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= 018027
         (362 letters)

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

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



>pdb|1MQS|A Chain A, Crystal Structure Of Sly1p In Complex With An N-Terminal
           Peptide Of Sed5p
          Length = 671

 Score = 34.3 bits (77), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 33/113 (29%), Positives = 55/113 (48%), Gaps = 15/113 (13%)

Query: 49  QMPEKTGGGNSGMRFHVALTATDAIYSQWQSRIMYYWYKKVKDMPRSDM-GKFTRILHSG 107
           ++PE T   N+ +  H  + A  A+ SQ +S+ +  +++  +D   +    +F  IL  G
Sbjct: 391 KLPELTAKKNT-IDTHXNIFA--ALLSQLESKSLDTFFEVEQDPGSTKTRSRFLDILKDG 447

Query: 108 KADNLMDEIPSFVVDPLPE--GLDRGYIVLNRPWAFVQWLEKATIEEEYILMA 158
           K +NL D++ SF+V  L    GL         P  FVQ +E    E +Y + A
Sbjct: 448 KTNNLEDKLRSFIVLYLTSTTGL---------PKDFVQNVENYFKENDYDINA 491


>pdb|1CYX|A Chain A, Quinol Oxidase (Periplasmic Fragment Of Subunit Ii With
           Engineered Cu-A Binding Site)(Cyoa)
          Length = 205

 Score = 28.9 bits (63), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 10/54 (18%)

Query: 52  EKTGGGNSGMRFHVALTATDAIYSQWQSRIMYYWYKKVKDMPR--SDMGKFTRI 103
           E  G G+SGM+F    T   A + QW +        K K  P   SDM  F ++
Sbjct: 99  EICGPGHSGMKFKAIATPDRAAFDQWVA--------KAKQSPNTMSDMAAFEKL 144


>pdb|1TUF|A Chain A, Crystal Structure Of Diaminopimelate Decarboxylase From M.
           Jannaschi
 pdb|1TUF|B Chain B, Crystal Structure Of Diaminopimelate Decarboxylase From M.
           Jannaschi
          Length = 434

 Score = 28.5 bits (62), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 16/31 (51%)

Query: 280 WDPEVGKRFILHYTYGCDYNLKGELTYGKIG 310
           W+ E GK FI+ Y Y  + NL       K+G
Sbjct: 54  WEEETGKEFIVAYAYXANANLAITRLLAKLG 84


>pdb|1TWI|A Chain A, Crystal Structure Of Diaminopimelate Decarboxylase From M.
           Jannaschii In Co-Complex With L-Lysine
 pdb|1TWI|B Chain B, Crystal Structure Of Diaminopimelate Decarboxylase From M.
           Jannaschii In Co-Complex With L-Lysine
 pdb|1TWI|C Chain C, Crystal Structure Of Diaminopimelate Decarboxylase From M.
           Jannaschii In Co-Complex With L-Lysine
 pdb|1TWI|D Chain D, Crystal Structure Of Diaminopimelate Decarboxylase From M.
           Jannaschii In Co-Complex With L-Lysine
          Length = 434

 Score = 28.1 bits (61), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 16/31 (51%)

Query: 280 WDPEVGKRFILHYTYGCDYNLKGELTYGKIG 310
           W+ E GK FI+ Y Y  + NL       K+G
Sbjct: 54  WEEETGKEFIVAYAYKANANLAITRLLAKLG 84


  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    0.139    0.438 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,640,838
Number of Sequences: 62578
Number of extensions: 456361
Number of successful extensions: 894
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 890
Number of HSP's gapped (non-prelim): 14
length of query: 362
length of database: 14,973,337
effective HSP length: 100
effective length of query: 262
effective length of database: 8,715,537
effective search space: 2283470694
effective search space used: 2283470694
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)