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= 0013.0269.p
         (342 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...   466   e-132
gi|300312695|ref|YP_003776787.1| AraC family transcription regul...    70   4e-13
gi|300311760|ref|YP_003775852.1| transcription regulator protein...    63   3e-11

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

 Score =  466 bits (1198), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 224/301 (74%), Positives = 261/301 (86%), Gaps = 2/301 (0%)

Query: 44  RAAQRELVALIARLTEGAEGSLETGIEGFFLHRITNPQGPKHAVQKPVFAVIAQGAKRLF 103
           +A Q+EL+ L+   T G EG LET I    ++RIT P GPKHAVQKPVFAVIAQG+KR+F
Sbjct: 38  QAMQQELLQLLEHYTTGVEGMLETAIPNMEIYRITCPSGPKHAVQKPVFAVIAQGSKRIF 97

Query: 104 VGDDIYDYDPMHYLVSSVDLPMVGKVTMSSPETPYLGLRIDLDTREIGSLIGDEHLPQG- 162
           VGD+IY+YDPMHYLV+SVDLP+VGKV ++SP+ PYLGLR++LDT+EIG LIGDE+LP   
Sbjct: 98  VGDEIYEYDPMHYLVASVDLPVVGKVMVTSPDEPYLGLRLELDTQEIGELIGDENLPAAA 157

Query: 163 -IPSDASRGLFVNRLDITLLDAVLRLLRLLDTPRDIPILAPMVKREILYRLLMNGQGALL 221
            +   A+RGL+VNRLD+ LLDAVLRLLRL + P D+PILAPM++REILYRLLMNGQGALL
Sbjct: 158 QVSEGAARGLYVNRLDVDLLDAVLRLLRLQERPADVPILAPMIRREILYRLLMNGQGALL 217

Query: 222 RQTVLQDSQMNRIAKAIRMMKESFAQPLRVDDIARDVHMSVSSLHHHFKVVTAMSPLQYQ 281
           RQTVLQDSQMNR+AKAIR++KE + Q LR+DDIARDVHMSVSSLHHHFK+VTAMSPLQYQ
Sbjct: 218 RQTVLQDSQMNRVAKAIRLIKEGYDQALRIDDIARDVHMSVSSLHHHFKLVTAMSPLQYQ 277

Query: 282 KNLRLQEARRLMLADDVSVATASQTVGYESPSQFSREYSRMFGAPPLRDKRRWLEEEAPA 341
           KNLRLQEAR+L+L  D SVATA+  VGYES SQFSREYSR+FGAPPLRDKRRW EEEAP 
Sbjct: 278 KNLRLQEARKLILTADASVATAAHRVGYESSSQFSREYSRLFGAPPLRDKRRWQEEEAPV 337

Query: 342 L 342
           L
Sbjct: 338 L 338


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

 Score = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 114/245 (46%), Gaps = 15/245 (6%)

Query: 94  VIAQGAKRLFVGDDIYDYDPMHYLVSSVDLPMVGKVTMSS-PETPYLGLRIDLD----TR 148
           VI   + + FVGD I D+ P + +++  +LP      + +  + P   L +        R
Sbjct: 40  VITASSGKFFVGDFIGDFGPGNLVLTGPNLPHNWVSNLGAHQQVPARDLVLQFSRPFAER 99

Query: 149 EIGSLIGDEHLP-QGIPSDASRGL-FVNRLDITLLDAVLRLLRLLDTPRDIPILAPMVKR 206
            +G++   E  P Q +   A+RGL F + L  ++   +++ L      R + ++  +++R
Sbjct: 100 VVGAI--PELSPLQEMLDGAARGLQFPDALGASI-TPLMQELAQASGARRVVLMMSVLER 156

Query: 207 --EILYRLLMNGQGALLRQTVLQDSQMNRIAKAIRMMKESFAQPLRVDDIARDVHMSVSS 264
                 R  + G G  L       S +N++   IR   ++    LR  D+A    MSVSS
Sbjct: 157 LASCPERKPLAGPGYDLNAQRHMSSTLNQVLSCIR---QNLGGNLRETDLAELAGMSVSS 213

Query: 265 LHHHFKVVTAMSPLQYQKNLRLQEARRLMLADDVSVATASQTVGYESPSQFSREYSRMFG 324
               FK  T  + +QYQ  LRL EA  L++  ++SV      VG+ + S F+R++    G
Sbjct: 214 FTRFFKRHTGCTFIQYQNGLRLNEACELLMCTELSVTEVCYRVGFNNLSNFNRQFLASKG 273

Query: 325 APPLR 329
            PP R
Sbjct: 274 MPPSR 278


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

 Score = 63.2 bits (152), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/95 (37%), Positives = 51/95 (53%)

Query: 233 RIAKAIRMMKESFAQPLRVDDIARDVHMSVSSLHHHFKVVTAMSPLQYQKNLRLQEARRL 292
           R+A+AIR +    AQ   V  +AR   +S SS    F+    ++P+ Y    R+  A+RL
Sbjct: 204 RLAQAIRALHAQPAQDWNVPRLARVAALSRSSFFERFRREVGLTPMDYLLAWRMALAKRL 263

Query: 293 MLADDVSVATASQTVGYESPSQFSREYSRMFGAPP 327
           +L  D S+A  +  VGY S S FS  +SR  G PP
Sbjct: 264 LLRADGSIAEVALQVGYSSASTFSVAFSRHVGLPP 298


  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    0.136    0.389 

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: 915,545
Number of extensions: 33568
Number of successful extensions: 138
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 140
Number of HSP's successfully gapped: 3
Length of query: 342
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 256
Effective length of database: 1,212,660
Effective search space: 310440960
Effective search space used: 310440960
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 (21.8 bits)
S2: 131 (55.1 bits)