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= 0013.0054.p
         (344 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310256|ref|YP_003774348.1| AraC family transcription regul...   695   0.0  
gi|300309356|ref|YP_003773448.1| AraC family transcription regul...    84   1e-17

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

 Score =  695 bits (1794), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 342/344 (99%), Positives = 342/344 (99%)

Query: 1   MLKKTCDTAPIPFSFVEDALGCLVRQGYDTEPVLQEAGLTTDEVGPVSAEQYGALWLAIA 60
           MLKKTCDTAPIPFSFVEDALGCLVRQGYDTEPVLQEAGLTTDEVGPVSAEQYGALWLAIA
Sbjct: 1   MLKKTCDTAPIPFSFVEDALGCLVRQGYDTEPVLQEAGLTTDEVGPVSAEQYGALWLAIA 60

Query: 61  RITDDEFFGLSARPMRQGSFTLLCHAVLHAESLGQALRRALRFLRIVLDEPYGELRIDDG 120
           RITDDEFFGLSARPMRQGSFTLLCHAVLHAESLGQALRRALRFLRIVLDEPYGELRIDDG
Sbjct: 61  RITDDEFFGLSARPMRQGSFTLLCHAVLHAESLGQALRRALRFLRIVLDEPYGELRIDDG 120

Query: 121 KAHIILIKNRSPYPAFAYRTFLLLLLGLACWLVGRRIPLQSIDFSCALPEGRPDYLEFFG 180
           KAHIILIKNRSPYPAFAYRTFLLLLLGLACWLVGRRIPLQ IDFSCALPEGRPDYLEFFG
Sbjct: 121 KAHIILIKNRSPYPAFAYRTFLLLLLGLACWLVGRRIPLQCIDFSCALPEGRPDYLEFFG 180

Query: 181 VPVNFNKPRCCLSFESIYLDLPVIRSDAALKPFLRDVPANLLVRYRHDTGWVTRLRACLK 240
           VPVNFNKPRCCLSFESIYLDLPVIRSDAALKPFLRDVPANLLVRYRHDTGWVTRLRACLK
Sbjct: 181 VPVNFNKPRCCLSFESIYLDLPVIRSDAALKPFLRDVPANLLVRYRHDTGWVTRLRACLK 240

Query: 241 QSPPTDWTDFEAMAERLGVSPATLRRRLRDEGQSYASLKDEIRSGIAQTLLGANELSVAA 300
           QS PTDWTDFEAMAERLGVSPATLRRRLRDEGQSYASLKDEIRSGIAQTLLGANELSVAA
Sbjct: 241 QSSPTDWTDFEAMAERLGVSPATLRRRLRDEGQSYASLKDEIRSGIAQTLLGANELSVAA 300

Query: 301 IAAQLGFTEASAFHRAFRKWTGKSPGVYRRDLLQVRVVDSQRCG 344
           IAAQLGFTEASAFHRAFRKWTGKSPGVYRRDLLQVRVVDSQRCG
Sbjct: 301 IAAQLGFTEASAFHRAFRKWTGKSPGVYRRDLLQVRVVDSQRCG 344


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

 Score = 84.0 bits (206), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 53/176 (30%), Positives = 89/176 (50%), Gaps = 1/176 (0%)

Query: 158 PLQSIDFSCALPEGRPDYLEFFGVPVNFNKPRCCLSFESIYLDLPVIRSDAALKPFLRDV 217
           PL+ I F      G+ ++   FG P+ F++    +      L+ P+  +DA L   +R+ 
Sbjct: 172 PLE-IRFEHGALHGKEEHEHIFGAPIQFSQGTNAIVLRGSDLNAPMPGADAHLHSLMRNN 230

Query: 218 PANLLVRYRHDTGWVTRLRACLKQSPPTDWTDFEAMAERLGVSPATLRRRLRDEGQSYAS 277
              L +    +   V ++RA ++          + +A  LG++  TL+RRLR  G +Y  
Sbjct: 231 LRQLGLIAATEETLVDKVRAVIRLRLDDSEPTLDEIASALGMANWTLQRRLRTAGLTYQE 290

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


  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    0.140    0.434 

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: 1,122,005
Number of extensions: 48273
Number of successful extensions: 239
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 239
Number of HSP's successfully gapped: 2
Length of query: 344
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 258
Effective length of database: 1,212,660
Effective search space: 312866280
Effective search space used: 312866280
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)