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= 0045.0015.p         (91 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

RSc0222 Non COG                                                       117   4e-27
PA4581 [KT] COG4650 Sigma54-dependent transcription regulator co...   113   1e-25
STM3522 [KT] COG4650 Sigma54-dependent transcription regulator c...   107   5e-24
rtcR [KT] COG4650 Sigma54-dependent transcription regulator cont...   107   9e-24
ECs4265 [KT] COG4650 Sigma54-dependent transcription regulator c...   106   1e-23

>RSc0222 Non COG
          Length = 535

 Score =  117 bits (294), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 62/79 (78%), Positives = 66/79 (83%)

Query: 1   LLRSAHKRLLFLDEIGELGLDEQAMLFKAIEEKRFLPIGADVEAESSCQLIAGTHRDLAR 60
           LLRSA   LLFLDEIGELGLDEQAML KAIEEKRFLP G+D EA+S  QLIAGT RDL +
Sbjct: 277 LLRSADGGLLFLDEIGELGLDEQAMLLKAIEEKRFLPFGSDREAQSDFQLIAGTVRDLRQ 336

Query: 61  EVAAGRFREDLFARIKLWS 79
            VA GRFREDLFARI LW+
Sbjct: 337 WVAEGRFREDLFARINLWT 355


>PA4581 [KT] COG4650 Sigma54-dependent transcription regulator containing
           an AAA-type ATPase domain and a DNA-binding domain Pae
           Pseudomonas aeruginosa
          Length = 531

 Score =  113 bits (282), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 58/79 (73%), Positives = 63/79 (79%)

Query: 1   LLRSAHKRLLFLDEIGELGLDEQAMLFKAIEEKRFLPIGADVEAESSCQLIAGTHRDLAR 60
           LLR+A   +LFLDEIGELG DEQAML KAIEEKRF P+G+D E ES  QLIAGTHRDL  
Sbjct: 280 LLRAADGGMLFLDEIGELGADEQAMLLKAIEEKRFFPLGSDREVESDFQLIAGTHRDLRG 339

Query: 61  EVAAGRFREDLFARIKLWS 79
            VA G FREDLFARI LW+
Sbjct: 340 RVAEGLFREDLFARINLWT 358


>STM3522 [KT] COG4650 Sigma54-dependent transcription regulator containing
           an AAA-type ATPase domain and a DNA-binding domain Sty
           Salmonella typhimurium LT2
          Length = 527

 Score =  107 bits (268), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 54/79 (68%), Positives = 61/79 (77%)

Query: 1   LLRSAHKRLLFLDEIGELGLDEQAMLFKAIEEKRFLPIGADVEAESSCQLIAGTHRDLAR 60
           LLRSA   +LFLDE+GELG DEQAML KAIEEKRF P G+D +  S  QLIAGT RDL +
Sbjct: 277 LLRSADGGMLFLDEVGELGADEQAMLLKAIEEKRFYPFGSDQQVSSDFQLIAGTVRDLRQ 336

Query: 61  EVAAGRFREDLFARIKLWS 79
            VA G FREDL+ARI LW+
Sbjct: 337 RVAEGTFREDLYARINLWT 355


>rtcR [KT] COG4650 Sigma54-dependent transcription regulator containing
           an AAA-type ATPase domain and a DNA-binding domain Eco
           Escherichia coli K12
          Length = 532

 Score =  107 bits (266), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 54/79 (68%), Positives = 62/79 (78%)

Query: 1   LLRSAHKRLLFLDEIGELGLDEQAMLFKAIEEKRFLPIGADVEAESSCQLIAGTHRDLAR 60
           LLRSA+  +LFLDEIGELG DEQAML KAIEEK F P G+D +  S  QLIAGT RDL +
Sbjct: 277 LLRSANGGMLFLDEIGELGADEQAMLLKAIEEKTFYPFGSDRQVSSDFQLIAGTVRDLRQ 336

Query: 61  EVAAGRFREDLFARIKLWS 79
            VA G+FREDL+ARI LW+
Sbjct: 337 LVAEGKFREDLYARINLWT 355


>ECs4265 [KT] COG4650 Sigma54-dependent transcription regulator containing
           an AAA-type ATPase domain and a DNA-binding domain Ecs
           Escherichia coli O157:H7
          Length = 532

 Score =  106 bits (265), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 54/79 (68%), Positives = 62/79 (78%)

Query: 1   LLRSAHKRLLFLDEIGELGLDEQAMLFKAIEEKRFLPIGADVEAESSCQLIAGTHRDLAR 60
           LLRSA+  +LFLDEIGELG DEQAML KAIEEK F P G+D +  S  QLIAGT RDL +
Sbjct: 277 LLRSANGGMLFLDEIGELGADEQAMLLKAIEEKTFYPFGSDRQVSSDFQLIAGTVRDLRQ 336

Query: 61  EVAAGRFREDLFARIKLWS 79
            VA G+FREDL+ARI LW+
Sbjct: 337 LVADGKFREDLYARINLWT 355