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= 0029.0053.p
         (315 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312817|ref|YP_003776909.1| transcription regulator protein...   366   e-102
gi|300312806|ref|YP_003776898.1| transcription regulator protein...    86   5e-18
gi|300311738|ref|YP_003775830.1| RpiR family transcription regul...    85   7e-18

>gi|300312817|ref|YP_003776909.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 293

 Score =  366 bits (940), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 185/284 (65%), Positives = 226/284 (79%), Gaps = 14/284 (4%)

Query: 41  PADFAELDALIRANYAGMRPQFQAGAAFLLDNPGEVAVSTMRAVX-RAGVQPSTLVRLSQ 99
           P+ F+EL+ALIR  +  MRPQFQAGAAFLLDNPGEVAVSTMRA+  +A VQPST VRL+Q
Sbjct: 8   PSSFSELEALIRERFIDMRPQFQAGAAFLLDNPGEVAVSTMRALSQKAQVQPSTFVRLAQ 67

Query: 100 YLGFPGWGELRALFVERLAVTPKAYAYKAQNLVKRNNSDILIAEIFQAQRANLDASEPKN 159
           +LGF GW ELRALFVERLA  PKAYA+KA+++V+R+NSD L+AE+F AQRANLDASEPK+
Sbjct: 68  HLGFAGWAELRALFVERLAGEPKAYAFKAKSIVRRSNSDKLVAELFTAQRANLDASEPKS 127

Query: 160 ADELLRAARTLTKARHVHIAGFRAAYSVAFMLEYLYRLFRPSVTLIKGTAGSLAMELRAV 219
           AD +L AAR L KA HVHIAGFRAA+S++F+L YLYRLFR SV+L++G+ GS+ +ELRA+
Sbjct: 128 ADRMLGAARALLKAHHVHIAGFRAAFSISFLLHYLYRLFRTSVSLVRGSEGSIELELRAI 187

Query: 220 APQDATIVISFAPYSIEAVQVAEATKRAGSKLIALTDSAV-------------GRRRGGG 266
           A  DA IV+SFAPYS EAV+VAEA K+AG+KLIALTDSAV                    
Sbjct: 188 AAHDAVIVVSFAPYSTEAVRVAEAAKQAGAKLIALTDSAVAPIALKADHCILFSHESPSF 247

Query: 267 KPDRXAAVAVAESLIELVISLDDDKAVKRLEHAEEELYQSGAYV 310
            P   AA A+AESLIELVIS+DD+ AV+RLE AE +L+ +GAY+
Sbjct: 248 FPSMAAATAIAESLIELVISIDDEHAVRRLELAESDLHSTGAYI 291


>gi|300312806|ref|YP_003776898.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 319

 Score = 85.5 bits (210), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 65/199 (32%), Positives = 109/199 (54%), Gaps = 8/199 (4%)

Query: 67  AFLLDNPGEVAVSTMRAVXRA-GVQPSTLVRLSQYLGFPGWGELRALFVERLAVTPKA-Y 124
           A L++ P EVAV ++  +  + GV  STL RL+  LG+ G+ + + +F + LA + +  Y
Sbjct: 54  AKLVERPEEVAVRSITDLAASLGVNASTLTRLATRLGYSGFVDFQNVFRDGLASSHRNFY 113

Query: 125 AYKAQNLVK----RNNSDIL-IAEIFQAQRANLDASEPK-NADELLRAARTLTKARHVHI 178
           + +AQ L+     R+  D+L +A++      N+++   + +A EL  A + L +ARHV I
Sbjct: 114 SQQAQRLITDGPGRHEGDVLAVAQLAAESARNMESCLAQLSAVELRGAVKLLARARHVRI 173

Query: 179 AGFRAAYSVAFMLEYLYRLFRPSVTLIKGTAGSLAMELRAVAPQDATIVISFAPYSIEAV 238
            G R  +S+A  L Y   + R  V+L+      +A  L  +   D  +V S +PY+    
Sbjct: 174 YGVRQMHSLASFLCYGLGMIRSEVSLLDAPGQGIAEGLAQLQRGDVLVVASVSPYTRIVA 233

Query: 239 QVAEATKRAGSKLIALTDS 257
           +VA+A   AG  +IALTD+
Sbjct: 234 EVAQAASNAGLNVIALTDN 252


>gi|300311738|ref|YP_003775830.1| RpiR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 281

 Score = 85.1 bits (209), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 59/219 (26%), Positives = 103/219 (47%), Gaps = 9/219 (4%)

Query: 51  IRANYAGMRPQFQAGAAFLLDNPGEVAVSTMRAVX-RAGVQPSTLVRLSQYLGFPGWGEL 109
           + A Y  +  Q +  A ++  +   + +  +  +  +  VQPS +VR +++ GF G+ E+
Sbjct: 4   VAAQYHSLSRQLKVIATYVEQHKTSLMLERISDIAEQCQVQPSAIVRFAKHFGFSGFSEM 63

Query: 110 RALFVERL---AVTPKAYAYKAQNLVK----RNNSDILIAEIFQAQRANLDASEPKNADE 162
           +A+F E     A+  + Y  + +NL++    R  S  L  E  Q+ RA LD       +E
Sbjct: 64  QAVFREAYTAQAIPSRNYQRRIRNLIQSKPTRVTSGALAHEFIQSSRAGLDELLAGFDEE 123

Query: 163 LLRAA-RTLTKARHVHIAGFRAAYSVAFMLEYLYRLFRPSVTLIKGTAGSLAMELRAVAP 221
              AA + L KA ++++ G R ++ +A  L Y  +     V LI G  G    E+R++  
Sbjct: 124 QFEAAVKLLLKAENIYVIGVRRSFPIANHLAYALQHTNKRVHLISGAGGMFREEVRSIDK 183

Query: 222 QDATIVISFAPYSIEAVQVAEATKRAGSKLIALTDSAVG 260
            D  I ISF PY  E            ++ + +TDS + 
Sbjct: 184 HDVLIAISFTPYGQETQACVRLAHHRQARTLVITDSQLS 222


  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
   0.320    0.132    0.369 

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: 814,579
Number of extensions: 28063
Number of successful extensions: 119
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 115
Number of HSP's successfully gapped: 4
Length of query: 315
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 230
Effective length of database: 1,217,395
Effective search space: 280000850
Effective search space used: 280000850
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 (21.8 bits)
S2: 130 (54.7 bits)