BLASTP 2.2.18 [Mar-02-2008]


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= 0317.0003.p
         (98 letters)

Database: COG 
           115,334 sequences; 38,378,431 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

BS_yqiD [H] COG0142 Geranylgeranyl pyrophosphate synthase              51   5e-07
slr0739 [H] COG0142 Geranylgeranyl pyrophosphate synthase              50   1e-06
PA4043 [H] COG0142 Geranylgeranyl pyrophosphate synthase               48   3e-06
alr0213 [H] COG0142 Geranylgeranyl pyrophosphate synthase              48   3e-06

>BS_yqiD [H] COG0142 Geranylgeranyl pyrophosphate synthase
          Length = 272

 Score = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 41/66 (62%), Gaps = 1/66 (1%)

Query: 17 LRQPLKEYIAEISSLVMSELEAALPEEWSVPGNLKDAMNYSLQAGGKRLRPLLVIAACEA 76
          +   L  ++A+    + ++L +   E+  +P +LK +M YSLQAGGKRLRPL+V+A   A
Sbjct: 1  MTNKLTSFLADRKKTIENQL-SVYTEKLDMPDSLKKSMLYSLQAGGKRLRPLIVLAVLNA 59

Query: 77 LGGSRQ 82
           G S +
Sbjct: 60 YGKSEK 65


>slr0739 [H] COG0142 Geranylgeranyl pyrophosphate synthase
          Length = 211

 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 6/47 (12%), Positives = 11/47 (23%), Gaps = 2/47 (4%)

Query: 36 LEAALPEEWSV--PGNLKDAMNYSLQAGGKRLRPLLVIAACEALGGS 80
                    +        A + S+     +L P+    A     G 
Sbjct: 23 ELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGV 69


>PA4043 [H] COG0142 Geranylgeranyl pyrophosphate synthase
          Length = 295

 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/64 (45%), Positives = 38/64 (59%), Gaps = 4/64 (6%)

Query: 25 IAEISSLVMSELEAALPEEWSVP----GNLKDAMNYSLQAGGKRLRPLLVIAACEALGGS 80
          IA   +   + ++AAL   +  P      L +AM YS+  GGKR+RPLL  AACEALGG+
Sbjct: 2  IAAYQARCQARVDAALDALFVAPREELQRLYEAMRYSVMNGGKRVRPLLAYAACEALGGA 61

Query: 81 RQAA 84
           Q A
Sbjct: 62 PQRA 65


>alr0213 [H] COG0142 Geranylgeranyl pyrophosphate synthase
          Length = 359

 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 7/64 (10%), Positives = 17/64 (26%), Gaps = 2/64 (3%)

Query: 21 LKEYIAEISSLVMSELEAALPEEWSVPGNLKDAMNYSLQAGGKRLRPLLVIAACEALGGS 80
           +      +S +++ ++A               +  +   G  RL   L + A       
Sbjct: 18 QRLRELAPASKMVAVVKANAYGHG--LLETARTLPDADAFGVARLEEALRLRAGGITKPV 75

Query: 81 RQAA 84
              
Sbjct: 76 LLLE 79


  Database: COG
    Posted date:  Aug 3, 2010  9:58 AM
  Number of letters in database: 38,378,431
  Number of sequences in database:  115,334
  
Lambda     K      H
   0.314    0.131    0.388 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 115334
Number of Hits to DB: 6,953,958
Number of extensions: 226003
Number of successful extensions: 431
Number of sequences better than 1.0e-05: 4
Number of HSP's gapped: 435
Number of HSP's successfully gapped: 4
Length of query: 98
Length of database: 38,378,431
Length adjustment: 67
Effective length of query: 31
Effective length of database: 30,651,053
Effective search space: 950182643
Effective search space used: 950182643
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 109 (46.6 bits)