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= 0033.0012.p
         (555 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...    96   1e-19
CAC0790 [P] COG0614 ABC-type Fe3+-hydroxamate transport system, ...    82   2e-15
BH0851 [K] COG2207 AraC-type DNA-binding domain-containing proteins    81   4e-15
BH3842 [T] COG4753 Response regulator containing CheY-like recei...    81   4e-15
SMa0319 [K] COG2207 AraC-type DNA-binding domain-containing prot...    77   1e-13

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

 Score = 95.9 bits (237), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 4/100 (4%), Positives = 13/100 (13%)

Query: 180 SMERSITYLENHFSEKITREHLAAIAGVSRSHYSTLFKQLTGFTLNEYLSRLRVHRAKEL 239
           +         +  S                +  +    +                R    
Sbjct: 164 NGVDLEGLARHRGSAFGRTLQPQLSQASFENLLAAEMLKTDARQNLRLWVLEDESRMIGS 223

Query: 240 LLNSSGTLREIALKVGYKDEFYLSRRFKQETGTSPSGYNR 279
                     +        E     R ++         + 
Sbjct: 224 NHLPECLRERMTQAAIAVVEDPFEIRLERLNEEYFLRMHH 263


>CAC0790 [P] COG0614 ABC-type Fe3+-hydroxamate transport system, periplasmic
           component
          Length = 307

 Score = 82.0 bits (201), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 58/217 (26%), Positives = 110/217 (50%), Gaps = 23/217 (10%)

Query: 341 LLEANIELIIAAR--QHLDQLRLSPGELRAVAPIVEIPWMEMGWKDHLRLIGQAIQRSER 398
           ++E   +LIIA    ++LD+L         +AP V   + ++G+ D +  IG+ I + ++
Sbjct: 104 IIELKPDLIIAGSTDKNLDKLS-------KIAPTVSYTYNKLGYLDQVIEIGKLINKKKQ 156

Query: 399 AEQWLADFEKEEAEARAIVQQSTGGKEIITILVIKPDGLLVYGSRNVGC---VIYQSLGL 455
           A++W+ +F+K  ++A   ++   G    +TIL      L V+GS N G    ++YQ++GL
Sbjct: 157 AQEWVNNFKKRASDAGEKIKNKIGNNSTVTILGGDNKQLYVFGS-NWGRGSEILYQAMGL 215

Query: 456 RAPALIEAEMKKLGDQFHSFPIDISELAEYAGDRLLVVVFPDAKGSTAHTEAVFRSPHWK 515
           + PA + A   K G     + I    L +Y GD L+ +    A  S  +T+       +K
Sbjct: 216 KMPAKVTANALKPG----YYVISSEVLPQYIGDYLIYIKDSAADNSFQNTDT------YK 265

Query: 516 RLPAVQRKNVHWLERDEWVPYNPVSIRLQLGRAVALF 552
            +PAV+   V  ++ +++   +P+S+  +L   +  F
Sbjct: 266 NIPAVKNNRVLEVDANKFYFNDPISLDYELDTFINYF 302


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

 Score = 81.3 bits (199), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 39/97 (40%), Positives = 63/97 (64%)

Query: 181 MERSITYLENHFSEKITREHLAAIAGVSRSHYSTLFKQLTGFTLNEYLSRLRVHRAKELL 240
           M+ +I+Y+ NH  E ++  H+A+  G S  H+S LFK+ TG +   Y+S LR+ +AKELL
Sbjct: 8   MDVAISYIHNHLYEPLSLSHIASYVGYSSYHFSRLFKEKTGLSPLYYVSSLRLQKAKELL 67

Query: 241 LNSSGTLREIALKVGYKDEFYLSRRFKQETGTSPSGY 277
           LN++ T+R+I L++G +     + RF +  G SPS +
Sbjct: 68  LNTNLTVRDIGLEIGQQSLGTFTTRFTKCVGMSPSHF 104


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

 Score = 81.3 bits (199), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 44/96 (45%), Positives = 62/96 (64%), Gaps = 1/96 (1%)

Query: 187 YLENHFSEKITREHLAAIAGVSRSHYSTLFKQLTGFTLNEYLSRLRVHRAKELLLNSSGT 246
           Y+ +HF E +T + LA   G+S  + S LFK+    T +EY+++LRV  AK+LL  +  +
Sbjct: 423 YVHDHFREPLTLDDLAKHIGLSPYYVSKLFKERFDLTFSEYVTQLRVEHAKQLLSLTQKS 482

Query: 247 LREIALKVGYKDEFYLSRRFKQETGTSPSGYNRKPI 282
           L+EI  ++GYKD  Y SR FK+ TG SPS Y RK I
Sbjct: 483 LKEITYEIGYKDPNYFSRVFKKLTGKSPSDY-RKSI 517


>SMa0319 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 333

 Score = 76.6 bits (187), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 37/99 (37%), Positives = 57/99 (57%)

Query: 181 MERSITYLENHFSEKITREHLAAIAGVSRSHYSTLFKQLTGFTLNEYLSRLRVHRAKELL 240
           + R++ +LE H +E      LA   G+S  H+S LFK+ TG + + Y  R RV RA+ LL
Sbjct: 234 LRRAVAHLEEHLAEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLL 293

Query: 241 LNSSGTLREIALKVGYKDEFYLSRRFKQETGTSPSGYNR 279
             +  ++ EI + VGY    + ++ F++ETG  PS Y R
Sbjct: 294 QETDTSIIEIGMSVGYSSPSHFAQVFRRETGLPPSHYRR 332


  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
   0.318    0.134    0.386 

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: 39,521,170
Number of extensions: 1584894
Number of successful extensions: 4316
Number of sequences better than 1.0e-05: 834
Number of HSP's gapped: 4302
Number of HSP's successfully gapped: 834
Length of query: 555
Length of database: 38,378,431
Length adjustment: 111
Effective length of query: 444
Effective length of database: 25,576,357
Effective search space: 11355902508
Effective search space used: 11355902508
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 118 (50.1 bits)