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= 0004.0111.p
         (325 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...    64   1e-11

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

 Score = 64.3 bits (155), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 53/220 (24%), Positives = 106/220 (48%), Gaps = 6/220 (2%)

Query: 100 RRERKSTQFVPGILAL-DMGQPMRMLRPTYAHVLAFFLPRAMVEAEIADADALHGQVLAY 158
           R++ + +  +PG  ++ D  +P  +      HVL+F +PR  V + +A       + +  
Sbjct: 94  RQDGQESMVLPGDFSIVDSTRPYFLDYQGDWHVLSFRIPREQVISRLASPYKATARRVDG 153

Query: 159 TSPLTRLLLAHLVALSRDLRGMS-ATAAEEAIRVCVDLLLA-AFGKQQRLTSSARAAAQS 216
            + +   L+A   A S +   +   +  ++ +   ++ ++A A G         R   + 
Sbjct: 154 KAGMG--LVASRFARSLEQVDLDMGSGVQDCLSAALNSIIAIALGATLEAQERDRLPVRE 211

Query: 217 VLRSQIQRHVQSRLYSKDLTPENVLRAFDLSRPTLYRMFENEG-GLGTYIRNFRLREAAE 275
            +R  ++ +++  L    L P+ +   F +SR TLY +FE     + + IR  RL+ +A 
Sbjct: 212 AIRLAVETYIRDHLEEPHLGPDMLASRFKVSRRTLYSLFEEAPLSVSSLIRELRLQRSAR 271

Query: 276 ELVSMRRTAVMEIAYGLGFGSASDFTRAFRRAYGMTPQDF 315
           +L+S     V+ +A   GF  AS F+R F+R +G+ P++F
Sbjct: 272 DLLSPGHPGVLAVALRWGFSDASHFSRLFKRRFGVCPREF 311


  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
   0.325    0.135    0.385 

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: 869,188
Number of extensions: 31160
Number of successful extensions: 154
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 156
Number of HSP's successfully gapped: 1
Length of query: 325
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 240
Effective length of database: 1,217,395
Effective search space: 292174800
Effective search space used: 292174800
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: 131 (55.1 bits)