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= 0229.0050.p
         (187 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312695|ref|YP_003776787.1| AraC family transcription regul...   174   4e-45
gi|300310394|ref|YP_003774486.1| AraC family transcription regul...   114   5e-27
gi|300311694|ref|YP_003775786.1| AraC family transcription regul...    58   6e-10

>gi|300312695|ref|YP_003776787.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 293

 Score =  174 bits (441), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 87/174 (50%), Positives = 116/174 (66%), Gaps = 1/174 (0%)

Query: 1   MQNLLDDARLGAQFGEDAEVRADEALSAMLTASDARRVILFLDLLDYLSRAP-RVMLASP 59
           +Q +LD A  G QF +         +  +  AS ARRV+L + +L+ L+  P R  LA P
Sbjct: 110 LQEMLDGAARGLQFPDALGASITPLMQELAQASGARRVVLMMSVLERLASCPERKPLAGP 169

Query: 60  SYDPGVDQRRNAVINQVLSYILENYTSDLREADLAELTRMSCATFSRFFRKHTGLTFVQY 119
            YD    +  ++ +NQVLS I +N   +LRE DLAEL  MS ++F+RFF++HTG TF+QY
Sbjct: 170 GYDLNAQRHMSSTLNQVLSCIRQNLGGNLRETDLAELAGMSVSSFTRFFKRHTGCTFIQY 229

Query: 120 VNHLRLNRACELLMHSELPVTDICYRVGFNNVSHFNHQFLQKKQMSPSKFRACH 173
            N LRLN ACELLM +EL VT++CYRVGFNN+S+FN QFL  K M PS+FR+ H
Sbjct: 230 QNGLRLNEACELLMCTELSVTEVCYRVGFNNLSNFNRQFLASKGMPPSRFRSLH 283


>gi|300310394|ref|YP_003774486.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 294

 Score =  114 bits (285), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 59/137 (43%), Positives = 91/137 (66%), Gaps = 2/137 (1%)

Query: 36  RRVILFLDLLDYLSRAPRV-MLASPSYDPGVDQRRNAVINQVLSYILENYTSDLREADLA 94
           +R+ LF +LLD L+ AP   +LAS SY   +    ++ +N+ ++Y+ E+ T D+ E DLA
Sbjct: 145 KRLALFWELLDVLANAPEPEVLASLSYKLDLSGVNSSGLNRAIAYLREHLTDDIGEQDLA 204

Query: 95  ELTRMSCATFSRFFRKHTGLTFVQYVNHLRLNRAC-ELLMHSELPVTDICYRVGFNNVSH 153
           ++   + ++FSR F++HTG T V+Y N LR++ AC  LL   +  +TDICY  GF+N+S+
Sbjct: 205 DMVGQNLSSFSRAFKRHTGTTLVRYKNQLRVDLACLALLTRPQARITDICYETGFSNLSN 264

Query: 154 FNHQFLQKKQMSPSKFR 170
           FN  F + K MSPS+FR
Sbjct: 265 FNRHFHKIKGMSPSEFR 281


>gi|300311694|ref|YP_003775786.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 375

 Score = 57.8 bits (138), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 30/108 (27%), Positives = 55/108 (50%)

Query: 63  PGVDQRRNAVINQVLSYILENYTSDLREADLAELTRMSCATFSRFFRKHTGLTFVQYVNH 122
           PG  + R+  I + L ++ E+ +S +  ++ A+   MS   F R F++ TG T   ++  
Sbjct: 245 PGEKRHRSERIQKALIWLDEHMSSSINMSEAADHVSMSERNFQREFKRETGETPHCFLTK 304

Query: 123 LRLNRACELLMHSELPVTDICYRVGFNNVSHFNHQFLQKKQMSPSKFR 170
           +R+  AC  L  ++LP+  I  R G  +  H    F +   +SP ++R
Sbjct: 305 IRIEAACLYLKETDLPIEKIARRCGLVSGEHLARLFRKHHGVSPGEYR 352


  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    0.133    0.385 

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: 500,440
Number of extensions: 17124
Number of successful extensions: 106
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 105
Number of HSP's successfully gapped: 3
Length of query: 187
Length of database: 1,619,870
Length adjustment: 80
Effective length of query: 107
Effective length of database: 1,241,070
Effective search space: 132794490
Effective search space used: 132794490
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: 128 (53.9 bits)