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= 0001.4374.p
         (418 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313775|ref|YP_003777867.1| AraC family xylose operon trans...   835   0.0  
gi|300311694|ref|YP_003775786.1| AraC family transcription regul...    58   1e-09
gi|300311952|ref|YP_003776044.1| AraC family transcription regul...    57   4e-09

>gi|300313775|ref|YP_003777867.1| AraC family xylose operon
           transcription regulator protein [Herbaspirillum
           seropedicae SmR1]
          Length = 442

 Score =  835 bits (2157), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 403/418 (96%), Positives = 410/418 (98%)

Query: 1   VAKAPTVHRIALLFNGNKIFDREIIAGIGEYISSTRASWDLYLEEDFRCRPQGIERWAGH 60
           VAKAPTVHRIALLFNGNKIFDREIIAGIGEYISSTRASWDLYLEEDFRCRPQGIERWAGH
Sbjct: 25  VAKAPTVHRIALLFNGNKIFDREIIAGIGEYISSTRASWDLYLEEDFRCRPQGIERWAGH 84

Query: 61  GIIADFDDPVTTAALEGVQLPVVAIGGSYADPSQYPANRPYVATDNYKMVKLAYDHLIEA 120
           GIIADFDDPVTTAALEGVQLPVVAIGGSYADPSQYPANRPYVATDNYKMVKLAYDHLIEA
Sbjct: 85  GIIADFDDPVTTAALEGVQLPVVAIGGSYADPSQYPANRPYVATDNYKMVKLAYDHLIEA 144

Query: 121 GLQHFALFSLPESPCNRWAQERERIFTDLTGADGITGHIYRGVGTSAQSWDTAVEQQIAW 180
           GLQHFALFSLPES CNRWAQERERIFTDLTGADGI GHIYRGVGTSAQSWDTAVEQQIAW
Sbjct: 145 GLQHFALFSLPESDCNRWAQERERIFTDLTGADGIAGHIYRGVGTSAQSWDTAVEQQIAW 204

Query: 181 VRSLPKPVGIIAVTDARARQLLQACLFAGIAVPEQVALIGIDNDPLARVLTRIPLSSVIQ 240
           VRSLPKPVGIIAVTDARARQLLQACLFAGIAVPEQVALIGIDNDPLARVLTRIPLSSVIQ
Sbjct: 205 VRSLPKPVGIIAVTDARARQLLQACLFAGIAVPEQVALIGIDNDPLARVLTRIPLSSVIQ 264

Query: 241 GSVEMGRTAAHLLHQMLHGARFPDTRIMVPPVGINVLASSRHEVRNHPHVMQALHFIRQY 300
           GSVEMGRTAAHLLHQMLHGARFPDTRIMVPPVGINVLASSRHEVRNHPHVMQALHFIRQY
Sbjct: 265 GSVEMGRTAAHLLHQMLHGARFPDTRIMVPPVGINVLASSRHEVRNHPHVMQALHFIRQY 324

Query: 301 ACQGIKTDQVADYVGISRSSLEWYFRRELGRSVHDEILRFKLDAAKRMLEQAGSHAAEIA 360
           ACQGIKTDQVADYVGISRSSLEWYFRRELGRSVHDEILRFKLDAAKR+LEQAGSHAAEIA
Sbjct: 325 ACQGIKTDQVADYVGISRSSLEWYFRRELGRSVHDEILRFKLDAAKRLLEQAGSHAAEIA 384

Query: 361 VSCGFTTVQYLHAVFKRELGCTPREYQEQFAAGLERSPAPAPRPKKKTAGPSLLTTTK 418
           VSCGFT+VQY+HAVFKRELGCTPREYQEQFAAGLER+ APA R KKK+AG +LL  T+
Sbjct: 385 VSCGFTSVQYMHAVFKRELGCTPREYQEQFAAGLERAAAPAARQKKKSAGTTLLEPTR 442


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

 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 62/113 (54%), Gaps = 5/113 (4%)

Query: 290 VMQALHFIRQYACQGIKTDQVADYVGISRSSLEWYFRRELGRSVHDEILRFKLDAAKRML 349
           + +AL ++ ++    I   + AD+V +S  + +  F+RE G + H  + + +++AA   L
Sbjct: 255 IQKALIWLDEHMSSSINMSEAADHVSMSERNFQREFKRETGETPHCFLTKIRIEAACLYL 314

Query: 350 EQAGSHAAEIAVSCGFTTVQYLHAVFKRELGCTPREYQEQFAAGLERSPAPAP 402
           ++      +IA  CG  + ++L  +F++  G +P EY+++     E +P PAP
Sbjct: 315 KETDLPIEKIARRCGLVSGEHLARLFRKHHGVSPGEYRKK-----ENAPRPAP 362


>gi|300311952|ref|YP_003776044.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 322

 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 32/111 (28%), Positives = 59/111 (53%), Gaps = 3/111 (2%)

Query: 280 SRHEV--RNHPHVMQALHFIRQYACQGIKTDQVADYVGISRSSLEWYFRRELGRSVHDEI 337
           +R EV  R    ++QA   + Q   +    D++A  VG+++  L+  FR   GR+VH  +
Sbjct: 206 ARGEVGTREQRQLLQARQLLEQRYAESWSVDRLAQAVGLNQKKLQAGFRAMAGRTVHAHL 265

Query: 338 LRFKLDAAKRMLEQAGSHAAEIAVSCGFTTVQYLHAVFKRELGCTPREYQE 388
              +L AA  ML + G   A+ A++ GF+ + +    F++  G TP ++++
Sbjct: 266 RELRLHAAAAMLAE-GMGVADTALAVGFSNLSHFSKSFRQTHGVTPSQWKQ 315


  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    0.136    0.414 

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: 1,300,254
Number of extensions: 55210
Number of successful extensions: 196
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 197
Number of HSP's successfully gapped: 3
Length of query: 418
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 330
Effective length of database: 1,203,190
Effective search space: 397052700
Effective search space used: 397052700
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 (21.9 bits)
S2: 132 (55.5 bits)