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= 0037.0028.p
         (139 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310443|ref|YP_003774535.1| LysR family transcription regul...    67   7e-13
gi|300313964|ref|YP_003778056.1| LysR family transcription regul...    62   1e-11
gi|300309845|ref|YP_003773937.1| LysR family transcription regul...    58   3e-10

>gi|300310443|ref|YP_003774535.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 295

 Score = 66.6 bits (161), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 44/134 (32%), Positives = 69/134 (51%), Gaps = 10/134 (7%)

Query: 1   VPLCSPALLRD----KPDALTLADIADMTLIQSTLNPVRWSDWFALNGMKLPPGRPMPSF 56
           VPL SPA +R+    KP     AD+  + LI+S ++ V+W+DWF        P +    F
Sbjct: 164 VPLASPAFIREYRLRKP-----ADLLGVKLIRSNVSVVQWADWFGEFADVRAPEQFAVRF 218

Query: 57  DRASLALAAAVNSVGIALESTRLAEQEIANGELVRLDGGELKSVLRETHFLSYREGEKNS 116
           DRA ++L AA   +G+ALES  +A + +   +L  + G E +++  + HF  Y       
Sbjct: 219 DRAQMSLDAATQGLGVALESATVAARHLEEKKLKPIFGLE-RAIKVKAHFAVYPAHHARR 277

Query: 117 KKIMRFRDWLFLQA 130
             +  F +WL  QA
Sbjct: 278 PAVAAFLEWLREQA 291


>gi|300313964|ref|YP_003778056.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 314

 Score = 62.4 bits (150), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 42/130 (32%), Positives = 61/130 (46%), Gaps = 3/130 (2%)

Query: 1   VPLCSPALLRDKPDALTLADIADMTLIQSTLNPVRWSDWFALNGMKLPPGRPMPSFDRAS 60
           V LC P L R  P   ++AD++   LI + + P  W+ W   +G +L   +      +  
Sbjct: 181 VALCHPRLWRQHP-VRSVADLSQHRLIHTAIRPDAWAHWLQQHGSRLGARQAGMECSQYP 239

Query: 61  LALAAAVNSVGIALESTRLAEQEIANGELVRLDGGELKSVLRETHFLSYREGEKNSKKIM 120
           +AL AA+N  GIAL  + LAE       L RL GG   S     ++L       +   + 
Sbjct: 240 VALQAAMNGEGIALVPSVLAESFDPQHRLRRLFGGPTPSA--GQYYLLTPGDRYDDSAVR 297

Query: 121 RFRDWLFLQA 130
           RFR WL +QA
Sbjct: 298 RFRQWLLMQA 307


>gi|300309845|ref|YP_003773937.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 294

 Score = 58.2 bits (139), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 45/137 (32%), Positives = 65/137 (47%), Gaps = 14/137 (10%)

Query: 1   VPLCSPALLR----DKPDALTLADIADMTLIQSTLNPVRWSDWFALNGMKLPPGRPMPSF 56
           +P+ SP  L     D PD L LA      LIQS  + ++W +WFA     L P R    F
Sbjct: 162 IPMASPDFLARHRIDTPDDLVLA-----PLIQSRGSLLQWPEWFARYAPDLRPERIALRF 216

Query: 57  DRASLALAAAVNSVGIALESTRLAEQEIANGEL--VRLDGGELKSVLRETHFLSYREGEK 114
           DRA +++ AAV  +G+  ES       +A+G L  V  DG  L+      H+       K
Sbjct: 217 DRAMMSIEAAVQGLGVVFESDAFGAVALASGRLQPVFADGLALEIT---QHYAVCPARNK 273

Query: 115 NSKKIMRFRDWLFLQAG 131
           +  ++M F  WL  ++G
Sbjct: 274 SRPEVMLFLQWLREESG 290


  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
   0.319    0.134    0.394 

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: 404,772
Number of extensions: 13438
Number of successful extensions: 69
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 70
Number of HSP's successfully gapped: 3
Length of query: 139
Length of database: 1,619,870
Length adjustment: 76
Effective length of query: 63
Effective length of database: 1,260,010
Effective search space: 79380630
Effective search space used: 79380630
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 (21.7 bits)
S2: 126 (53.1 bits)