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= 0012.0166.p
         (285 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310271|ref|YP_003774363.1| AraC family transcription regul...    73   2e-14
gi|300313268|ref|YP_003777360.1| transcription regulator protein...    57   2e-09

>gi|300310271|ref|YP_003774363.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 350

 Score = 73.2 bits (178), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 92/174 (52%), Gaps = 12/174 (6%)

Query: 105 QRQAAXAALGHLAARSFGRTGIERMVREQISSAFRECHTMPLRSGNVVANTILQLVGSAL 164
           +R    A +G +A+R F R+ +E+ V   + S  ++C +  L S   +A      +G+ L
Sbjct: 149 RRVDGKAGMGLVASR-FARS-LEQ-VDLDMGSGVQDCLSAALNSIIAIA------LGATL 199

Query: 165 EASNDNPAGAAMGLRQRIVQFIDEHLSDEHLTVARIAEAFGYSSRQIHRMFSDETGMTVA 224
           EA   +       +R  +  +I +HL + HL    +A  F  S R ++ +F +E  ++V+
Sbjct: 200 EAQERDRLPVREAIRLAVETYIRDHLEEPHLGPDMLASRFKVSRRTLYSLF-EEAPLSVS 258

Query: 225 QYLWQRRLAQSLKDLQDSEQAGCTITEIAFRWGFSNAAHFSHAFRQAYGLSPRE 278
             + + RL +S +DL      G  +  +A RWGFS+A+HFS  F++ +G+ PRE
Sbjct: 259 SLIRELRLQRSARDLLSPGHPG--VLAVALRWGFSDASHFSRLFKRRFGVCPRE 310


>gi|300313268|ref|YP_003777360.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 288

 Score = 56.6 bits (135), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/104 (35%), Positives = 54/104 (51%), Gaps = 3/104 (2%)

Query: 180 QRIVQFIDEHLSDEHLTVARIAEAFGYSSRQIHRMFSDETGMTVAQYLWQRRLAQSLKDL 239
           +R++  I+ HL    L V ++A    +S     R F+D TG+ VA+Y+   RL  +   L
Sbjct: 14  ERVLDHIEAHLHAP-LEVEQLANVAHFSRFHFQRQFADFTGVGVARYILLMRLKHA--SL 70

Query: 240 QDSEQAGCTITEIAFRWGFSNAAHFSHAFRQAYGLSPRECRVAA 283
           Q + Q    I +IA   GF N   F+ AFR A+G SP + R A 
Sbjct: 71  QLAFQPQRRIIDIALEAGFENPESFTRAFRSAFGQSPSQFRRAP 114


  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
   0.322    0.133    0.402 

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: 818,422
Number of extensions: 30459
Number of successful extensions: 129
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 144
Number of HSP's successfully gapped: 3
Length of query: 285
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 201
Effective length of database: 1,222,130
Effective search space: 245648130
Effective search space used: 245648130
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 (22.0 bits)
S2: 130 (54.7 bits)