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= 0042.0014.p
         (120 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311424|ref|YP_003775516.1| LysR family transcription regul...    62   2e-11
gi|300311458|ref|YP_003775550.1| LysR family transcription regul...    59   1e-10
gi|300312334|ref|YP_003776426.1| transcription regulator protein...    58   3e-10
gi|300311233|ref|YP_003775325.1| LysR family transcription regul...    57   6e-10

>gi|300311424|ref|YP_003775516.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 327

 Score = 61.6 bits (148), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/113 (32%), Positives = 54/113 (47%), Gaps = 1/113 (0%)

Query: 2   PQTPDDLLQHACLHHRFATNGKLERWPLRRGRKDLTLDLPTTAVVNTIEPLIHMAEAGLG 61
           PQ P DLL HACL    +    L+ W L        + + +   VN  E ++     G+G
Sbjct: 180 PQQPADLLNHACLQL-VSPISPLDEWILEGPEGGTVVAVKSNFQVNVAEAMLTAIREGMG 238

Query: 62  IACLPDFSIREQERKGTLVSVLDSYIHHSGTFRMLWPSSPYLSPKLRAFVDFM 114
           I  LP +S  +  R GT+V VL  +   +     L+PS  YL  K+  +VD+M
Sbjct: 239 IGVLPIYSAVDALRAGTIVRVLPQHRLQNMGVYALYPSRQYLDAKISTWVDWM 291


>gi|300311458|ref|YP_003775550.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 303

 Score = 58.9 bits (141), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 36/117 (30%), Positives = 59/117 (50%), Gaps = 2/117 (1%)

Query: 2   PQTPDDLLQHACLHHRFATNGKLERWPLRRGRKDLTLDLPTTAVVNTIEPLIHMAEAGLG 61
           P+ P+DL +H CL+  F+       W +      L + + +  V N+   L  +A AG+G
Sbjct: 179 PEQPEDLSRHNCLN--FSHEYLRHHWHVNTNGGVLDVPIVSKVVSNSGVLLRDLALAGMG 236

Query: 62  IACLPDFSIREQERKGTLVSVLDSYIHHSGTFRMLWPSSPYLSPKLRAFVDFMAAHL 118
           I   P +S+ +  R G LV VL  +        M++PS   LS K+R+F +F++A  
Sbjct: 237 IVLRPSYSLGDDLRSGRLVQVLPGFDMGQVIMSMVYPSRRLLSAKVRSFAEFISARF 293


>gi|300312334|ref|YP_003776426.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 302

 Score = 57.8 bits (138), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 35/113 (30%), Positives = 57/113 (50%), Gaps = 2/113 (1%)

Query: 2   PQTPDDLLQHACLHHRFATNGKLERWPLRRGRKDLTLDLPTTAVVNTIEPLIHMAEAGLG 61
           PQ+PD+L++H CL    ++ G    W LR+  K     +    V N  E L + A AG G
Sbjct: 178 PQSPDELMRHNCLA--MSSEGSQRGWTLRQSGKVSVYKVGGNMVCNDGEVLHNWALAGRG 235

Query: 62  IACLPDFSIREQERKGTLVSVLDSYIHHSGTFRMLWPSSPYLSPKLRAFVDFM 114
           +A    + +      G LV+VLD +   + +   ++    +L  ++RAFVDF+
Sbjct: 236 LAWRSMWEVGAAIEAGELVTVLDKFAAPAPSIYAVFAQRRHLPLRIRAFVDFL 288


>gi|300311233|ref|YP_003775325.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 315

 Score = 56.6 bits (135), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 37/120 (30%), Positives = 57/120 (47%), Gaps = 5/120 (4%)

Query: 2   PQTPDDLLQHACLHHRFATNGKLERWPLRRGRKDLTLDLPTTAVVNTIEPLIHMAEAGLG 61
           P  P  L +H+C++     +    RW  RR  K + +++      N     +      LG
Sbjct: 184 PAHPQALKEHSCIY--LGESPADARWRFRRQGKSVNVEVRGRYAANHTGVRLDAVLRHLG 241

Query: 62  IACLPDFSIREQERKGTLVSVLDSY---IHHSGTFRMLWPSSPYLSPKLRAFVDFMAAHL 118
           IA LP F  R    +G+LV VL  +    H+ G    L+P++ +L P+L AFV F+A  L
Sbjct: 242 IASLPYFIARPALEEGSLVQVLPQWSFRTHYCGELWALYPATRHLPPRLGAFVQFLAQRL 301


  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
   0.325    0.139    0.441 

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: 399,622
Number of extensions: 15359
Number of successful extensions: 79
Number of sequences better than 1.0e-08: 7
Number of HSP's gapped: 81
Number of HSP's successfully gapped: 7
Length of query: 120
Length of database: 1,619,870
Length adjustment: 74
Effective length of query: 46
Effective length of database: 1,269,480
Effective search space: 58396080
Effective search space used: 58396080
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)