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= 0002.0413.p
         (128 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312300|ref|YP_003776392.1| LysR family transcription regul...    63   7e-12
gi|300310059|ref|YP_003774151.1| LysR family transcription regul...    57   5e-10

>gi|300312300|ref|YP_003776392.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 305

 Score = 63.2 bits (152), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 34/114 (29%), Positives = 56/114 (49%), Gaps = 5/114 (4%)

Query: 12  WKRTARNKRQFIGYGEALQGGP--HQAWLAQYADGAPYVMTANDFSLLHQACRAGLGLTI 69
           W     ++R FIG     Q  P   +AWL    D   Y +  ND   +  A  +G+GL +
Sbjct: 191 WLERPESERSFIGLD---QESPCRQKAWLESQVDQRRYALRTNDIRAMCHAAMSGIGLAL 247

Query: 70  LPHFIARGDAELTGFDSGQPPWQRELWLTVHPDLRRSPRVQRIAELVAEIVQER 123
           LP F+   D  L      + P    L+L +H D+RR+PR++  A+ + +++Q +
Sbjct: 248 LPRFMVAEDTRLVAIPMPETPPPCPLYLVMHSDVRRAPRIRATADFLIDLIQSQ 301


>gi|300310059|ref|YP_003774151.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 283

 Score = 57.0 bits (136), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 35/101 (34%), Positives = 50/101 (49%), Gaps = 3/101 (2%)

Query: 14  RTARNKRQFIGYGEALQGGPHQAWLAQYADGAPYVMTANDFSLLHQACRAGLGLTILPHF 73
           R  R     IGY +++   P   WLA +ADG P  + +        A RAG+GL +LP +
Sbjct: 177 RHQRGSAPVIGYDDSVPDIPETRWLAAHADGNPVRLRSASLVAQCMAARAGVGLALLPSY 236

Query: 74  IARGDAELTGFDSGQPPWQRELWLTVHPDLRRSPRVQRIAE 114
           +     EL   +S  P   RELW   H DL+  PR++ + E
Sbjct: 237 LL--APELQTVES-TPQLVRELWAVFHRDLKALPRLRAVLE 274


  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
   0.324    0.137    0.442 

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: 419,409
Number of extensions: 17249
Number of successful extensions: 80
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 78
Number of HSP's successfully gapped: 2
Length of query: 128
Length of database: 1,619,870
Length adjustment: 75
Effective length of query: 53
Effective length of database: 1,264,745
Effective search space: 67031485
Effective search space used: 67031485
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 125 (52.8 bits)