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= 0034.0008.p
         (423 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

STM0563 [K] COG2207 AraC-type DNA-binding domain-containing prot...    68   2e-11
TM0563 [GEPR] COG0477 Permeases of the major facilitator superfa...    68   2e-11

>STM0563 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 284

 Score = 68.2 bits (165), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 10/236 (4%), Positives = 37/236 (15%), Gaps = 7/236 (2%)

Query: 67  ALTTLVNVAQIGVAFLIQKLPSRKWAMVTFIGLHRVLWSSTGLVPFIFPKEHWVTAFIVL 126
                + +       L                       S   +     + H  + + + 
Sbjct: 46  QGEAQLEMPTGDAMTLTPGKVVILPQNSAHRLRQS--GESPTHIVCGSLRLHTTSRYFLT 103

Query: 127 YTIAFIANTAGGVLWSSVISDLVPARVRGRYFGIRNTFLNALGSLVMYGGGLVLDRYPGG 186
                +         +S+  +     ++                       L +  +   
Sbjct: 104 ALPEVLCLAPPPHSPASIWINATILLLQQESERHLPGADVLYSQQCATLFTLAVRDWLS- 162

Query: 187 HGFLILYXXXXXXXXXXXXXXXXYPDVPFEKSEEKDFLPMLKKPLHDTLFMKSTLFLSAW 246
                                  +                L + +H +    + LF    
Sbjct: 163 -QAGTAKSVLNLLLHPRLGRVILHMLETPAHPWTV--ET-LAQRVHMSRASFAQLFRDVS 218

Query: 247 LLLQNLTVPLYSYVMLQLLHINYETLSLLNVSQTIFMMASFYVWGNLNAKYSNKRL 302
                  +      +            ++      +   S +    +         
Sbjct: 219 ATTPLAVLTTLRLQIAAQTLSREVLPVMVIAESVGYASESSFHKAFVREFGCTPGE 274


>TM0563 [GEPR] COG0477 Permeases of the major facilitator superfamily
          Length = 459

 Score = 68.2 bits (165), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 57/236 (24%), Positives = 104/236 (44%), Gaps = 7/236 (2%)

Query: 67  ALTTLVNVAQIGVAFLIQKLPSRKWAMVTFIGLHRVLWSSTGLVPFIFPKEHWVTAFIVL 126
           A+  ++   Q+  +F +QK   R++ +  F    R  +S   L+ F+   +     FIV 
Sbjct: 46  AIPPMMQFFQLFASFFVQKYRKRRFLVNVFNAFSR--FSFAFLIVFLLLGKTEPLIFIVA 103

Query: 127 YTIAFIANTAGGVLWSSVISDLVPARVRGRYFGIRNTFLNALGSLVMYGGGLVLDRYPGG 186
             I+ I        W+S + DLVP   RGR FG RN FL+   +L++Y    ++D +   
Sbjct: 104 LVISQIFAALSSSTWNSWMRDLVPPEERGRVFGNRNMFLSIGNALIIYLYSSIVDHFSS- 162

Query: 187 HGFLILYXXXXXXXXXXXXXXXXYPDVPFEKSEEKDFLPMLKKPLHDTLFMKSTLFLSAW 246
            GF+++                  PDVP +++     +P LK    D  FMK   F   W
Sbjct: 163 -GFVLVLLISTVGTVLSILAMNKIPDVPVKETGTG--IP-LKVVFKDENFMKFVFFTFYW 218

Query: 247 LLLQNLTVPLYSYVMLQLLHINYETLSLLNVSQTIFMMASFYVWGNLNAKYSNKRL 302
            +    +   Y Y +L+ L ++Y  ++ + +      M  + + G ++ +  +K +
Sbjct: 219 NMAVTFSSAFYHYHLLKNLGVDYTYIAYMMIVNNFVAMLVYRILGKVSDRVGHKTI 274


  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
   0.327    0.142    0.446 

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: 26,294,217
Number of extensions: 960977
Number of successful extensions: 3659
Number of sequences better than 1.0e-05: 5
Number of HSP's gapped: 3655
Number of HSP's successfully gapped: 5
Length of query: 423
Length of database: 38,378,431
Length adjustment: 109
Effective length of query: 314
Effective length of database: 25,807,025
Effective search space: 8103405850
Effective search space used: 8103405850
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 117 (49.7 bits)