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= 0225.0052.p
         (282 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313854|ref|YP_003777946.1| LysR family transcription regul...   288   3e-79
gi|300313153|ref|YP_003777245.1| transcription regulator protein...   213   1e-56

>gi|300313854|ref|YP_003777946.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 310

 Score =  288 bits (738), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 158/252 (62%), Positives = 179/252 (71%), Gaps = 43/252 (17%)

Query: 1   MEIKWVEDFLSVVETLNFSRSAKLRNVTQP-------------GAQATVKFAF------- 40
           MEIKWVEDFLSVVETLNFSRSAKLRNVTQP             GA+   + ++       
Sbjct: 1   MEIKWVEDFLSVVETLNFSRSAKLRNVTQPAFGRRIRSLETWLGAELFDRSSYPCTLTQA 60

Query: 41  -----------------------SXLAGAQATVKFAMPHTLLLTLYPKLLSEIEKCTGAM 77
                                    LAGAQ+ V+ AMPHTLLLT++PKLLSEIEK  GA+
Sbjct: 61  GESFVPIAKEMLNQSMQARLVLRGQLAGAQSAVRLAMPHTLLLTVFPKLLSEIEKSIGAI 120

Query: 78  ATTVQATNVHDAVMALVERHCDLLICYHHPQQGIDLDAERYAMLSLGKEPLRPYVKAVAK 137
           +TTV A NVHDAVMALVER+CDLL+CY H QQGI LD ERY +LSLGKEPLRPYVK +  
Sbjct: 121 STTVMAGNVHDAVMALVERNCDLLLCYDHRQQGIALDTERYDVLSLGKEPLRPYVKTLPN 180

Query: 138 GVPKYALPGTAAEPVPFLSYSSYSSLSRIVEKQLSASPRPVHVFRRFESDLAEGLKSMVL 197
           G+PKY LPG   +P PFLSYS YSSLSRIVEK L +SPR VH+FRRFE+DLAEGLKSM +
Sbjct: 181 GLPKYVLPGAPNDPQPFLSYSPYSSLSRIVEKALHSSPRQVHLFRRFETDLAEGLKSMAV 240

Query: 198 EGHGVAWLPASA 209
           EGHG+AWLPASA
Sbjct: 241 EGHGIAWLPASA 252


>gi|300313153|ref|YP_003777245.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 331

 Score =  213 bits (542), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 112/252 (44%), Positives = 150/252 (59%), Gaps = 43/252 (17%)

Query: 1   MEIKWVEDFLSVVETLNFSRSAKLRNVTQPGAQATVKFAFSXL----------------A 44
           ME KW+EDF+S+ ET +FSRSA+LR+VTQP     ++   + L                A
Sbjct: 1   MESKWLEDFVSLAETRSFSRSAELRHVTQPAFSRRIQSLEAWLGTDLIDRTSYPTRLTAA 60

Query: 45  G---------------------------AQATVKFAMPHTLLLTLYPKLLSEIEKCTGAM 77
           G                           AQ T+ FA+PHTL LT  PK LS +E   GA+
Sbjct: 61  GEVFYEQAVAMLGQINNTRALLRGKRPTAQTTIDFAVPHTLSLTYMPKWLSALESGFGAI 120

Query: 78  ATTVQATNVHDAVMALVERHCDLLICYHHPQQGIDLDAERYAMLSLGKEPLRPYVKAVAK 137
            T + A NVHDAVM +VE  CDLL+CYHHP+Q + LD+ RY ML++G E LRPY +    
Sbjct: 121 NTRLIALNVHDAVMTIVEGGCDLLLCYHHPRQPVQLDSSRYDMLTMGTETLRPYSRCDRN 180

Query: 138 GVPKYALPGTAAEPVPFLSYSSYSSLSRIVEKQLSASPRPVHVFRRFESDLAEGLKSMVL 197
           G P Y  PG+A  PVPFLSY+S + L R+VE  ++ + RP+H+ + +E+D++E LK M L
Sbjct: 181 GKPDYVFPGSAKAPVPFLSYTSNAYLGRMVELMMADTKRPLHLDKHYETDMSESLKMMAL 240

Query: 198 EGHGVAWLPASA 209
           EGHGVA+LP S+
Sbjct: 241 EGHGVAFLPESS 252


  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    0.132    0.390 

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: 703,962
Number of extensions: 24753
Number of successful extensions: 126
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 126
Number of HSP's successfully gapped: 3
Length of query: 282
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 198
Effective length of database: 1,222,130
Effective search space: 241981740
Effective search space used: 241981740
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: 130 (54.7 bits)