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= 0228.0003.p
         (414 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309661|ref|YP_003773753.1| AraC family transcription regul...   155   5e-39
gi|300310404|ref|YP_003774496.1| AraC family transcription regul...    62   7e-11
gi|300311835|ref|YP_003775927.1| AraC family ethanolamine operon...    55   8e-09

>gi|300309661|ref|YP_003773753.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 338

 Score =  155 bits (392), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 80/165 (48%), Positives = 108/165 (65%)

Query: 240 GAPKKXYVEASGAELQEAFLRLIRLLNKPQDIAAMSRILKLEIMYRLITAQNGDVLYHTV 299
           GA +  YV     +L +A LRL+RL  +P D+  ++ +++ EI+YRL+    G +L  TV
Sbjct: 162 GAARGLYVNRLDVDLLDAVLRLLRLQERPADVPILAPMIRREILYRLLMNGQGALLRQTV 221

Query: 300 LSHYQERGVNDAIQWIKQHYAEPMSIEKLARQVRMSVSALHHRFKATTVMSPLQYQKQTR 359
           L   Q   V  AI+ IK+ Y + + I+ +AR V MSVS+LHH FK  T MSPLQYQK  R
Sbjct: 222 LQDSQMNRVAKAIRLIKEGYDQALRIDDIARDVHMSVSSLHHHFKLVTAMSPLQYQKNLR 281

Query: 360 LLEARRMLMAGGVEAATVAYQVGYESPSQFSREYRRLFGASPLQD 404
           L EAR++++      AT A++VGYES SQFSREY RLFGA PL+D
Sbjct: 282 LQEARKLILTADASVATAAHRVGYESSSQFSREYSRLFGAPPLRD 326



 Score = 73.6 bits (179), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 32/107 (29%), Positives = 59/107 (55%)

Query: 44  VATTIPYLSFIRICRPTDLSRGMLQPSMCLVVQGRKKVLIGKDVNDYGSGSYVLSAIDLP 103
           + T IP +   RI  P+     + +P   ++ QG K++ +G ++ +Y    Y+++++DLP
Sbjct: 59  LETAIPNMEIYRITCPSGPKHAVQKPVFAVIAQGSKRIFVGDEIYEYDPMHYLVASVDLP 118

Query: 104 VSGQIVEADDAAPYYGVRIDLDPKEIAAFIIELNIPAGGFVGGSCRR 150
           V G+++      PY G+R++LD +EI   I + N+PA   V     R
Sbjct: 119 VVGKVMVTSPDEPYLGLRLELDTQEIGELIGDENLPAAAQVSEGAAR 165


>gi|300310404|ref|YP_003774496.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 344

 Score = 62.4 bits (150), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 42/156 (26%), Positives = 74/156 (47%), Gaps = 20/156 (12%)

Query: 261 LIRLLNKPQDIAAMSRILKLEIMYRLITAQNGDVLYHTVLSHYQERGVNDAIQWIK---- 316
           ++ LL+  +   A++RI    I+ RL      DVL  +++  + E   +DA  WI     
Sbjct: 188 VLALLDAMEREVALNRIGACGILARL-----ADVLAASIIRGWVECACSDASGWIAAVRC 242

Query: 317 -----------QHYAEPMSIEKLARQVRMSVSALHHRFKATTVMSPLQYQKQTRLLEARR 365
                      QH     S+ +LA  +  S S+   +F A    +P +Y  + ++ +AR 
Sbjct: 243 PQVGRVLAAVHQHPERDWSVAELAALMGASRSSFIDKFSAAVGETPAKYVARVKMFQARH 302

Query: 366 MLMAGGVEAATVAYQVGYESPSQFSREYRRLFGASP 401
            +   G+  A VA ++GY+S + FSR ++R+ G  P
Sbjct: 303 WIAREGLRVAVVANRLGYDSEASFSRAFKRIIGHPP 338


>gi|300311835|ref|YP_003775927.1| AraC family ethanolamine operon
           transcription regulator protein [Herbaspirillum
           seropedicae SmR1]
          Length = 332

 Score = 55.5 bits (132), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 51/101 (50%), Gaps = 5/101 (4%)

Query: 306 RGVNDAIQWIKQHYAEPMSIEKLARQVRMSVSALHHRFKATTVMSPLQYQKQTRLLEARR 365
           R VNDA ++   H   P+++  L   V +S   L + F+    MSP+ Y +  RL   RR
Sbjct: 222 RIVNDAREFAMAHQDSPVTVPMLCEAVHVSRRTLQYCFEDVLGMSPMSYLRSLRLNGVRR 281

Query: 366 MLMAGGVEAAT-----VAYQVGYESPSQFSREYRRLFGASP 401
            L  G    A      +A   G+ + SQFS +Y++LFG +P
Sbjct: 282 ALCHGDGRQAVGSIGDIAAAWGFANFSQFSCDYKKLFGQTP 322


  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
   0.322    0.135    0.391 

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: 1,220,543
Number of extensions: 48895
Number of successful extensions: 200
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 208
Number of HSP's successfully gapped: 5
Length of query: 414
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 326
Effective length of database: 1,203,190
Effective search space: 392239940
Effective search space used: 392239940
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 (22.0 bits)
S2: 132 (55.5 bits)