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= 0397.0013.p
         (425 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

lin2267 [K] COG2207 AraC-type DNA-binding domain-containing prot...   377   e-104
CAC1451 [K] COG2207 AraC-type DNA-binding domain-containing prot...    92   1e-18
lin0157 [K] COG2207 AraC-type DNA-binding domain-containing prot...    86   8e-17
BH3679 [T] COG4753 Response regulator containing CheY-like recei...    80   7e-15
L0229 [K] COG2207 AraC-type DNA-binding domain-containing proteins     79   1e-14

>lin2267 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 292

 Score =  377 bits (967), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 175/292 (59%), Positives = 221/292 (75%)

Query: 111 MSIYLELPDVDKHFPFRSLICGGDELCYPHWHKEIEIIYVTKGRLNLGINDTPIRMEQGE 170
           MS YLE+P+++K FPFRS +  G+ L YPHWHKEIEIIY  KG LNLG+ND PI++ +GE
Sbjct: 1   MSEYLEIPELNKAFPFRSFVNEGEVLVYPHWHKEIEIIYALKGSLNLGVNDMPIQLNEGE 60

Query: 171 VQFINGGDVHYFLASPESERVVIQFDLNLFQEVAALGSSGYSLRDLFTEMEHSSPSWPEA 230
           +Q INGGDVHYFLASP SER+VIQFDL+LFQE   +     +LR++ TEM H S  WPE 
Sbjct: 61  IQIINGGDVHYFLASPNSERIVIQFDLSLFQEEMQMDGQNGTLREMLTEMAHLSREWPEE 120

Query: 231 ATAKVISLIESIYEEDTQRREGYAYLIKARMFELLTVILREIPKNRTQRQPKFSEDTLTQ 290
            TAKV SLI +I+ E +    G  Y++KA +  ++ +I REIP+ +TQ     SE  + +
Sbjct: 121 TTAKVQSLIRNIHLESSNDSPGKHYILKADLLAIIGLIYREIPQKKTQPDSVISEKAVLK 180

Query: 291 SRETMERLERIFAYVELHYQKSISLNEVARYMGFSPYYFTKLFKRNTGMTFVAFLNEYRL 350
           S+ET+++L++IF+YVE HYQ+ +SL EVA Y GFS YYFTK FKRNTGMTFV FLN+YRL
Sbjct: 181 SKETLQKLDQIFSYVEKHYQEPVSLQEVADYTGFSTYYFTKFFKRNTGMTFVTFLNDYRL 240

Query: 351 NKAKWILLNEDLPMSAVAEAAGFGSVKTFHHFFKEATGISPLKYHKTIFRNN 402
           NKAKW+LLNE  P++ VAE AGF SVKTFHH FK A G++PLKY KTI+ NN
Sbjct: 241 NKAKWMLLNEAFPVTEVAELAGFSSVKTFHHAFKRAMGVAPLKYRKTIYGNN 292


>CAC1451 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 295

 Score = 92.4 bits (228), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/265 (23%), Positives = 121/265 (45%), Gaps = 23/265 (8%)

Query: 140 HWHKEIEIIYVTKGRLNLGINDTPIRMEQGEVQFINGGDVHYFLASPESERVVIQFDLNL 199
           HWH+ ++I Y T G   L        +  G +  IN  ++HY  +   + +         
Sbjct: 36  HWHEHLQIYYFTAGTAYLECAQNKFDVTTGSIAIINSNELHYLESHSNNLK--------- 86

Query: 200 FQEVAALGSSGYSLRDLFTEMEHSSPSWPEAATAK--------VISLIESIYEEDTQRRE 251
           F  +    +  +S ++   + ++ +P      T K        ++  I++I +E + +  
Sbjct: 87  FYTIRIEPTFLFSNKEDLLQTKYLAPLALNRITFKNLIENDLQILECIKTILKEYSSKNI 146

Query: 252 GYAYLIKARMFELLTVILREIPKNRTQRQPKFSEDTLTQSRETMERLERIFAYVELHYQK 311
           GY   +KA +++L+  +LR             +E+   + +  + + + +F  +E  Y +
Sbjct: 147 GYELAVKANIYQLIVYLLRGYV------DKILNENEFEERKRILNKFQCVFRLIEEKYTE 200

Query: 312 SISLNEVARYMGFSPYYFTKLFKRNTGMTFVAFLNEYRLNKAKWILLNEDLPMSAVAEAA 371
            ++LNE+A  + FS ++F + FK+ TG T   ++N  RL K+   L   DL ++ +A   
Sbjct: 201 KLTLNELADCVNFSTHHFCRTFKQMTGKTTTDYINGIRLYKSTNYLKQTDLNITEIAIKC 260

Query: 372 GFGSVKTFHHFFKEATGISPLKYHK 396
           GF +   F   FK+   ++P KY K
Sbjct: 261 GFDNNNYFSRLFKKHYDMTPTKYRK 285


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

 Score = 86.3 bits (212), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 65/253 (25%), Positives = 116/253 (45%), Gaps = 14/253 (5%)

Query: 140 HWHKEIEIIYVTKGRLNLGINDTPIRMEQGEVQFINGGDVHYFLASPESERVVIQFDLNL 199
           H H  +EI  + +G +   I    + +E+G++   N G  HY +  P      +      
Sbjct: 30  HHHDFLEISIICEGNVIYDIEGERVALEKGDMLIFNPGVNHYDITEPGMTNAQLHIGFRN 89

Query: 200 FQEVAALGSSGYSLRDLFTEMEHSSPSWPEAATAKVISLIESIYEEDTQRREGYAYLIKA 259
           F         GYS      +         E+A   ++S+ + I EE    + GY  ++KA
Sbjct: 90  F------ALEGYSRNTFPFKKAFLRKKEDESA---ILSISKQIIEEKDAEKPGYDLILKA 140

Query: 260 RMFELLTVILRE-IPKNRTQRQPKFSEDTLTQSRETMERLERIFAYVELHYQKSISLNEV 318
            + +L+  +LRE  P+       K S D   Q ++ +  +  I  Y+E H+ + +SL+ +
Sbjct: 141 FVMQLIIHVLREATPEQLENNGVKLSTDE--QQKQML--VNEIIHYMEKHHTEDVSLSTL 196

Query: 319 ARYMGFSPYYFTKLFKRNTGMTFVAFLNEYRLNKAKWILLNEDLPMSAVAEAAGFGSVKT 378
           ++ M  SP Y +K+FK  TG + + +L + RL +A+ +L N+D+ +   A   G+     
Sbjct: 197 SQTMYISPAYISKVFKEETGESPINYLIKIRLTRAEELLKNKDVTVKQAANMVGYNDAYY 256

Query: 379 FHHFFKEATGISP 391
           F   FK+  G  P
Sbjct: 257 FSKLFKKYYGFPP 269


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

 Score = 79.7 bits (195), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 36/93 (38%), Positives = 55/93 (59%)

Query: 304 YVELHYQKSISLNEVARYMGFSPYYFTKLFKRNTGMTFVAFLNEYRLNKAKWILLNEDLP 363
           Y++ H  + I L +VA+ +  +P Y + LFK  T MTF  +L   RL  AK +L++ D P
Sbjct: 162 YIDAHLDQKIGLKDVAKSVHLNPSYLSALFKEKTNMTFSEYLTRKRLQHAKHLLVSTDRP 221

Query: 364 MSAVAEAAGFGSVKTFHHFFKEATGISPLKYHK 396
           +S +AE  G+ + K F   FKE  G++P +Y K
Sbjct: 222 ISDIAEKCGYQTAKYFIKIFKEHEGMTPTQYRK 254


>L0229 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 327

 Score = 79.3 bits (194), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/261 (23%), Positives = 117/261 (44%), Gaps = 20/261 (7%)

Query: 139 PHWHKEIEIIYVTKGRLNLGINDTPIRMEQGEVQFINGGDVHYFLASPESERVVIQFDLN 198
           PH H +IE+ +V +G   +   +    ++ G+    N   VH   +S   + +++QF   
Sbjct: 30  PHLHFDIELAFVLEGAGQVITQEQCFEIKAGQAIIFNSCQVHELSSSDSMKLLILQFSSE 89

Query: 199 LFQEVAALGSSGYSLRDLFTEMEHSSPSWPEAATAKVISLIESIYEE--DTQRREGYAYL 256
           +F+ +       Y     F     +  + PE     + + +    ++  ++ R  GY  L
Sbjct: 90  IFKIIFPQLDKIY-----FESHPFNLKNQPETLKLLLQAALSYFADDKNNSLRTHGYTSL 144

Query: 257 IKARMFELLTVILREIPKNRTQRQPKFSEDTLTQSRETMERLERIFAYVELHYQKSISLN 316
           +  R   LL++    I  +  Q +            +  ER+ERI +Y+  +Y   ISL 
Sbjct: 145 LLDR---LLSISEYSILSSSEQNKL----------MDLQERMERISSYIHENYDHKISLE 191

Query: 317 EVARYMGFSPYYFTKLFKRNTGMTFVAFLNEYRLNKAKWILLNEDLPMSAVAEAAGFGSV 376
            +A + G S  YF+  FK N G+ F  +LN+ R  KA+ +L +    +  +A   GF  +
Sbjct: 192 MIASHEGLSRTYFSHFFKSNFGINFNEYLNKIRSEKARTLLSSSKDNLLNIAYMCGFSDI 251

Query: 377 KTFHHFFKEATGISPLKYHKT 397
           +T +  F ++ G+ P ++ K 
Sbjct: 252 RTLNTAFLKSYGVLPKEFRKN 272


  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    0.136    0.399 

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: 25,698,600
Number of extensions: 965375
Number of successful extensions: 2605
Number of sequences better than 1.0e-05: 68
Number of HSP's gapped: 2582
Number of HSP's successfully gapped: 68
Length of query: 425
Length of database: 38,378,431
Length adjustment: 109
Effective length of query: 316
Effective length of database: 25,807,025
Effective search space: 8155019900
Effective search space used: 8155019900
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: 117 (49.7 bits)