BLASTP 2.2.21 [Jun-14-2009]

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= 0030.0213.p         (250 letters)

Database: COGmodified 
           192,987 sequences; 59,019,183 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

STM3124 [K] COG2771 DNA-binding HTH domain-containing proteins S...    67   3e-11
PA4074 [K] COG2771 DNA-binding HTH domain-containing proteins Pa...    67   5e-11
RSc3373 [K] COG2771 DNA-binding HTH domain-containing proteins R...    62   1e-09

>STM3124 [K] COG2771 DNA-binding HTH domain-containing proteins Sty
           Salmonella typhimurium LT2
          Length = 227

 Score = 67.0 bits (162), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 53/186 (28%), Positives = 91/186 (48%), Gaps = 21/186 (11%)

Query: 63  NMDPANLANYERYYQYCDPIT---FELQRLSVPTLVTQVMPMEQLRRTEFFNDFLARDGL 119
           N+  +    Y  ++Q  DP++   F  Q ++V T+   +      R   ++++F+  + +
Sbjct: 48  NISNSTHQQYLEHFQPLDPLSPSRFGQQVVTVATMTPGICA----RHRHYYHEFMLPNHV 103

Query: 120 CFGVNMFAYDGDRNIGDLRIWRSARRENFDRDALKLLALIRPAFTLALQRARAHCSAAAA 179
           C  + +F   G R I  + + R     + +R  L+  A ++P   LA+        +   
Sbjct: 104 CDMIEIFIRRGHRIIAGISLMRDIPFSSEER--LRAQA-VQPLLGLAIH------DSLQE 154

Query: 180 SPDAGALLTPTPLSERESHLAQCICRGLSDKEIARELHIEFSTVRTHITRIFKKLNVGNR 239
             D  ++LT     ERE  +   +C G S+K IAR+L+I  STV+TH+  IF K  V NR
Sbjct: 155 DNDLESILTA---KERE--IVGMVCEGASNKLIARQLNISLSTVKTHLRNIFAKTEVINR 209

Query: 240 TQLVKR 245
           T+LV R
Sbjct: 210 TELVSR 215


>PA4074 [K] COG2771 DNA-binding HTH domain-containing proteins Pae
           Pseudomonas aeruginosa
          Length = 222

 Score = 66.6 bits (161), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 57/188 (30%), Positives = 88/188 (46%), Gaps = 20/188 (10%)

Query: 66  PANLA-NYERYYQYCDPITFELQRLSVPTLVTQVMPMEQ------LRRTEFFNDFLARDG 118
           PA +  +Y R+Y+  DP    LQ        + V+P+ Q         +  +  FL R G
Sbjct: 46  PAGMHRDYLRHYRDYDP----LQPRHCLASASPVVPLRQGIARQPAEDSALYQGFLRRHG 101

Query: 119 LCFGVNMFAYDGDRNIGDLRIWRSARRENFDRDALKLLALIRPAFTLALQRARAHCSAAA 178
           +C  V + A+   R +  L + R AR   F    L+ L  +     LA Q     C+   
Sbjct: 102 ICDVVEVLAHAHQRPVAALSLLRDARLGAFSDQELRQLRALHGLMELAAQA----CATPT 157

Query: 179 ASPDAGALLTPTPLSERESHLAQCICRGLSDKEIARELHIEFSTVRTHITRIFKKLNVGN 238
           AS +    LTP     RE  +A  +  G+S+K +A+ L +   TV+TH+  +F+K    +
Sbjct: 158 ASAERLQGLTP-----REREIALLLRDGVSNKCLAQCLGLGLPTVKTHLLNLFRKTGARS 212

Query: 239 RTQLVKRL 246
           RT+LVKRL
Sbjct: 213 RTELVKRL 220


>RSc3373 [K] COG2771 DNA-binding HTH domain-containing proteins Rso
           Ralstonia solanacearum
          Length = 336

 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 46/162 (28%), Positives = 75/162 (46%), Gaps = 3/162 (1%)

Query: 24  SVEVRDFVSTRLLKLLDADYFASYTWDDANHRFGNTVSVNMDPANLANYERYYQYCDPIT 83
           S+  R  ++ +L  LL  D  +   W D       T +    P   A Y++++   DPI+
Sbjct: 25  SLVERPEITQKLSALLGVDVISHIVWKDHGRTPVQTTTWGRAPDMNAEYQQHFHGVDPIS 84

Query: 84  FELQRLSVPTLVTQVMPMEQLRRTEFFNDFLARDGLCFGVNMFAYDGDRNIGDLRIWRSA 143
             L+      LV  ++  + L+RTE+F DFL R  +  G++M+  D    + D R+  S 
Sbjct: 85  PLLRSRPDALLVEGLINRKTLQRTEYFTDFLTRYKIYPGLSMYLEDSGGILLDYRLGTSD 144

Query: 144 RRENFDRDALKLLALIRPAFTLALQRARAHCSAA--AASPDA 183
            ++ F      +L L+RP    A QR R+  +A      PDA
Sbjct: 145 PKQTFGERERLILDLLRPHLINA-QRLRSALNAHRDPTGPDA 185