   PP  TD +  G DA       
Sbjct: 39  SLLDIELPKPAPAGHDILVEVKAVSVNPVDYKVRRS--TPPDGTDWKVIGYDAAGIVSAV 96

Query: 165 ------FKPNEE 170
                 F+P +E
Sbjct: 97  GPDVTLFRPGDE 108


>pdb|1EF8|A Chain A, Crystal Structure Of Methylmalonyl Coa Decarboxylase
 pdb|1EF8|B Chain B, Crystal Structure Of Methylmalonyl Coa Decarboxylase
 pdb|1EF8|C Chain C, Crystal Structure Of Methylmalonyl Coa Decarboxylase
 pdb|1EF9|A Chain A, The Crystal Structure Of Methylmalonyl Coa Decarboxylase
          Complexed With 2s-Carboxypropyl Coa
          Length = 261

 Score = 29.3 bits (64), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 13/37 (35%), Positives = 22/37 (59%)

Query: 54 LMNLCRTQTECLIVLVPNGNKLKSIKPNIEKWPSSNR 90
          L +L R +  C+I+  P+G+K+ S   +I + PS  R
Sbjct: 40 LSDLNRPEIRCIILRAPSGSKVFSAGHDIHELPSGGR 76


  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
   0.318    0.131    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,975,916
Number of Sequences: 62578
Number of extensions: 177156
Number of successful extensions: 377
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 375
Number of HSP's gapped (non-prelim): 3
length of query: 180
length of database: 14,973,337
effective HSP length: 93
effective length of query: 87
effective length of database: 9,153,583
effective search space: 796361721
effective search space used: 796361721
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)