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= 0541.0004.p
         (351 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

BH0793 [T] COG4753 Response regulator containing CheY-like recei...    75   2e-13
BH3842 [T] COG4753 Response regulator containing CheY-like recei...    74   4e-13
BH3679 [T] COG4753 Response regulator containing CheY-like recei...    74   5e-13
lin1152 [K] COG2207 AraC-type DNA-binding domain-containing prot...    72   1e-12
BH2109 [T] COG4753 Response regulator containing CheY-like recei...    72   1e-12

>BH0793 [T] COG4753 Response regulator containing CheY-like receiver domain
           and AraC-type DNA-binding domain
          Length = 508

 Score = 75.1 bits (183), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/105 (35%), Positives = 60/105 (57%)

Query: 243 NPTLQPAFDFIYSNKHENFSLEAMARLCHISPSYFSRLFVRESGENFSAYVSRLKIGQAK 302
           +P +Q     I+ +  ++ SL+ +    HI+P Y  +LF RE G +F+ Y+++L+I +AK
Sbjct: 402 SPIIQTVLQHIHQHFSQDLSLKTLGHSFHINPIYLGQLFQREVGCSFTKYLNQLRIDRAK 461

Query: 303 QLLETTGLSVNEISDHLSFCDAGYFIKIFKKYEQRTPAAYRSFIK 347
           +LL  +     +I   + + DA YF K FKKYE  TP  +R   K
Sbjct: 462 KLLLNSYDRAGQIGKKVGYGDATYFYKQFKKYEAMTPTEWRKVHK 506


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

 Score = 73.6 bits (179), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 36/100 (36%), Positives = 59/100 (59%)

Query: 249 AFDFIYSNKHENFSLEAMARLCHISPSYFSRLFVRESGENFSAYVSRLKIGQAKQLLETT 308
           A D+++ +  E  +L+ +A+   +SP Y S+LF       FS YV++L++  AKQLL  T
Sbjct: 420 ARDYVHDHFREPLTLDDLAKHIGLSPYYVSKLFKERFDLTFSEYVTQLRVEHAKQLLSLT 479

Query: 309 GLSVNEISDHLSFCDAGYFIKIFKKYEQRTPAAYRSFIKG 348
             S+ EI+  + + D  YF ++FKK   ++P+ YR  I G
Sbjct: 480 QKSLKEITYEIGYKDPNYFSRVFKKLTGKSPSDYRKSING 519


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

 Score = 73.6 bits (179), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 62/104 (59%)

Query: 241 CTNPTLQPAFDFIYSNKHENFSLEAMARLCHISPSYFSRLFVRESGENFSAYVSRLKIGQ 300
            ++ ++  A  +I ++  +   L+ +A+  H++PSY S LF  ++   FS Y++R ++  
Sbjct: 151 SSSDSIHEALHYIDAHLDQKIGLKDVAKSVHLNPSYLSALFKEKTNMTFSEYLTRKRLQH 210

Query: 301 AKQLLETTGLSVNEISDHLSFCDAGYFIKIFKKYEQRTPAAYRS 344
           AK LL +T   +++I++   +  A YFIKIFK++E  TP  YR 
Sbjct: 211 AKHLLVSTDRPISDIAEKCGYQTAKYFIKIFKEHEGMTPTQYRK 254


>lin1152 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 183

 Score = 72.4 bits (176), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 40/111 (36%), Positives = 61/111 (54%)

Query: 237 SVVTCTNPTLQPAFDFIYSNKHENFSLEAMARLCHISPSYFSRLFVRESGENFSAYVSRL 296
           S  +  +  ++ A  +I  N H + +LE +A   ++SP Y S+LF  E   NF  YV+  
Sbjct: 73  SKTSGEHKEIKQAIRYIKKNIHRSITLEEVANYVYLSPFYLSKLFKNELNINFINYVNEQ 132

Query: 297 KIGQAKQLLETTGLSVNEISDHLSFCDAGYFIKIFKKYEQRTPAAYRSFIK 347
           K+  AK+ LE +  +V+ I+ +L F  A YF K+FKK    TP  YR  +K
Sbjct: 133 KMLYAKEQLEKSDWAVHTIAKNLGFSRASYFCKVFKKEFDMTPKEYRDSLK 183


>BH2109 [T] COG4753 Response regulator containing CheY-like receiver domain
           and AraC-type DNA-binding domain
          Length = 525

 Score = 72.0 bits (175), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 58/93 (62%)

Query: 252 FIYSNKHENFSLEAMARLCHISPSYFSRLFVRESGENFSAYVSRLKIGQAKQLLETTGLS 311
           +I ++ HEN SL+++A L +++P Y  +LF +  G  F  Y+ +L++ +AK+LL  T + 
Sbjct: 429 YIENHYHENISLKSIASLFYMNPVYMGQLFKKTFGVYFKEYLLKLRMNEAKKLLRQTDMR 488

Query: 312 VNEISDHLSFCDAGYFIKIFKKYEQRTPAAYRS 344
           V E+++ + F    YF+  F+K  + TP  YR+
Sbjct: 489 VYEVAERVGFGSTDYFVTQFEKINKMTPTEYRN 521


  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
   0.320    0.132    0.382 

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: 23,692,722
Number of extensions: 929590
Number of successful extensions: 2924
Number of sequences better than 1.0e-05: 44
Number of HSP's gapped: 2925
Number of HSP's successfully gapped: 44
Length of query: 351
Length of database: 38,378,431
Length adjustment: 107
Effective length of query: 244
Effective length of database: 26,037,693
Effective search space: 6353197092
Effective search space used: 6353197092
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 (21.8 bits)
S2: 116 (49.3 bits)