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= 0542.0005.p
         (304 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

BH3679 [T] COG4753 Response regulator containing CheY-like recei...    75   1e-13
CAC2818 [K] COG2207 AraC-type DNA-binding domain-containing prot...    75   2e-13
BH0851 [K] COG2207 AraC-type DNA-binding domain-containing proteins    72   1e-12
lin1114_2 [K] COG2207 AraC-type DNA-binding domain-containing pr...    72   2e-12
VC1825 [K] COG2207 AraC-type DNA-binding domain-containing proteins    70   3e-12

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

 Score = 75.1 bits (183), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 36/99 (36%), Positives = 57/99 (57%)

Query: 203 EALSYINDHLDQPLELGTLAGRAAISPAHFSRVFKQRLGMNVTDYIATKRIFAAKDSLLQ 262
           EAL YI+ HLDQ + L  +A    ++P++ S +FK++  M  ++Y+  KR+  AK  L+ 
Sbjct: 158 EALHYIDAHLDQKIGLKDVAKSVHLNPSYLSALFKEKTNMTFSEYLTRKRLQHAKHLLVS 217

Query: 263 SSYTIEQIAMACGFESLPHFYRTFKRITSMTPAAYRKSN 301
           +   I  IA  CG+++  +F + FK    MTP  YRK  
Sbjct: 218 TDRPISDIAEKCGYQTAKYFIKIFKEHEGMTPTQYRKGT 256


>CAC2818 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 279

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 64/270 (23%), Positives = 115/270 (42%), Gaps = 12/270 (4%)

Query: 32  LLDYKETKSPQRELPDHQHDWYEFIYVYGGKGSFFIDQTFYEMHPGDIIVVPGNTVHRGF 91
           L   K+ KS   E   H HD+ + I    GK ++ I+   YE+ P DI++V  + VH+  
Sbjct: 14  LFHLKDRKSQSFEF--HYHDFNKIIIFISGKVTYLIEGKAYELKPWDILLVNNHDVHKPI 71

Query: 92  PDNEEPVTSSALFFSPALIHNHTYSESYPYLKLFDAAKTNKQYKYTLSPEHAEILQNDIE 151
            D+ +      ++ +   I  H Y +      L +  K  ++  + L     E LQ++++
Sbjct: 72  IDSSKVYERIIIWANSDFIKKHNYEDC----DLSNCFKLARERSFNLVRLKTE-LQDNMK 126

Query: 152 EIHREREQ---NQQDGGQA-XXXXXXXXXXXXNRYCLPQTAEPVASSPLLPEWFREALSY 207
            I    EQ   +++ G +              NR  L         +    +   + L Y
Sbjct: 127 FIINSLEQSLKSKEFGSKLFSNSLFIQLIIYLNRVHLENMYLTGKETLRYDKQIEKILKY 186

Query: 208 INDHLDQPLELGTLAGRAAISPAHFSRVFKQRLGMNVTDYIATKRIFAAKDSLLQSSYTI 267
           IN +L   L    LA    +S  +    FK+  G  + +Y+  KR+  +KD +++    I
Sbjct: 187 INANLKGELSTEALAREFYMSKYYLMHKFKKETGYTLHNYVLQKRLLLSKD-MIKKGDAI 245

Query: 268 EQIAMACGFESLPHFYRTFKRITSMTPAAY 297
            +  M CGF+    F+R FK++   +P  +
Sbjct: 246 TKAYMQCGFKDYSSFFRAFKKMFGRSPREF 275


>BH0851 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 261

 Score = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 35/97 (36%), Positives = 60/97 (61%)

Query: 204 ALSYINDHLDQPLELGTLAGRAAISPAHFSRVFKQRLGMNVTDYIATKRIFAAKDSLLQS 263
           A+SYI++HL +PL L  +A     S  HFSR+FK++ G++   Y+++ R+  AK+ LL +
Sbjct: 11  AISYIHNHLYEPLSLSHIASYVGYSSYHFSRLFKEKTGLSPLYYVSSLRLQKAKELLLNT 70

Query: 264 SYTIEQIAMACGFESLPHFYRTFKRITSMTPAAYRKS 300
           + T+  I +  G +SL  F   F +   M+P+ +R+S
Sbjct: 71  NLTVRDIGLEIGQQSLGTFTTRFTKCVGMSPSHFRES 107


>lin1114_2 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 145

 Score = 71.6 bits (174), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 31/100 (31%), Positives = 59/100 (59%)

Query: 201 FREALSYINDHLDQPLELGTLAGRAAISPAHFSRVFKQRLGMNVTDYIATKRIFAAKDSL 260
            R+AL YI  +L++P+ L  +A    +S  +FS++FK+ + +N  +Y+  K++  AKD L
Sbjct: 44  IRKALKYIEKNLNRPITLDEVASHVYLSSYYFSKLFKKEMNVNFINYVNQKKMSLAKDML 103

Query: 261 LQSSYTIEQIAMACGFESLPHFYRTFKRITSMTPAAYRKS 300
               ++I+ +A   GF    +F + F++   +TP  YR++
Sbjct: 104 KNPRWSIDNVARNLGFTQTSYFCKVFRKEFDVTPKGYRET 143


>VC1825 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 279

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 56/94 (59%)

Query: 207 YINDHLDQPLELGTLAGRAAISPAHFSRVFKQRLGMNVTDYIATKRIFAAKDSLLQSSYT 266
           YI ++  +P+   ++A R +IS  H SR+F+Q+  M + DYI   R+  AK  L + ++ 
Sbjct: 185 YIQENFHRPITRESIASRFSISANHLSRLFRQQGHMTLADYITWVRVDRAKFMLKKYNFK 244

Query: 267 IEQIAMACGFESLPHFYRTFKRITSMTPAAYRKS 300
           + ++++ CGF+ + +F R FK  T  TP  YR S
Sbjct: 245 LNEVSLRCGFKDVNYFCRVFKNRTGRTPTDYRAS 278


  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    0.418 

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: 22,436,565
Number of extensions: 892721
Number of successful extensions: 2948
Number of sequences better than 1.0e-05: 830
Number of HSP's gapped: 2938
Number of HSP's successfully gapped: 830
Length of query: 304
Length of database: 38,378,431
Length adjustment: 106
Effective length of query: 198
Effective length of database: 26,153,027
Effective search space: 5178299346
Effective search space used: 5178299346
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: 115 (48.9 bits)