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= 0389.0008.p
         (309 letters)

Database: COG 
           115,334 sequences; 38,378,431 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

BS_ybbB_1 [K] COG2207 AraC-type DNA-binding domain-containing pr...    75   1e-13
lin0157 [K] COG2207 AraC-type DNA-binding domain-containing prot...    74   3e-13
BH0989 [K] COG2207 AraC-type DNA-binding domain-containing proteins    72   1e-12
BH3679 [T] COG4753 Response regulator containing CheY-like recei...    70   3e-12
BH3842 [T] COG4753 Response regulator containing CheY-like recei...    69   1e-11

>BS_ybbB_1 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 364

 Score = 75.5 bits (184), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 5/95 (5%), Positives = 16/95 (16%)

Query: 212 IHEVANYVSQHPGAMHRVEDLAARAGLSPRYFSIKFKEITGSSVQSYVIRTRIERAQHLL 271
             ++         A  R               + +  +          +     R     
Sbjct: 165 GVDLEGLARHRGSAFGRTLQPQLSQASFENLLAAEMLKTDARQNLRLWVLEDESRMIGSN 224

Query: 272 LYAGMNVTEVADALGYRDIFFFSRQFKQHTGKSPS 306
                    +  A        F  + ++   +   
Sbjct: 225 HLPECLRERMTQAAIAVVEDPFEIRLERLNEEYFL 259


>lin0157 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 277

 Score = 74.3 bits (181), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 47/136 (34%), Positives = 75/136 (55%), Gaps = 10/136 (7%)

Query: 182 LILK----QLMIHLLREDQVMPVERH------VSNQLAEVIHEVANYVSQHPGAMHRVED 231
           LILK    QL+IH+LRE     +E +         Q   +++E+ +Y+ +H      +  
Sbjct: 136 LILKAFVMQLIIHVLREATPEQLENNGVKLSTDEQQKQMLVNEIIHYMEKHHTEDVSLST 195

Query: 232 LAARAGLSPRYFSIKFKEITGSSVQSYVIRTRIERAQHLLLYAGMNVTEVADALGYRDIF 291
           L+    +SP Y S  FKE TG S  +Y+I+ R+ RA+ LL    + V + A+ +GY D +
Sbjct: 196 LSQTMYISPAYISKVFKEETGESPINYLIKIRLTRAEELLKNKDVTVKQAANMVGYNDAY 255

Query: 292 FFSRQFKQHTGKSPSE 307
           +FS+ FK++ G  PSE
Sbjct: 256 YFSKLFKKYYGFPPSE 271


>BH0989 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 278

 Score = 72.4 bits (176), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 37/127 (29%), Positives = 71/127 (55%)

Query: 183 ILKQLMIHLLREDQVMPVERHVSNQLAEVIHEVANYVSQHPGAMHRVEDLAARAGLSPRY 242
           I  + + + +  D ++     ++ +   VI +V  Y+  H      V+ LA  +G+  + 
Sbjct: 141 IQAKALFYTIFHDMLICARNRLNRESQLVIEQVVEYIHHHYMEPMTVKKLADMSGMGVKP 200

Query: 243 FSIKFKEITGSSVQSYVIRTRIERAQHLLLYAGMNVTEVADALGYRDIFFFSRQFKQHTG 302
           FS  FK+  G     Y+I+ R++RA++LL+ +  ++ ++A+++GY D  +FSR FK+H G
Sbjct: 201 FSYLFKKYIGMFPIDYLIQYRLKRAKNLLVSSNSSIADIAESIGYLDALYFSRLFKKHIG 260

Query: 303 KSPSEIR 309
            SP+  R
Sbjct: 261 CSPTAFR 267


>BH3679 [T] COG4753 Response regulator containing CheY-like receiver domain
           and AraC-type DNA-binding domain
          Length = 257

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 58/101 (57%)

Query: 209 AEVIHEVANYVSQHPGAMHRVEDLAARAGLSPRYFSIKFKEITGSSVQSYVIRTRIERAQ 268
           ++ IHE  +Y+  H      ++D+A    L+P Y S  FKE T  +   Y+ R R++ A+
Sbjct: 153 SDSIHEALHYIDAHLDQKIGLKDVAKSVHLNPSYLSALFKEKTNMTFSEYLTRKRLQHAK 212

Query: 269 HLLLYAGMNVTEVADALGYRDIFFFSRQFKQHTGKSPSEIR 309
           HLL+     ++++A+  GY+   +F + FK+H G +P++ R
Sbjct: 213 HLLVSTDRPISDIAEKCGYQTAKYFIKIFKEHEGMTPTQYR 253


>BH3842 [T] COG4753 Response regulator containing CheY-like receiver domain
           and AraC-type DNA-binding domain
          Length = 530

 Score = 68.6 bits (166), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 38/93 (40%), Positives = 53/93 (56%)

Query: 217 NYVSQHPGAMHRVEDLAARAGLSPRYFSIKFKEITGSSVQSYVIRTRIERAQHLLLYAGM 276
           +YV  H      ++DLA   GLSP Y S  FKE    +   YV + R+E A+ LL     
Sbjct: 422 DYVHDHFREPLTLDDLAKHIGLSPYYVSKLFKERFDLTFSEYVTQLRVEHAKQLLSLTQK 481

Query: 277 NVTEVADALGYRDIFFFSRQFKQHTGKSPSEIR 309
           ++ E+   +GY+D  +FSR FK+ TGKSPS+ R
Sbjct: 482 SLKEITYEIGYKDPNYFSRVFKKLTGKSPSDYR 514


  Database: COG
    Posted date:  Aug 3, 2010  9:58 AM
  Number of letters in database: 38,378,431
  Number of sequences in database:  115,334
  
Lambda     K      H
   0.321    0.136    0.402 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 115334
Number of Hits to DB: 22,603,196
Number of extensions: 913693
Number of successful extensions: 2457
Number of sequences better than 1.0e-05: 64
Number of HSP's gapped: 2453
Number of HSP's successfully gapped: 64
Length of query: 309
Length of database: 38,378,431
Length adjustment: 106
Effective length of query: 203
Effective length of database: 26,153,027
Effective search space: 5309064481
Effective search space used: 5309064481
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: 116 (49.3 bits)