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= 0011.0060.p
         (289 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...   200   1e-52
gi|300311760|ref|YP_003775852.1| transcription regulator protein...    64   2e-11
gi|300312695|ref|YP_003776787.1| AraC family transcription regul...    60   3e-10

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

 Score =  200 bits (508), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 111/274 (40%), Positives = 164/274 (59%), Gaps = 7/274 (2%)

Query: 10  GRDGLAHTPIAGLTIVRATEVSELLYAISRPLVCLVLQGGKRVAMGAQAFAFSAGDSLLI 69
           G +G+  T I  + I R T  S   +A+ +P+  ++ QG KR+ +G + + +     L+ 
Sbjct: 54  GVEGMLETAIPNMEIYRITCPSGPKHAVQKPVFAVIAQGSKRIFVGDEIYEYDPMHYLVA 113

Query: 70  TADVPTVSQITHASLAAPYLSLVLELDPAVIADLAMQMEAAPASAQAP------VRVDPT 123
           + D+P V ++   S   PYL L LELD   I +L +  E  PA+AQ        + V+  
Sbjct: 114 SVDLPVVGKVMVTSPDEPYLGLRLELDTQEIGEL-IGDENLPAAAQVSEGAARGLYVNRL 172

Query: 124 DAEVADAALRLMRLLDRPAALPVLQTQLTRELHYWLLAGKHGAAIRNLGWPDSQARRVAR 183
           D ++ DA LRL+RL +RPA +P+L   + RE+ Y LL    GA +R     DSQ  RVA+
Sbjct: 173 DVDLLDAVLRLLRLQERPADVPILAPMIRREILYRLLMNGQGALLRQTVLQDSQMNRVAK 232

Query: 184 AVEVLRTDFAQALPVERLAAVAGMSPSSFHQHFRSVTSLSPLQFQKQLRLIEARRLMLTD 243
           A+ +++  + QAL ++ +A    MS SS H HF+ VT++SPLQ+QK LRL EAR+L+LT 
Sbjct: 233 AIRLIKEGYDQALRIDDIARDVHMSVSSLHHHFKLVTAMSPLQYQKNLRLQEARKLILTA 292

Query: 244 GVSASSAAFAVGYESVPQFTREYGRMFGLPPAKD 277
             S ++AA  VGYES  QF+REY R+FG PP +D
Sbjct: 293 DASVATAAHRVGYESSSQFSREYSRLFGAPPLRD 326


>gi|300311760|ref|YP_003775852.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 319

 Score = 63.5 bits (153), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/97 (38%), Positives = 53/97 (54%)

Query: 180 RVARAVEVLRTDFAQALPVERLAAVAGMSPSSFHQHFRSVTSLSPLQFQKQLRLIEARRL 239
           R+A+A+  L    AQ   V RLA VA +S SSF + FR    L+P+ +    R+  A+RL
Sbjct: 204 RLAQAIRALHAQPAQDWNVPRLARVAALSRSSFFERFRREVGLTPMDYLLAWRMALAKRL 263

Query: 240 MLTDGVSASSAAFAVGYESVPQFTREYGRMFGLPPAK 276
           +L    S +  A  VGY S   F+  + R  GLPP++
Sbjct: 264 LLRADGSIAEVALQVGYSSASTFSVAFSRHVGLPPSQ 300


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

 Score = 59.7 bits (143), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 29/96 (30%), Positives = 53/96 (55%)

Query: 181 VARAVEVLRTDFAQALPVERLAAVAGMSPSSFHQHFRSVTSLSPLQFQKQLRLIEARRLM 240
           + + +  +R +    L    LA +AGMS SSF + F+  T  + +Q+Q  LRL EA  L+
Sbjct: 183 LNQVLSCIRQNLGGNLRETDLAELAGMSVSSFTRFFKRHTGCTFIQYQNGLRLNEACELL 242

Query: 241 LTDGVSASSAAFAVGYESVPQFTREYGRMFGLPPAK 276
           +   +S +   + VG+ ++  F R++    G+PP++
Sbjct: 243 MCTELSVTEVCYRVGFNNLSNFNRQFLASKGMPPSR 278


  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
   0.320    0.131    0.371 

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: 773,859
Number of extensions: 26391
Number of successful extensions: 203
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 205
Number of HSP's successfully gapped: 3
Length of query: 289
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 205
Effective length of database: 1,222,130
Effective search space: 250536650
Effective search space used: 250536650
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)