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= 0006.0011.p
         (83 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311835|ref|YP_003775927.1| AraC family ethanolamine operon...   123   3e-30
gi|300313240|ref|YP_003777332.1| AraC family transcription regul...    79   7e-17
gi|300310610|ref|YP_003774702.1| AraC family transcription regul...    79   9e-17
gi|300312820|ref|YP_003776912.1| AraC family transcription regul...    78   1e-16
gi|300312312|ref|YP_003776404.1| AraC family ethanolamine operon...    73   3e-15

>gi|300311835|ref|YP_003775927.1| AraC family ethanolamine operon
           transcription regulator protein [Herbaspirillum
           seropedicae SmR1]
          Length = 332

 Score =  123 bits (309), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 58/81 (71%), Positives = 69/81 (85%), Gaps = 2/81 (2%)

Query: 1   VSRRTLQYCFEDVLGISPMTYLRSLRLNGVRRQLMQGAAAVSPHAVRVGDVAAAWGFSNF 60
           VSRRTLQYCFEDVLG+SPM+YLRSLRLNGVRR L  G    +  +  +GD+AAAWGF+NF
Sbjct: 250 VSRRTLQYCFEDVLGMSPMSYLRSLRLNGVRRALCHGDGRQAVGS--IGDIAAAWGFANF 307

Query: 61  SQFSCDYKKLFGESPSSALRA 81
           SQFSCDYKKLFG++PS+ L+A
Sbjct: 308 SQFSCDYKKLFGQTPSAMLQA 328


>gi|300313240|ref|YP_003777332.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 328

 Score = 79.0 bits (193), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 37/80 (46%), Positives = 52/80 (65%), Gaps = 4/80 (5%)

Query: 1   VSRRTLQYCFEDVLGISPMTYLRSLRLNGVRRQLMQGAAAVSPHAVRVGDVAAAWGFSNF 60
           VSRRT+Q  F+ V   +P+ YLR +RLNGVRR+L+    + +     +GD+A+ WGF + 
Sbjct: 245 VSRRTVQNSFQTVAETTPLNYLRCVRLNGVRRELL----STTHQEASIGDIASRWGFFHL 300

Query: 61  SQFSCDYKKLFGESPSSALR 80
           S F+ DY+ LFGE PS   R
Sbjct: 301 SHFAEDYQALFGELPSQTAR 320


>gi|300310610|ref|YP_003774702.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 324

 Score = 78.6 bits (192), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 38/80 (47%), Positives = 51/80 (63%), Gaps = 4/80 (5%)

Query: 1   VSRRTLQYCFEDVLGISPMTYLRSLRLNGVRRQLMQGAAAVSPHAVRVGDVAAAWGFSNF 60
           VSRRT+Q  F+ V   +P  YLR +RLNGVRR LM    + S   + +GD+A+ WGF + 
Sbjct: 238 VSRRTVQNSFQTVTETTPRNYLRCVRLNGVRRALM----STSAEQITIGDIASRWGFFHL 293

Query: 61  SQFSCDYKKLFGESPSSALR 80
           S F+ DY+ LF E PS  +R
Sbjct: 294 SHFAEDYRALFCELPSQTIR 313


>gi|300312820|ref|YP_003776912.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 331

 Score = 77.8 bits (190), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 40/86 (46%), Positives = 58/86 (67%), Gaps = 3/86 (3%)

Query: 1   VSRRTLQYCFEDVLGISPMTYLRSLRLNGVRRQLMQGAAAVSPH--AVRVGDVAAAWGFS 58
           VSRRTLQYCFE+ L ISP+ YL++LRLN   R++ +       H     +G++AA  GF+
Sbjct: 244 VSRRTLQYCFEERLDISPLQYLKALRLNAAHREIKRRTGEDRAHDRHATIGNLAALCGFN 303

Query: 59  NFSQFSCDYKKLFGESPS-SALRAAA 83
           + S+F+ +YKK+FG  PS + LRA +
Sbjct: 304 HPSRFASEYKKMFGVLPSETVLRAVS 329


>gi|300312312|ref|YP_003776404.1| AraC family ethanolamine operon
           transcription regulator protein [Herbaspirillum
           seropedicae SmR1]
          Length = 358

 Score = 73.2 bits (178), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 36/79 (45%), Positives = 52/79 (65%), Gaps = 2/79 (2%)

Query: 1   VSRRTLQYCFEDVLGISPMTYLRSLRLNGVRRQLMQGAAAVSPHAVRVGDVAAAWGFSNF 60
           VSRR LQ CF   +GI  + ++R+ RLN VR+ L++  A  +   V +GD+AA WGF + 
Sbjct: 262 VSRRHLQTCFNTSVGIPAIEFVRAERLNQVRKALVE--ARRAGLEVSIGDIAADWGFWHL 319

Query: 61  SQFSCDYKKLFGESPSSAL 79
           S+F+ DY+ +FGE PS  L
Sbjct: 320 SRFAADYRDMFGELPSKTL 338


  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
   0.324    0.133    0.397 

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: 242,151
Number of extensions: 8153
Number of successful extensions: 61
Number of sequences better than 1.0e-08: 5
Number of HSP's gapped: 62
Number of HSP's successfully gapped: 5
Length of query: 83
Length of database: 1,619,870
Length adjustment: 54
Effective length of query: 29
Effective length of database: 1,364,180
Effective search space: 39561220
Effective search space used: 39561220
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: 123 (52.0 bits)