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= 0567.0053.p
         (299 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

BH3506_2 [S] COG3708 Uncharacterized protein conserved in bacteria    139   7e-33
CAC0426_1 [K] COG2207 AraC-type DNA-binding domain-containing pr...    89   6e-18
YPO0456 [K] COG2207 AraC-type DNA-binding domain-containing prot...    86   5e-17
STM0581 [K] COG2207 AraC-type DNA-binding domain-containing prot...    84   2e-16
BS_ydeE_1 [K] COG2207 AraC-type DNA-binding domain-containing pr...    82   7e-16

>BH3506_2 [S] COG3708 Uncharacterized protein conserved in bacteria
          Length = 167

 Score =  139 bits (349), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 74/176 (42%), Positives = 104/176 (59%), Gaps = 12/176 (6%)

Query: 125 PVIVQKPAFKVAGYGIETNVAEGNYTKDIASFWSHYEGENLESKMYDILNPPKHGXXXXG 184
           P  V KPAF + GY ++T  A+G   KDI  FW HY    L++K+   +  P H     G
Sbjct: 2   PKFVTKPAFHIIGYELKTKNADGQNNKDIPEFWQHY----LKNKLGCTIPNPLHKHVELG 57

Query: 185 LCVP-AFDSGNAVYLLGVIVEDFSRVTDEMITVDVPEAEYAVFTTPPVDTSEGKDQEEFV 243
           +C     ++G  VY++G+ VE  ++  + M+    PE EYAVFTTP  +      +E F 
Sbjct: 58  ICTEFNPETGEFVYVIGMEVEKGTKAPEGMVYKSFPELEYAVFTTPKAN------EESFT 111

Query: 244 QTIKSTWKYIFEEWFPGSGYVYDEGKLNFEFYDERCHSRVDTVMEIYVPVKKRAGK 299
            +I+STW YIF EWFP S Y ++ G + FE YDERCH   +  M+IY+PVKKR+G+
Sbjct: 112 SSIQSTWNYIFTEWFPQSDYEHN-GVVEFELYDERCHGTENIEMDIYIPVKKRSGE 166


>CAC0426_1 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 127

 Score = 89.4 bits (220), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 41/102 (40%), Positives = 69/102 (67%), Gaps = 1/102 (0%)

Query: 1   LNYSKDIERCVEYIEVNIKRNLTAEEIAAEAGYSLYHFSRVFSLCKGMSVMEYVRSRKLS 60
           +N+  D+   + Y+E N++RN+ + E+A  A  S ++F R+F +  GM++ +Y+R RKLS
Sbjct: 1   MNWIGDMNNALRYVEENLERNIESGEVANAAHMSKFYFLRIFKILTGMTLGDYIRERKLS 60

Query: 61  LAAVELFS-GKRIIDIALDYGFETQSGFTKAFRKAFGYSPSQ 101
           LA  ++ S  ++IIDI+  YG+ET   FTKAF++  G SP++
Sbjct: 61  LATKDIVSTNQKIIDISYKYGYETPEAFTKAFKRLNGISPTE 102


>YPO0456 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 288

 Score = 86.3 bits (212), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 52/165 (31%), Positives = 85/165 (51%), Gaps = 9/165 (5%)

Query: 7   IERCVEYIEVNIKRNLTAEEIAAEAGYSLYHFSRVFSLCKGMSVMEYVRSRKLSLAAVEL 66
           I   + ++E ++ + L  + +AA+AGYS +H  R+F    G ++  Y+R+R+LS AAV L
Sbjct: 7   IRDLLSWLESHLDQPLALDNVAAKAGYSKWHLQRMFKDVTGNAIGAYIRARRLSKAAVAL 66

Query: 67  -FSGKRIIDIALDYGFETQSGFTKAFRKAFGYSPSQYAARMEGFLQMG--SKIDIGGYMM 123
             + + I+DIAL Y F++Q  FT+AF+K F  +P+ Y  R E +   G    I +G Y +
Sbjct: 67  RLTSRPILDIALQYRFDSQQTFTRAFKKQFAQTPALY-RRAEDWHSSGICPPIRLGTYTL 125

Query: 124 -NPVIVQKPAFKVAG----YGIETNVAEGNYTKDIASFWSHYEGE 163
             P  +  P   + G    Y         +  +    FW  Y G+
Sbjct: 126 PQPEFITLPEQHLVGITQSYSCTLEQISTHRAELRLHFWQQYLGD 170


>STM0581 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 113

 Score = 84.3 bits (207), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/103 (40%), Positives = 61/103 (59%), Gaps = 1/103 (0%)

Query: 7   IERCVEYIEVNIKRNLTAEEIAAEAGYSLYHFSRVFSLCKGMSVMEYVRSRKLSLAAVEL 66
           I+  VE+I+ N+ + L  ++IA  AGYS +H  R+F   KG S+  YVR RKL LAA +L
Sbjct: 8   IDTIVEWIDDNLNQPLRIDDIARHAGYSKWHLQRLFMQYKGESLGRYVRERKLKLAARDL 67

Query: 67  F-SGKRIIDIALDYGFETQSGFTKAFRKAFGYSPSQYAARMEG 108
             + +++ DI L YGF++Q  FT+ F + F   P  Y     G
Sbjct: 68  LDTDQKVYDICLKYGFDSQQTFTRIFTRTFNLPPGAYRKEKHG 110


>BS_ydeE_1 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 127

 Score = 82.4 bits (202), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 44/105 (41%), Positives = 66/105 (62%), Gaps = 3/105 (2%)

Query: 5   KDIERCVEYIEVNIKRNLTAEEIAAEAGYSLYHFSRVFSLCKGMSVMEYVRSRKLSLAAV 64
           K + R ++YIE N+  ++  +E A  A  S YHF R+FS   G+S+ EY+R R+L+LAA 
Sbjct: 5   KSMNRALKYIEENLTNDIDFQEAAKLAFCSEYHFKRMFSFLAGISLSEYIRRRRLTLAAF 64

Query: 65  ELF-SGKRIIDIALDYGFETQSGFTKAFRKAFGYSPSQYAARMEG 108
           EL  S  ++IDIA+ YG+ +   F +AF+   G +PS+  AR  G
Sbjct: 65  ELKDSNVKVIDIAIKYGYNSPDSFARAFQNLHGINPSK--ARFNG 107


  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
   0.319    0.137    0.405 

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: 22,235,538
Number of extensions: 852760
Number of successful extensions: 4793
Number of sequences better than 1.0e-05: 763
Number of HSP's gapped: 4155
Number of HSP's successfully gapped: 763
Length of query: 299
Length of database: 38,378,431
Length adjustment: 106
Effective length of query: 193
Effective length of database: 26,153,027
Effective search space: 5047534211
Effective search space used: 5047534211
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 (21.7 bits)
S2: 115 (48.9 bits)