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= 0001.2839.p
         (345 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...   596   e-172
gi|300309356|ref|YP_003773448.1| AraC family transcription regul...    81   1e-16

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

 Score =  596 bits (1536), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 296/341 (86%), Positives = 317/341 (92%), Gaps = 2/341 (0%)

Query: 1   MLKKASDTPSIPFAFVEDALGCLLRQGYETAPVLQQAGLVSNEDELGPVTAEQYGALWLA 60
           MLKK  DT  IPF+FVEDALGCL+RQGY+T PVLQ+AGL +  DE+GPV+AEQYGALWLA
Sbjct: 1   MLKKTCDTAPIPFSFVEDALGCLVRQGYDTEPVLQEAGLTT--DEVGPVSAEQYGALWLA 58

Query: 61  IARITDDEFFGLSARPMRQGSFTLLCHAVLHSQSLGQALRRALRFLRIVLDEPYGELHVE 120
           IARITDDEFFGLSARPMRQGSFTLLCHAVLH++SLGQALRRALRFLRIVLDEPYGEL ++
Sbjct: 59  IARITDDEFFGLSARPMRQGSFTLLCHAVLHAESLGQALRRALRFLRIVLDEPYGELRID 118

Query: 121 DGKAHIILIKNRSPYPAFAYRTFLLLLLGLACWLVGRRIPLQRIDFSCALPEGRPDYLEF 180
           DGKAHIILIKNRSPYPAFAYRTFLLLLLGLACWLVGRRIPLQ IDFSCALPEGRPDYLEF
Sbjct: 119 DGKAHIILIKNRSPYPAFAYRTFLLLLLGLACWLVGRRIPLQCIDFSCALPEGRPDYLEF 178

Query: 181 FGVPVNFNKPRCCLSFDAVYLDLPVIRSDIALKPFLRDVPANLLVRYRHDTGWVTRLRDS 240
           FGVPVNFNKPRCCLSF+++YLDLPVIRSD ALKPFLRDVPANLLVRYRHDTGWVTRLR  
Sbjct: 179 FGVPVNFNKPRCCLSFESIYLDLPVIRSDAALKPFLRDVPANLLVRYRHDTGWVTRLRAC 238

Query: 241 LKQSSPTDWPDFDVIAERFEVSPATLRRRLRDEGQSYASLKDEIRSGLAQALLGKNELSV 300
           LKQSSPTDW DF+ +AER  VSPATLRRRLRDEGQSYASLKDEIRSG+AQ LLG NELSV
Sbjct: 239 LKQSSPTDWTDFEAMAERLGVSPATLRRRLRDEGQSYASLKDEIRSGIAQTLLGANELSV 298

Query: 301 AQISTQLGFTEPSAFHRAFRKWTGKSPGAFRRDLLKIRVGD 341
           A I+ QLGFTE SAFHRAFRKWTGKSPG +RRDLL++RV D
Sbjct: 299 AAIAAQLGFTEASAFHRAFRKWTGKSPGVYRRDLLQVRVVD 339


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

 Score = 80.9 bits (198), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 51/176 (28%), Positives = 87/176 (49%), Gaps = 1/176 (0%)

Query: 160 PLQRIDFSCALPEGRPDYLEFFGVPVNFNKPRCCLSFDAVYLDLPVIRSDIALKPFLRDV 219
           PL+ I F      G+ ++   FG P+ F++    +      L+ P+  +D  L   +R+ 
Sbjct: 172 PLE-IRFEHGALHGKEEHEHIFGAPIQFSQGTNAIVLRGSDLNAPMPGADAHLHSLMRNN 230

Query: 220 PANLLVRYRHDTGWVTRLRDSLKQSSPTDWPDFDVIAERFEVSPATLRRRLRDEGQSYAS 279
              L +    +   V ++R  ++       P  D IA    ++  TL+RRLR  G +Y  
Sbjct: 231 LRQLGLIAATEETLVDKVRAVIRLRLDDSEPTLDEIASALGMANWTLQRRLRTAGLTYQE 290

Query: 280 LKDEIRSGLAQALLGKNELSVAQISTQLGFTEPSAFHRAFRKWTGKSPGAFRRDLL 335
           L  E+R  +A   L   +L +++++  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    0.141    0.432 

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: 1,146,532
Number of extensions: 49587
Number of successful extensions: 207
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 207
Number of HSP's successfully gapped: 2
Length of query: 345
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 259
Effective length of database: 1,212,660
Effective search space: 314078940
Effective search space used: 314078940
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)