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= 0013.0008.p
         (252 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313159|ref|YP_003777251.1| AraC family transcription regul...    82   6e-17
gi|300313797|ref|YP_003777889.1| AraC family transcription regul...    70   2e-13
gi|300311952|ref|YP_003776044.1| AraC family transcription regul...    60   2e-10
gi|300313912|ref|YP_003778004.1| AraC family transcription regul...    55   5e-09

>gi|300313159|ref|YP_003777251.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 280

 Score = 81.6 bits (200), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 107/243 (44%), Gaps = 11/243 (4%)

Query: 13  YAMHRHDTYAIGITLGGVQSFQYKKSMRHSLPGNTMALYPDEPHDGQAGSEAGFRYRMLY 72
           YA H HD+++IGI   G   F   +  +   PG+ + +   + H         + YRM +
Sbjct: 39  YAPHTHDSFSIGIVDAGHSIFALAEHSQPIAPGDVVLVRAGDVHCCNPADLQCWSYRMFH 98

Query: 73  IE----PSLLQDALGGVALPF-IEGGISTDPRLFGAVRNLLLHMDDEVEPLQQDDGIFEL 127
           IE     +LL +      LP  +   +   P+    +  + L +D +    ++   +   
Sbjct: 99  IEHGWLSTLLAETPATRGLPERMRSQVLRSPQAVQLLDRMTLALDHDAS--ERVAEVITC 156

Query: 128 ARALDAVSGKRPRRHAADFR--AAQLAREYIH--GALDRTLTLDELAQASGRDRWSLTRD 183
            + +  +  +     AA     A  L R Y H      R+++LDELA+ +G  R+ L R 
Sbjct: 157 LQEIMLLCAEACAHDAAPLTEDAHGLGRAYAHLQQHCRRSVSLDELAEVAGMGRYQLIRQ 216

Query: 184 FRSFFGTSPYRYLSMRRLDMARRLMAQGLPLADAAAMSGFADQSHMTRLFTKTYGIAPAH 243
           FR  +G +P+      ++  AR L+ QG   ADAA  +GFADQSH  R F       P  
Sbjct: 217 FRRRYGMTPHALQLDMKIRQARTLLQQGASAADAAYDTGFADQSHFHRAFKSRVAATPLQ 276

Query: 244 WLR 246
           + R
Sbjct: 277 YTR 279


>gi|300313797|ref|YP_003777889.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 294

 Score = 69.7 bits (169), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/95 (37%), Positives = 57/95 (60%), Gaps = 1/95 (1%)

Query: 153 REYIHGALDRTLTLDELAQASGRDRWSLTRDFRSFFGTSPYRYLSMRRLDMARRLMAQ-G 211
           R+++   L + L+L E+A  SG  R   +R F+  FG SP+ +L  +R+ +A RL+ + G
Sbjct: 197 RDFMLSHLAQRLSLAEIAAQSGLSRAHFSRAFKQSFGLSPHAWLQQQRIALACRLLHEGG 256

Query: 212 LPLADAAAMSGFADQSHMTRLFTKTYGIAPAHWLR 246
             +   A   GF+DQSH +R+F +  G+ PA WLR
Sbjct: 257 KSMTTIALECGFSDQSHFSRVFKQVQGMGPAAWLR 291


>gi|300311952|ref|YP_003776044.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 322

 Score = 60.1 bits (144), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/93 (32%), Positives = 54/93 (58%)

Query: 152 AREYIHGALDRTLTLDELAQASGRDRWSLTRDFRSFFGTSPYRYLSMRRLDMARRLMAQG 211
           AR+ +      + ++D LAQA G ++  L   FR+  G + + +L   RL  A  ++A+G
Sbjct: 221 ARQLLEQRYAESWSVDRLAQAVGLNQKKLQAGFRAMAGRTVHAHLRELRLHAAAAMLAEG 280

Query: 212 LPLADAAAMSGFADQSHMTRLFTKTYGIAPAHW 244
           + +AD A   GF++ SH ++ F +T+G+ P+ W
Sbjct: 281 MGVADTALAVGFSNLSHFSKSFRQTHGVTPSQW 313


>gi|300313912|ref|YP_003778004.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 313

 Score = 55.1 bits (131), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 34/93 (36%), Positives = 49/93 (52%), Gaps = 1/93 (1%)

Query: 150 QLAREYIHGALDRTLTLDELAQASGRDRWSLTRDFRSFFGTSPYRYLSMRRLDMARRLMA 209
           Q A  Y    L R LT++ELA+ +       TR F S  G SP + +   RL+ AR ++ 
Sbjct: 212 QDALNYARRNLKRALTVEELAEQANLSARQFTRVFTSETGQSPAKAIEGLRLEAARLMIE 271

Query: 210 QGL-PLADAAAMSGFADQSHMTRLFTKTYGIAP 241
           Q   PL   A  +GF D+ HM  +F + +G+AP
Sbjct: 272 QSRHPLEVVARETGFRDRRHMREVFLRGFGVAP 304


  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
   0.324    0.139    0.419 

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: 837,829
Number of extensions: 34575
Number of successful extensions: 132
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 136
Number of HSP's successfully gapped: 4
Length of query: 252
Length of database: 1,619,870
Length adjustment: 83
Effective length of query: 169
Effective length of database: 1,226,865
Effective search space: 207340185
Effective search space used: 207340185
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 129 (54.3 bits)