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= 0005.0295.p
         (262 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311571|ref|YP_003775663.1| LysR family transcription regul...   113   2e-26
gi|300310617|ref|YP_003774709.1| LysR family transcription regul...    56   3e-09

>gi|300311571|ref|YP_003775663.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 313

 Score =  113 bits (282), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 88/271 (32%), Positives = 136/271 (50%), Gaps = 16/271 (5%)

Query: 1   LLQRTTTGVVPTDAGLAFWHQAQLALRHVDEAARAAQHA--RMSGHVSVGFAPSTASVLA 58
           LL R+  GV+ TDAG  F+  A   L+ V +A +A   +  + SG V++G   S ++ LA
Sbjct: 47  LLHRSAQGVIATDAGKVFYEHALAILKQVQDAKQAVGQSADKPSGTVALGIPQSVSNALA 106

Query: 59  LTFMNGLRARYPDIRLHLVESLSGNLATMLNARQLDLAILFETDVAKRLSATPLLDER-L 117
           L  +N +R+ YP+I L L E L+GNL T L + +++LA+LF+       +ATP+++E  +
Sbjct: 107 LPLLNAVRSTYPEITLQLTEELTGNLITQLKSGRINLAVLFDDGQLSSFAATPMIEEEMM 166

Query: 118 FVVGSHQLIGMPKGKQVRLKDIGALPLVMPSGTHGLRAIVATAFAQAKREPNIVAEIDGL 177
           ++  +    G+   K V L      PL++P   HG+R  +           + V EI+ +
Sbjct: 167 YITRAKSQYGVAGRKSVPLARAIQAPLILPGLAHGVRPRIENLVRSQGMSLDNVIEINSV 226

Query: 178 AILMDVVRAGLAATIQPGAAASRLPASVVRLVQVADK--GVRRRNLLA-----SLPEDEL 230
           AIL   + A + ATI P A    L A + R   VA +  G R    LA     ++P   L
Sbjct: 227 AILKSAILADIGATILPVAP---LLADIERGEMVAHRIAGERISRTLALCASRNIP---L 280

Query: 231 SPAALATRIVLKDVVRELLSESHWMGASLHE 261
           + AA A   ++ DV  EL     W    L E
Sbjct: 281 TTAAAAVEQLVLDVTDELCRSGRWGHTELLE 311


>gi|300310617|ref|YP_003774709.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 303

 Score = 56.2 bits (134), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 65/251 (25%), Positives = 110/251 (43%), Gaps = 8/251 (3%)

Query: 1   LLQRTTTGVVPTDAGLAFWHQAQLALRHVDEAARAAQHARMS--GHVSVGFAPSTASVLA 58
           L QR   GV+PT+ G+    + +  L   ++     Q A  +  G V +G  PS A  L 
Sbjct: 47  LFQRNGRGVIPTELGMRVAPRVRAWLATTEQLTNDIQSAAGTPIGRVRMGILPSAAHPLV 106

Query: 59  LTFMNGLRARYPDIRLHLVESLSGNLATMLNARQLDLAILFETDVAKRLSATPLLDERLF 118
            T    ++ RYP I+L + E     L T L+   +DLA+LF      +     +     +
Sbjct: 107 STLYQQIQQRYPQIQLSVREGQGAQLDTWLDNGYVDLALLFRHGANAKNGDLYITKTDTY 166

Query: 119 VVGSHQLIGMPKGKQVRLKDIGALPLVMPSGTHGLRAIVATAFAQAKREPNIVAEIDGLA 178
           +VG+     + +G  V    +  LPLV     +  R  +     +     N+  E D L+
Sbjct: 167 LVGAPD-DPLVQGPTVPFASLDRLPLVSFCRPNSWRDRLDHLSIEHGITLNVQIEADSLS 225

Query: 179 ILMDVV-RAGLAATIQPGAAASRLPASVVRLVQVADKGVRRRNLLASLPEDELSPAALAT 237
           I   +V   G+ A + P A AS +  + ++  ++    + R   LA     EL+   LA 
Sbjct: 226 IQEHLVENGGVYALLGPYAIASAVRKNRLKAARIIAPEITRHIALAMSRHGELT---LAC 282

Query: 238 RIVLKDVVREL 248
           R V++ +++EL
Sbjct: 283 RTVMQ-LIKEL 292


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.321    0.133    0.373 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 804,929
Number of extensions: 33105
Number of successful extensions: 197
Number of sequences better than 1.0e-08: 5
Number of HSP's gapped: 200
Number of HSP's successfully gapped: 5
Length of query: 262
Length of database: 1,619,870
Length adjustment: 83
Effective length of query: 179
Effective length of database: 1,226,865
Effective search space: 219608835
Effective search space used: 219608835
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 (21.9 bits)
S2: 129 (54.3 bits)