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= 0423.0001.p
         (242 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

alr3988 [L] COG0419 ATPase involved in DNA repair                      66   5e-11
STM1636 [E] COG0765 ABC-type amino acid transport system, permea...    50   4e-06

>alr3988 [L] COG0419 ATPase involved in DNA repair
          Length = 673

 Score = 66.2 bits (160), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 9/183 (4%), Positives = 27/183 (14%), Gaps = 20/183 (10%)

Query: 3   PILLKVAGLQSYREQQEIDFGSLTETGLFGIFGPTGSGKSSVLDAITLAMYGKVERAVNG 62
               +   ++       +                T      +      A +       N 
Sbjct: 3   LNPGQQQAVEFVTGP-CLVLAGAGSGK---TRVITNKIAHLIRGCGYQARHIAAVTFTNK 58

Query: 63  TQGIMNHSEDQLSVSFTFELTSSSGPRRYRVERKFKRTGDQSVS---NTISRFIEVAADG 119
                   E         E    +                +         + F       
Sbjct: 59  --AAREMKERVGQTLGRKE----ARGLMISTFHTLGLDIIKREYAALGMKANFSLFDDTD 112

Query: 120 DHVLADKLADVTRCVEEHIGLKMDDFTRAVVLPQGKFAEFLSLRGVDRRQMLQRLFHLEQ 179
              L          + E +        + ++     +   L          +     +  
Sbjct: 113 QLALLK-------ELTEGLIEDDKVLLQQLISTISNWKNDLKTPSQAAASAIGERDRIFA 165

Query: 180 YGD 182
           +  
Sbjct: 166 HCY 168


>STM1636 [E] COG0765 ABC-type amino acid transport system, permease
           component
          Length = 226

 Score = 49.7 bits (117), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 8/136 (5%), Positives = 21/136 (15%), Gaps = 10/136 (7%)

Query: 27  ETGLFGIFGPTGSGKSSVLDAITLAMYGKVERAVNGTQGIMNHSEDQLS-VSFTFELTSS 85
                       S    +   I   +       V     +          +   F     
Sbjct: 22  GIKETCKLALIVSITGFLWGIIIFFLSLSHRPVVKAITRLYMDFFIGTPLILILFV---- 77

Query: 86  SGPRRYRVERKFKRTGDQSVSNTISRFIEVAADGDH-VLADKLADVTRCVEEHIGLKMDD 144
                 +                    + V A     +     A      E  +   ++ 
Sbjct: 78  IYYGLPQSGIHLSSF--TVAVT--GFTLNVGAYNAAYMTTAYNALNKYETEAAVVQGLNK 133

Query: 145 FTRAVVLPQGKFAEFL 160
               + +   +     
Sbjct: 134 RQVFLWIILPQVLLSS 149


  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
   0.318    0.135    0.376 

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: 15,688,193
Number of extensions: 538813
Number of successful extensions: 2905
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 2910
Number of HSP's successfully gapped: 2
Length of query: 242
Length of database: 38,378,431
Length adjustment: 103
Effective length of query: 139
Effective length of database: 26,499,029
Effective search space: 3683365031
Effective search space used: 3683365031
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 114 (48.5 bits)