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= 0225.0036.p
         (88 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300314079|ref|YP_003778171.1| LysR family transcription regul...   126   4e-31
gi|300310675|ref|YP_003774767.1| LysR family transcription regul...    66   4e-13
gi|300310448|ref|YP_003774540.1| transcription regulator protein...    65   8e-13
gi|300310335|ref|YP_003774427.1| transcription regulator protein...    60   5e-11
gi|300310812|ref|YP_003774904.1| LysR family transcription regul...    54   3e-09

>gi|300314079|ref|YP_003778171.1| LysR family transcription
          regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 319

 Score =  126 bits (316), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 65/74 (87%), Positives = 66/74 (89%), Gaps = 5/74 (6%)

Query: 1  MSFLTLDLNLLRVFDAVMTEQNLTRAANLLAMTQPAVSNALRRLRDTLNDELVIRTAHGV 60
          MSFLTLDLNLLRVFDAVMTEQNLTRAANLLAMTQPAVSNALRRLRDTLND+LVIRTAHGV
Sbjct: 1  MSFLTLDLNLLRVFDAVMTEQNLTRAANLLAMTQPAVSNALRRLRDTLNDDLVIRTAHGV 60

Query: 61 KPXS-----WPTAR 69
          KP       WPT R
Sbjct: 61 KPTPRAEELWPTVR 74


>gi|300310675|ref|YP_003774767.1| LysR family transcription
          regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 309

 Score = 66.2 bits (160), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 43/61 (70%)

Query: 2  SFLTLDLNLLRVFDAVMTEQNLTRAANLLAMTQPAVSNALRRLRDTLNDELVIRTAHGVK 61
          +F  +DLNLLRVF A+  E++LT A N L ++QPAVS AL RLR   +D L IRT  G++
Sbjct: 3  TFNNMDLNLLRVFQAIADERSLTLAGNRLHLSQPAVSYALGRLRQIFDDPLFIRTKEGMQ 62

Query: 62 P 62
          P
Sbjct: 63 P 63


>gi|300310448|ref|YP_003774540.1| transcription regulator protein
          [Herbaspirillum seropedicae SmR1]
          Length = 306

 Score = 65.5 bits (158), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 30/60 (50%), Positives = 41/60 (68%)

Query: 6  LDLNLLRVFDAVMTEQNLTRAANLLAMTQPAVSNALRRLRDTLNDELVIRTAHGVKPXSW 65
          +DLNLL VF  V  E+ ++  A  L ++QPAVSNAL RLR +  DEL +RTA G++P  +
Sbjct: 9  IDLNLLVVFQEVFQERQISSVARRLGLSQPAVSNALARLRRSFEDELFVRTAQGMQPTPF 68


>gi|300310335|ref|YP_003774427.1| transcription regulator protein
          [Herbaspirillum seropedicae SmR1]
          Length = 309

 Score = 59.7 bits (143), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 29/62 (46%), Positives = 44/62 (70%)

Query: 1  MSFLTLDLNLLRVFDAVMTEQNLTRAANLLAMTQPAVSNALRRLRDTLNDELVIRTAHGV 60
          M F  LDLNLL   DA++TE +++RAA  + ++Q A+SNAL RLR+  +DEL+I+    +
Sbjct: 1  MRFNKLDLNLLVALDALLTEMSISRAAEKIHLSQSAMSNALARLREYFDDELLIQVGRRM 60

Query: 61 KP 62
          +P
Sbjct: 61 EP 62


>gi|300310812|ref|YP_003774904.1| LysR family transcription
          regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 311

 Score = 53.5 bits (127), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 32/76 (42%), Positives = 44/76 (57%), Gaps = 6/76 (7%)

Query: 1  MSFLTLDLNLLRVFDAVMTEQNLTRAANLLAMTQPAVSNALRRLRDTLNDELVIRTAHGV 60
          M+    DLNLL+ F  +   ++LT AA  L +TQPAVS+ALRRLR+  +D L +R+   +
Sbjct: 4  MNIAAADLNLLKTFIVIWELRSLTAAAERLHLTQPAVSHALRRLREMFDDPLFVRSTSAM 63

Query: 61 KPXS------WPTARA 70
           P         P ARA
Sbjct: 64 VPTETAIRLHEPIARA 79


  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
   0.323    0.128    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: 192,906
Number of extensions: 4869
Number of successful extensions: 88
Number of sequences better than 1.0e-08: 6
Number of HSP's gapped: 88
Number of HSP's successfully gapped: 6
Length of query: 88
Length of database: 1,619,870
Length adjustment: 58
Effective length of query: 30
Effective length of database: 1,345,240
Effective search space: 40357200
Effective search space used: 40357200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 123 (52.0 bits)