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= 0284.0029.p
         (256 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

YPO0401 [K] COG2207 AraC-type DNA-binding domain-containing prot...    68   2e-11
BH0989 [K] COG2207 AraC-type DNA-binding domain-containing proteins    59   9e-09
RSp0044 [K] COG4977 Transcriptional regulator containing an amid...    59   1e-08
BH2728 [T] COG4753 Response regulator containing CheY-like recei...    57   3e-08
BH0483 [K] COG2207 AraC-type DNA-binding domain-containing proteins    55   1e-07

>YPO0401 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 291

 Score = 67.8 bits (164), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/102 (34%), Positives = 55/102 (53%)

Query: 155 LRKALYNNPGHPWTVSSMAEYLHISAGYLQTIYKSTFGISCMEDVIHCRIRLAKEKLVFG 214
           +R+ +  N   P T  S+A   HIS  YL  ++++   I   E V   R+  AK  L F 
Sbjct: 184 IREYIERNYSEPLTRESVAHVFHISPNYLSHLFRNAGNIGFNESVNSARLENAKILLKFY 243

Query: 215 PHKIAELASLCGYANVEHFCRQFRQHTGCSPRAYRDKHASRL 256
             KI E+A++CG+ +  +FCR FR+ T  +P  YR ++ S +
Sbjct: 244 EMKIKEVANVCGFIDSNYFCRLFRKETELTPSEYRQQYRSNM 285


>BH0989 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 278

 Score = 58.5 bits (140), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 34/132 (25%), Positives = 71/132 (53%), Gaps = 1/132 (0%)

Query: 119 NDYRELSIDYLFRIIFNKLHEASQDKLSPQYYKLLE-LRKALYNNPGHPWTVSSMAEYLH 177
            ++ E+    LF  IF+ +   ++++L+ +   ++E + + ++++   P TV  +A+   
Sbjct: 136 GNFPEIQAKALFYTIFHDMLICARNRLNRESQLVIEQVVEYIHHHYMEPMTVKKLADMSG 195

Query: 178 ISAGYLQTIYKSTFGISCMEDVIHCRIRLAKEKLVFGPHKIAELASLCGYANVEHFCRQF 237
           +       ++K   G+  ++ +I  R++ AK  LV     IA++A   GY +  +F R F
Sbjct: 196 MGVKPFSYLFKKYIGMFPIDYLIQYRLKRAKNLLVSSNSSIADIAESIGYLDALYFSRLF 255

Query: 238 RQHTGCSPRAYR 249
           ++H GCSP A+R
Sbjct: 256 KKHIGCSPTAFR 267


>RSp0044 [K] COG4977 Transcriptional regulator containing an amidase domain
           and an AraC-type DNA-binding HTH domain
          Length = 387

 Score = 58.5 bits (140), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/88 (34%), Positives = 45/88 (51%)

Query: 164 GHPWTVSSMAEYLHISAGYLQTIYKSTFGISCMEDVIHCRIRLAKEKLVFGPHKIAELAS 223
           G P  +  +A  L +SA  L+ ++K+  G S        R+R A   L      +A++A 
Sbjct: 247 GRPLPLEELAHKLDLSARQLERLFKAETGKSPQTFAKQVRLRTAAWLLTSSDRGVADIAF 306

Query: 224 LCGYANVEHFCRQFRQHTGCSPRAYRDK 251
            CG+A+  H  R+FR+  G  P AYRDK
Sbjct: 307 SCGFADASHLGREFRKQFGMPPAAYRDK 334


>BH2728 [T] COG4753 Response regulator containing CheY-like receiver domain
           and AraC-type DNA-binding domain
          Length = 510

 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 36/124 (29%), Positives = 60/124 (48%), Gaps = 19/124 (15%)

Query: 149 YYKLLELRK---ALYNNPG----------------HPWTVSSMAEYLHISAGYLQTIYKS 189
           +Y+ LE+ K   ++Y+N G                 P ++S +A Y H +  YL   ++ 
Sbjct: 380 FYQFLEVTKQIISVYSNEGSSSIQKMLAYIEEHHSEPLSLSQLANYFHFNPSYLSAYFRQ 439

Query: 190 TFGISCMEDVIHCRIRLAKEKLVFGPHKIAELASLCGYANVEHFCRQFRQHTGCSPRAYR 249
                  E +   RIR AKE L      I+E+ +L GY++  +FC+ F++ TG  P  YR
Sbjct: 440 HHDEGFSEYLNKVRIRKAKEWLKSSTIPISEIYALVGYSDHSYFCKVFKKRTGMPPSRYR 499

Query: 250 DKHA 253
            ++A
Sbjct: 500 RENA 503


>BH0483 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 769

 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 29/87 (33%), Positives = 46/87 (52%)

Query: 168 TVSSMAEYLHISAGYLQTIYKSTFGISCMEDVIHCRIRLAKEKLVFGPHKIAELASLCGY 227
           T+ S+AE LH +  YL +I++    IS  E +   R+ +AK+ L+     I E+A    Y
Sbjct: 683 TLESIAERLHYNPNYLSSIFRKETNISFSEYLSSYRLAMAKKWLLETSMPIREIAERLCY 742

Query: 228 ANVEHFCRQFRQHTGCSPRAYRDKHAS 254
            N ++F R F++  G +P  YR    S
Sbjct: 743 GNSQNFIRSFKKKEGMTPGKYRQSKVS 769


  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
   0.324    0.138    0.439 

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: 20,254,165
Number of extensions: 775743
Number of successful extensions: 2190
Number of sequences better than 1.0e-05: 28
Number of HSP's gapped: 2203
Number of HSP's successfully gapped: 28
Length of query: 256
Length of database: 38,378,431
Length adjustment: 104
Effective length of query: 152
Effective length of database: 26,383,695
Effective search space: 4010321640
Effective search space used: 4010321640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 114 (48.5 bits)