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= 0008.0138.p
         (326 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312962|ref|YP_003777054.1| AraC family transcription regul...   560   e-161
gi|300309734|ref|YP_003773826.1| transcription regulator protein...    72   8e-14
gi|300312312|ref|YP_003776404.1| AraC family ethanolamine operon...    59   6e-10
gi|300313240|ref|YP_003777332.1| AraC family transcription regul...    56   4e-09

>gi|300312962|ref|YP_003777054.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 340

 Score =  560 bits (1442), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 296/328 (90%), Positives = 308/328 (93%), Gaps = 2/328 (0%)

Query: 1   LYRRRVFHSTRKVDCHAQVANELAEHDLFWKGDDVDTVLFKAAIQQLQIFMLKYGAEVVV 60
           LYRRRVF S+RKVDCHAQVANEL+EHDLFWKGDDVDTVLFKAAIQQLQIFMLKYGAEV+V
Sbjct: 13  LYRRRVFQSSRKVDCHAQVANELSEHDLFWKGDDVDTVLFKAAIQQLQIFMLKYGAEVIV 72

Query: 61  RPRLFNGFALVHMTLSGSAEIESDGRKVCIPQGHTALIAPKKNLRLWWQAGSEQLILKVP 120
           RPRLFNGFALVHMTLSGSAEIESDGRKVCIPQGHTALIAPK+NLRLWWQAGSEQLILKVP
Sbjct: 73  RPRLFNGFALVHMTLSGSAEIESDGRKVCIPQGHTALIAPKRNLRLWWQAGSEQLILKVP 132

Query: 121 LALFEELRAVGQRGPMDVPSVFLLPQQAAPYWDLLIQSLLRVLALP--GQGAGQGEWVQH 178
           LALFEELRA GQ  P+++PSV LLP QAAPYWDLLIQSLLRVLALP  GQG GQGEWV+H
Sbjct: 133 LALFEELRAAGQSAPLELPSVLLLPPQAAPYWDLLIQSLLRVLALPEQGQGQGQGEWVRH 192

Query: 179 FERSAAQFLLSQLTSTVEPVHTSSSGQRAASESADSLVGAGKLQRLDMLERYIRSRLCAP 238
           FERSA QFLLSQLTSTVEPV + S  QR AS+ ADSLVGAGKLQRLDMLERYIRSRLCAP
Sbjct: 193 FERSAVQFLLSQLTSTVEPVTSPSGAQRGASQCADSLVGAGKLQRLDMLERYIRSRLCAP 252

Query: 239 LALADLAGAAGVSVRALNALCHQQYGVAPMDLLRNIRLDAVRERLLTHPEANITDTAFEF 298
           LALADLAGAAGVSVR LNALCHQQYGVAPMDLLRNIRLDAVRERLLTHP AN+TDTAFEF
Sbjct: 253 LALADLAGAAGVSVRTLNALCHQQYGVAPMDLLRNIRLDAVRERLLTHPGANVTDTAFEF 312

Query: 299 GFGHLGRFSAYYRERFGELPKQTRSVTR 326
           GFGHLGRFSAYYRERFGELPKQTR + R
Sbjct: 313 GFGHLGRFSAYYRERFGELPKQTRGMLR 340


>gi|300309734|ref|YP_003773826.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 345

 Score = 71.6 bits (174), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 40/93 (43%), Positives = 56/93 (60%), Gaps = 1/93 (1%)

Query: 230 YIRSRLCAPLALADLAGAAGVSVRALNALCHQQYGVAPMDLLRNIRLDAVRERLLTHP-E 288
           +I +RL AP+ LAD+A  A +SVR+L +   +   + PM+ LR  RL  VRE LL     
Sbjct: 242 FIMARLSAPITLADIAAHAAISVRSLQSGFRRYKEMTPMEFLRTQRLGRVREDLLDPAVP 301

Query: 289 ANITDTAFEFGFGHLGRFSAYYRERFGELPKQT 321
           A+I   A  +GF HL  F  YY+++FGE P+ T
Sbjct: 302 ADIQHIALSWGFTHLYLFMRYYKKQFGESPQAT 334


>gi|300312312|ref|YP_003776404.1| AraC family ethanolamine operon
           transcription regulator protein [Herbaspirillum
           seropedicae SmR1]
          Length = 358

 Score = 58.5 bits (140), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 35/102 (34%), Positives = 53/102 (51%), Gaps = 4/102 (3%)

Query: 224 LDMLERYIRSRLCAPLALADLAGAAGVSVRALNALCHQQYGVAPMDLLRNIRLDAVRERL 283
           +D   R +R        +  +A   GVS R L    +   G+  ++ +R  RL+ VR+ L
Sbjct: 236 IDQARRLMRGDAPERATMTQVAAHLGVSRRHLQTCFNTSVGIPAIEFVRAERLNQVRKAL 295

Query: 284 LTHP----EANITDTAFEFGFGHLGRFSAYYRERFGELPKQT 321
           +       E +I D A ++GF HL RF+A YR+ FGELP +T
Sbjct: 296 VEARRAGLEVSIGDIAADWGFWHLSRFAADYRDMFGELPSKT 337


>gi|300313240|ref|YP_003777332.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 328

 Score = 56.2 bits (134), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 29/59 (49%), Positives = 37/59 (62%), Gaps = 2/59 (3%)

Query: 265 VAPMDLLRNIRLDAVRERLL--THPEANITDTAFEFGFGHLGRFSAYYRERFGELPKQT 321
             P++ LR +RL+ VR  LL  TH EA+I D A  +GF HL  F+  Y+  FGELP QT
Sbjct: 260 TTPLNYLRCVRLNGVRRELLSTTHQEASIGDIASRWGFFHLSHFAEDYQALFGELPSQT 318


  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
   0.323    0.136    0.408 

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: 959,344
Number of extensions: 38834
Number of successful extensions: 147
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 150
Number of HSP's successfully gapped: 4
Length of query: 326
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 241
Effective length of database: 1,217,395
Effective search space: 293392195
Effective search space used: 293392195
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 131 (55.1 bits)