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= 0001.0735.p
         (353 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309356|ref|YP_003773448.1| AraC family transcription regul...   619   e-178
gi|300310256|ref|YP_003774348.1| AraC family transcription regul...    81   1e-16

>gi|300309356|ref|YP_003773448.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 353

 Score =  619 bits (1595), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 313/353 (88%), Positives = 327/353 (92%)

Query: 1   MSNAPRLSRASDHQSCILSAAATGLLEFIQSEGGDPERILGAAGADCDTIEQPTATLSLE 60
           M +APR+  ASD QSCILSAAATGLLEFIQSEGGDPERILGAAGADC+ IEQPTA LSL+
Sbjct: 1   MPSAPRVPPASDRQSCILSAAATGLLEFIQSEGGDPERILGAAGADCNAIEQPTARLSLD 60

Query: 61  IYCNAMEQAARQTQNAHFGLRFGQQFMPAGLGMLGYLGLTSPTVGEALCNMGAMFHHHQQ 120
           IYCNAMEQAARQTQN HFGLRFGQQFMPAGLGMLGYLGLTSPTVGEAL NMGAMFHHHQQ
Sbjct: 61  IYCNAMEQAARQTQNEHFGLRFGQQFMPAGLGMLGYLGLTSPTVGEALRNMGAMFHHHQQ 120

Query: 121 RSHLGVTHADGLAYVEYRITDPLITQRRQDAELSIGMFFNVLRQALGQQWRPLEIHFEHG 180
           RSHLG+T ADGLAYVEYRITDPLITQRRQDAELSIGMFFNVLRQALGQQW PLEI FEHG
Sbjct: 121 RSHLGLTQADGLAYVEYRITDPLITQRRQDAELSIGMFFNVLRQALGQQWSPLEIRFEHG 180

Query: 181 ALHGDEEHEHIFGAPIQFSQATNAIVLRGDELDAPMPGADVHLHSLMRNNLRQLGLTASV 240
           ALHG EEHEHIFGAPIQFSQ TNAIVLRG +L+APMPGAD HLHSLMRNNLRQLGL A+ 
Sbjct: 181 ALHGKEEHEHIFGAPIQFSQGTNAIVLRGSDLNAPMPGADAHLHSLMRNNLRQLGLIAAT 240

Query: 241 AETLVDKVRAAIRQRLDDREPTLDDIASALGMANWTLQRRLRAAGLTYQEVLLDVRKNMA 300
            ETLVDKVRA IR RLDD EPTLD+IASALGMANWTLQRRLR AGLTYQE+LL+VRK+MA
Sbjct: 241 EETLVDKVRAVIRLRLDDSEPTLDEIASALGMANWTLQRRLRTAGLTYQELLLEVRKDMA 300

Query: 301 LVYLKDPALQISELSFLLGYSEISAFSRAFQRWHGISPTEWRRQHLGGHPRVQ 353
           L YLKDP LQISEL+FLLGYSEISAFSRAFQRWHG+SPTEWRRQHL G PRVQ
Sbjct: 301 LEYLKDPDLQISELAFLLGYSEISAFSRAFQRWHGMSPTEWRRQHLVGRPRVQ 353


>gi|300310256|ref|YP_003774348.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 344

 Score = 80.9 bits (198), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 51/176 (28%), Positives = 86/176 (48%), Gaps = 1/176 (0%)

Query: 172 PLE-IHFEHGALHGDEEHEHIFGAPIQFSQATNAIVLRGDELDAPMPGADVHLHSLMRNN 230
           PL+ I F      G  ++   FG P+ F++    +      LD P+  +D  L   +R+ 
Sbjct: 158 PLQCIDFSCALPEGRPDYLEFFGVPVNFNKPRCCLSFESIYLDLPVIRSDAALKPFLRDV 217

Query: 231 LRQLGLTASVAETLVDKVRAAIRQRLDDREPTLDDIASALGMANWTLQRRLRAAGLTYQE 290
              L +        V ++RA ++Q         + +A  LG++  TL+RRLR  G +Y  
Sbjct: 218 PANLLVRYRHDTGWVTRLRACLKQSSPTDWTDFEAMAERLGVSPATLRRRLRDEGQSYAS 277

Query: 291 VLLDVRKNMALVYLKDPALQISELSFLLGYSEISAFSRAFQRWHGISPTEWRRQHL 346
           +  ++R  +A   L    L ++ ++  LG++E SAF RAF++W G SP  +RR  L
Sbjct: 278 LKDEIRSGIAQTLLGANELSVAAIAAQLGFTEASAFHRAFRKWTGKSPGVYRRDLL 333


  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    0.135    0.405 

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: 1,166,280
Number of extensions: 50127
Number of successful extensions: 191
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 191
Number of HSP's successfully gapped: 2
Length of query: 353
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 267
Effective length of database: 1,212,660
Effective search space: 323780220
Effective search space used: 323780220
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 (21.9 bits)
S2: 131 (55.1 bits)