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= 0025.0103.p
         (287 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...   176   2e-45
gi|300312695|ref|YP_003776787.1| AraC family transcription regul...    60   2e-10
gi|300313081|ref|YP_003777173.1| transcription regulator protein...    56   3e-09

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

 Score =  176 bits (447), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 109/279 (39%), Positives = 161/279 (57%), Gaps = 10/279 (3%)

Query: 7   EKQLESAIPRLAIGAFRQSEPT--IMAVSAGV-CLILQGAKQMMVGKTMLRYSAGGCFAS 63
           E  LE+AIP + I  +R + P+    AV   V  +I QG+K++ VG  +  Y       +
Sbjct: 56  EGMLETAIPNMEI--YRITCPSGPKHAVQKPVFAVIAQGSKRIFVGDEIYEYDPMHYLVA 113

Query: 64  LIELPTTCCIFEMDGDKPYIGTGLTLDHEMFTSLIAD--MPE--ERSKKEMLGFNVETVS 119
            ++LP    +     D+PY+G  L LD +    LI D  +P   + S+    G  V  + 
Sbjct: 114 SVDLPVVGKVMVTSPDEPYLGLRLELDTQEIGELIGDENLPAAAQVSEGAARGLYVNRLD 173

Query: 120 RDVLEAWDHLLALLDTPSDIPILAASRERELLYRLLQSPHGPLLRQIGREEGKLAQIRRA 179
            D+L+A   LL L + P+D+PILA    RE+LYRLL +  G LLRQ   ++ ++ ++ +A
Sbjct: 174 VDLLDAVLRLLRLQERPADVPILAPMIRREILYRLLMNGQGALLRQTVLQDSQMNRVAKA 233

Query: 180 IDWMRHHFDESFPIETVADIAGMSVASFNRHFRAATSTSPLQYQKTLRLQAARRL-LASD 238
           I  ++  +D++  I+ +A    MSV+S + HF+  T+ SPLQYQK LRLQ AR+L L +D
Sbjct: 234 IRLIKEGYDQALRIDDIARDVHMSVSSLHHHFKLVTAMSPLQYQKNLRLQEARKLILTAD 293

Query: 239 VDATRTAYAVGYESPSQFSREYSRLFGRPPKQDASQLRE 277
                 A+ VGYES SQFSREYSRLFG PP +D  + +E
Sbjct: 294 ASVATAAHRVGYESSSQFSREYSRLFGAPPLRDKRRWQE 332


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

 Score = 60.1 bits (144), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 35/113 (30%), Positives = 61/113 (53%), Gaps = 2/113 (1%)

Query: 174 AQIRRAIDWMRHHFDESFPIETVADIAGMSVASFNRHFRAATSTSPLQYQKTLRL-QAAR 232
           + + + +  +R +   +     +A++AGMSV+SF R F+  T  + +QYQ  LRL +A  
Sbjct: 181 STLNQVLSCIRQNLGGNLRETDLAELAGMSVSSFTRFFKRHTGCTFIQYQNGLRLNEACE 240

Query: 233 RLLASDVDATRTAYAVGYESPSQFSREYSRLFGRPPKQDASQLRENISDVSGI 285
            L+ +++  T   Y VG+ + S F+R++    G PP +  S  R N  DV  +
Sbjct: 241 LLMCTELSVTEVCYRVGFNNLSNFNRQFLASKGMPPSRFRSLHRLN-DDVRAV 292


>gi|300313081|ref|YP_003777173.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 330

 Score = 56.2 bits (134), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 31/101 (30%), Positives = 55/101 (54%), Gaps = 1/101 (0%)

Query: 170 EGKLAQIRRAIDWMRHHFDESFPIETVADIAGMSVASFNRHFRAATSTSPLQYQKTLRLQ 229
           +G   +IRRA+ + R H  ++  ++ +A++A +S   F+R F A T  +P +  + +R +
Sbjct: 207 DGGSERIRRALGFAREHLHQALTVDLLAEVACLSRRQFDRAFAAETGQTPARAIEQMRAE 266

Query: 230 AARRLLASDVDATRT-AYAVGYESPSQFSREYSRLFGRPPK 269
           AAR  +    D   + A A G+    +  R   RLFG+PP+
Sbjct: 267 AARLRIEQSQDTLESIARATGFGDADRMRRACLRLFGQPPQ 307


  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
   0.321    0.135    0.388 

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: 833,714
Number of extensions: 32123
Number of successful extensions: 146
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 151
Number of HSP's successfully gapped: 4
Length of query: 287
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 203
Effective length of database: 1,222,130
Effective search space: 248092390
Effective search space used: 248092390
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: 130 (54.7 bits)