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= 0001.0292.p
         (334 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...   596   e-172
gi|300312695|ref|YP_003776787.1| AraC family transcription regul...    77   3e-15
gi|300311760|ref|YP_003775852.1| transcription regulator protein...    64   1e-11

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

 Score =  596 bits (1537), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 297/338 (87%), Positives = 309/338 (91%), Gaps = 4/338 (1%)

Query: 1   MELDLHPVHDSSPL----TLVQEIDTVAQSVADDTRFTAMQQELLQLLQRYTTGAEGMLQ 56
           MELDLH + D++ L                  ++ RF AMQQELLQLL+ YTTG EGML+
Sbjct: 1   MELDLHTIQDAAALLSPEAHDAAPAPAPAPAGEEARFQAMQQELLQLLEHYTTGVEGMLE 60

Query: 57  TAIPDMEIYRITCPSGPKHAVQKPVFAVIAQGSKRIFVGDEIYEYDPMHYLVASVDLPVV 116
           TAIP+MEIYRITCPSGPKHAVQKPVFAVIAQGSKRIFVGDEIYEYDPMHYLVASVDLPVV
Sbjct: 61  TAIPNMEIYRITCPSGPKHAVQKPVFAVIAQGSKRIFVGDEIYEYDPMHYLVASVDLPVV 120

Query: 117 GKVMVTSPDEPYLGLRLELDTQEIGELIGDENLPAAAHLNEGAARGLYVNRLDVDLLDAV 176
           GKVMVTSPDEPYLGLRLELDTQEIGELIGDENLPAAA ++EGAARGLYVNRLDVDLLDAV
Sbjct: 121 GKVMVTSPDEPYLGLRLELDTQEIGELIGDENLPAAAQVSEGAARGLYVNRLDVDLLDAV 180

Query: 177 LRLLRLHESPRDVPILAPMIRREILYRLLMNGQGALLRQTVLQDSQMNRVAKAIRLIKDG 236
           LRLLRL E P DVPILAPMIRREILYRLLMNGQGALLRQTVLQDSQMNRVAKAIRLIK+G
Sbjct: 181 LRLLRLQERPADVPILAPMIRREILYRLLMNGQGALLRQTVLQDSQMNRVAKAIRLIKEG 240

Query: 237 YDQALRIEDIARDVHMSVSSLHHHFKLVTAMSPLQYQKNLRLQEARKLILTADASVATAA 296
           YDQALRI+DIARDVHMSVSSLHHHFKLVTAMSPLQYQKNLRLQEARKLILTADASVATAA
Sbjct: 241 YDQALRIDDIARDVHMSVSSLHHHFKLVTAMSPLQYQKNLRLQEARKLILTADASVATAA 300

Query: 297 HRVGYESSSQFSREYSRLFGAPPLRDKRRWQEEEAPVL 334
           HRVGYESSSQFSREYSRLFGAPPLRDKRRWQEEEAPVL
Sbjct: 301 HRVGYESSSQFSREYSRLFGAPPLRDKRRWQEEEAPVL 338


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

 Score = 76.6 bits (187), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 113/244 (46%), Gaps = 11/244 (4%)

Query: 84  VIAQGSKRIFVGDEIYEYDPMHYLVASVDLPVVGKVMVTSPDE-PYLGLRLELDTQEIGE 142
           VI   S + FVGD I ++ P + ++   +LP      + +  + P   L L+        
Sbjct: 40  VITASSGKFFVGDFIGDFGPGNLVLTGPNLPHNWVSNLGAHQQVPARDLVLQFSRPFAER 99

Query: 143 LIGDENLPAAAHLNE---GAARGL-YVNRLDVDLLDAVLRLLRLHESPRDVPILAPMIR- 197
           ++G   +P  + L E   GAARGL + + L   +   +  L +   + R V +++ + R 
Sbjct: 100 VVGA--IPELSPLQEMLDGAARGLQFPDALGASITPLMQELAQASGARRVVLMMSVLERL 157

Query: 198 REILYRLLMNGQGALLRQTVLQDSQMNRVAKAIRLIKDGYDQALRIEDIARDVHMSVSSL 257
                R  + G G  L       S +N+V   IR    G    LR  D+A    MSVSS 
Sbjct: 158 ASCPERKPLAGPGYDLNAQRHMSSTLNQVLSCIRQNLGG---NLRETDLAELAGMSVSSF 214

Query: 258 HHHFKLVTAMSPLQYQKNLRLQEARKLILTADASVATAAHRVGYESSSQFSREYSRLFGA 317
              FK  T  + +QYQ  LRL EA +L++  + SV    +RVG+ + S F+R++    G 
Sbjct: 215 TRFFKRHTGCTFIQYQNGLRLNEACELLMCTELSVTEVCYRVGFNNLSNFNRQFLASKGM 274

Query: 318 PPLR 321
           PP R
Sbjct: 275 PPSR 278


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

 Score = 64.3 bits (155), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 35/95 (36%), Positives = 53/95 (55%)

Query: 225 RVAKAIRLIKDGYDQALRIEDIARDVHMSVSSLHHHFKLVTAMSPLQYQKNLRLQEARKL 284
           R+A+AIR +     Q   +  +AR   +S SS    F+    ++P+ Y    R+  A++L
Sbjct: 204 RLAQAIRALHAQPAQDWNVPRLARVAALSRSSFFERFRREVGLTPMDYLLAWRMALAKRL 263

Query: 285 ILTADASVATAAHRVGYESSSQFSREYSRLFGAPP 319
           +L AD S+A  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    0.384 

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: 949,763
Number of extensions: 35677
Number of successful extensions: 155
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 156
Number of HSP's successfully gapped: 3
Length of query: 334
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 248
Effective length of database: 1,212,660
Effective search space: 300739680
Effective search space used: 300739680
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)