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= 0598.0015.p
         (110 letters)

Database: pfamseq 
           9,421,015 sequences; 3,060,696,203 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Q9KFJ6.1 Q9KFJ6_BACHD Transcriptional regulator (AraC/XylS family)     68   3e-10
B1D8A9.1 B1D8A9_9BACL Transcriptional regulator, AraC family           64   6e-09
B3KFU0.1 B3KFU0_9BACI Helix-turn-helix-domain containing protein...    60   6e-08
Q65FY6.1 Q65FY6_BACLD YtdP                                             56   1e-06

>Q9KFJ6.1 Q9KFJ6_BACHD Transcriptional regulator (AraC/XylS family)
          Length = 769

 Score = 67.8 bits (164), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 38/106 (35%), Positives = 58/106 (54%), Gaps = 1/106 (0%)

Query: 1   VYVPVRRIIEAAKAEVSKDKPAAGGRDDEFQIIGDHLDILRTSRTRLTVQLQGQTRQLKE 60
           +Y PV+ + +   A  S    A     DEF++I  H+  +      L  +LQGQ +QLK+
Sbjct: 325 IYRPVQELYQMITATFSAGS-AKKPPKDEFELIHAHIHNVLDLNNELEEKLQGQIKQLKQ 383

Query: 61  YFIRKLLLGQLKPSEINEKLDQLQYVSSGEWNCVLTVQIDTLKGTR 106
           +F+  L+ G + PSEI  K +  QY        VLT+QID+L+GT+
Sbjct: 384 FFVLNLIKGHMSPSEIETKYETFQYPKDWRQLHVLTLQIDSLEGTK 429


>B1D8A9.1 B1D8A9_9BACL Transcriptional regulator, AraC family
          Length = 768

 Score = 63.5 bits (153), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 36/109 (33%), Positives = 65/109 (59%), Gaps = 6/109 (5%)

Query: 1   VYVPVRRIIEAAKAEVSKDKPAAGGRDDEFQIIGDHLDILRTSRTRLTVQLQGQTRQLKE 60
           +Y P++ +++       + +     R +EFQ IG+ +  L  S+TRL  +LQ   +Q++ 
Sbjct: 320 MYSPIQMLLKQMNVRTPEIRQT---RKNEFQAIGEQIQQLFQSKTRLESELQQHLKQVRT 376

Query: 61  YFIRKLLLGQLKPSEINEKLDQLQY---VSSGEWNCVLTVQIDTLKGTR 106
            F+ K L GQ+K +++ EKL++  Y   ++S +   V+TVQID+L+ TR
Sbjct: 377 LFLAKALQGQVKNNDLTEKLERFGYSEQLNSWDVMAVITVQIDSLEDTR 425


>B3KFU0.1 B3KFU0_9BACI Helix-turn-helix-domain containing protein AraC type
          Length = 770

 Score = 60.1 bits (144), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 34/109 (31%), Positives = 59/109 (54%), Gaps = 6/109 (5%)

Query: 1   VYVPVRRIIEAAKAEVSKDKPAAGGRDDEFQIIGDHLDILRTSRTRLTVQLQGQTRQLKE 60
           +Y P+R I E     V +       +  E Q+I +H+  +  S T+L  +L+  ++Q++ 
Sbjct: 321 MYTPIRHIFENI---VERLPEIQANKKSELQVIDEHIRDMFNSNTKLRSELRQTSQQVRT 377

Query: 61  YFIRKLLLGQLKPSEINEKLDQLQY---VSSGEWNCVLTVQIDTLKGTR 106
           +F+ KL LG++ P E  E+++   +   VS+ E   V T+QID L  TR
Sbjct: 378 FFLHKLFLGKINPPEAMEQIEMFGFKEQVSTWEQLAVFTLQIDMLDETR 426


>Q65FY6.1 Q65FY6_BACLD YtdP
          Length = 769

 Score = 55.8 bits (133), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/109 (31%), Positives = 59/109 (54%), Gaps = 10/109 (9%)

Query: 2   YVPVRRIIEAAK-----AEVSKDKPAAGGRDDEFQIIGDHLDILRTSRTRLTVQLQGQTR 56
           Y P++ + E+       A+  ++KP      +EF++I  ++  ++     L V+++ Q  
Sbjct: 323 YRPIKVLYESVSGFSPGADSVQEKP-----KNEFELIERNIKEMKNKNHDLKVRVEQQVT 377

Query: 57  QLKEYFIRKLLLGQLKPSEINEKLDQLQYVSSGEWNCVLTVQIDTLKGT 105
           QLK+YF+ +LLLG+L   EI ++   L +        V T+QIDTLK T
Sbjct: 378 QLKQYFLTRLLLGKLSEEEIKDRFTGLGFPEDWSHLSVFTLQIDTLKDT 426


  Database: pfamseq
    Posted date:  Aug 5, 2010  3:22 PM
  Number of letters in database: 3,060,696,203
  Number of sequences in database:  9,421,015
  
Lambda     K      H
   0.319    0.137    0.384 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 9421015
Number of Hits to DB: 584,450,753
Number of extensions: 19836447
Number of successful extensions: 49624
Number of sequences better than 1.0e-05: 4
Number of HSP's gapped: 49625
Number of HSP's successfully gapped: 4
Length of query: 110
Length of database: 3,060,696,203
Length adjustment: 77
Effective length of query: 33
Effective length of database: 2,335,278,048
Effective search space: 77064175584
Effective search space used: 77064175584
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 126 (53.1 bits)