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= 0001.2247.p         (173 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

PA2050 [K] COG1595 DNA-directed RNA polymerase specialized sigma...   157   1e-38
RSp0849 [K] COG1595 DNA-directed RNA polymerase specialized sigm...   156   2e-38
PA2093 [K] COG1595 DNA-directed RNA polymerase specialized sigma...   137   9e-33
fecI [K] COG1595 DNA-directed RNA polymerase specialized sigma s...   137   1e-32
PA0472 [K] COG1595 DNA-directed RNA polymerase specialized sigma...   129   4e-30

>PA2050 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 168

 Score =  157 bits (397), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 80/158 (50%), Positives = 109/158 (68%)

Query: 14  RHDFLVTEFTNSYSWLKQYLRRQVKSLADAEDVASAAFLEMAGIPDVSIIREPRALLTTI 73
           R+  +   F N YSWL   LRR +     AED+AS  FL++  +PD + IREPRALLTTI
Sbjct: 7   RNRLVGLMFQNDYSWLSGRLRRYLGCPHSAEDIASETFLKVLALPDPASIREPRALLTTI 66

Query: 74  SQRLVFDLWRRRDLEAAYLAALATTEEANTPSPEVVLEVVQTLVNIDRLLYGLSKNARQA 133
           ++RL++D WRR+DLE AYL +LA   EA  PS E   +VV+TL+ ++R+L GLS  AR A
Sbjct: 67  ARRLMYDGWRRQDLERAYLESLAGLPEALAPSAEEQAQVVETLLRLERMLAGLSPKARAA 126

Query: 134 FLYSQLDGLTYREIAELLGVSVSMVRKYIAQALAKCYE 171
           F++SQ+ GLTY EIA LL VSVS + +Y+ +   +CY+
Sbjct: 127 FIHSQIGGLTYVEIACLLEVSVSRIHQYMVEGFKQCYQ 164


>RSp0849 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Rso Ralstonia solanacearum
          Length = 169

 Score =  156 bits (395), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 83/149 (55%), Positives = 99/149 (66%)

Query: 22  FTNSYSWLKQYLRRQVKSLADAEDVASAAFLEMAGIPDVSIIREPRALLTTISQRLVFDL 81
           F   Y+WL   + R+      AED+AS AF ++  +PD    REPRALLTTI+QRL++D+
Sbjct: 16  FRQHYAWLAGRMGRKTGCRFGAEDLASEAFAQLLQMPDWQGTREPRALLTTIAQRLLYDI 75

Query: 82  WRRRDLEAAYLAALATTEEANTPSPEVVLEVVQTLVNIDRLLYGLSKNARQAFLYSQLDG 141
           WRRRDLE AY A  A   EA  PSPE    V++ L  IDRLL GL   AR AFLYSQLDG
Sbjct: 76  WRRRDLELAYQAWAAAQPEATLPSPEERALVLEALATIDRLLDGLPVKARTAFLYSQLDG 135

Query: 142 LTYREIAELLGVSVSMVRKYIAQALAKCY 170
           LTY EIA  L VSV MV+KY+ QA+  CY
Sbjct: 136 LTYPEIAGRLNVSVRMVQKYMTQAMRLCY 164


>PA2093 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 169

 Score =  137 bits (346), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 71/149 (47%), Positives = 95/149 (63%)

Query: 22  FTNSYSWLKQYLRRQVKSLADAEDVASAAFLEMAGIPDVSIIREPRALLTTISQRLVFDL 81
           F  +Y WL + L  Q      AED+A+ AFL++  +PD + IR PRA L TI+QRL+++ 
Sbjct: 16  FQQNYDWLCKKLSYQTGCSHSAEDLAAEAFLQVWMLPDPASIRSPRAFLATIAQRLMYES 75

Query: 82  WRRRDLEAAYLAALATTEEANTPSPEVVLEVVQTLVNIDRLLYGLSKNARQAFLYSQLDG 141
           WRR+DLE AYL  LA   EA  PSP     ++++L  IDRLL GLS  AR  FL SQL+G
Sbjct: 76  WRRKDLERAYLQILAEAPEAVQPSPHEQWMLIESLQAIDRLLDGLSGQARAVFLMSQLEG 135

Query: 142 LTYREIAELLGVSVSMVRKYIAQALAKCY 170
           LTY +I E LG+S+  + + +  AL  CY
Sbjct: 136 LTYVQIGERLGLSLGRIHQLMKDALHCCY 164


>fecI [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Eco Escherichia coli K12
          Length = 173

 Score =  137 bits (344), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 69/148 (46%), Positives = 97/148 (65%)

Query: 22  FTNSYSWLKQYLRRQVKSLADAEDVASAAFLEMAGIPDVSIIREPRALLTTISQRLVFDL 81
           +   + WLK +L R+++S  DA+D+A   FL +     +S IR+PR+ L TI++R++ DL
Sbjct: 17  YGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDL 76

Query: 82  WRRRDLEAAYLAALATTEEANTPSPEVVLEVVQTLVNIDRLLYGLSKNARQAFLYSQLDG 141
           +RR  LE AYL  LA   E   PSPE     ++TL  +D +L GL+   R+AFL SQLDG
Sbjct: 77  FRRNALEKAYLEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDG 136

Query: 142 LTYREIAELLGVSVSMVRKYIAQALAKC 169
           LTY EIA  LGVS+S V+KY+A+A+  C
Sbjct: 137 LTYSEIAHKLGVSISSVKKYVAKAVEHC 164


>PA0472 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 172

 Score =  129 bits (323), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 69/155 (44%), Positives = 97/155 (62%)

Query: 16  DFLVTEFTNSYSWLKQYLRRQVKSLADAEDVASAAFLEMAGIPDVSIIREPRALLTTISQ 75
           +F+ + + +   WL  +L R +     AED++   F+ + G P++  +REPRA L  +++
Sbjct: 10  EFVGSLYRDHRGWLLAWLNRNLGCRQRAEDLSQDTFVRLLGRPELPGLREPRAFLAKVAR 69

Query: 76  RLVFDLWRRRDLEAAYLAALATTEEANTPSPEVVLEVVQTLVNIDRLLYGLSKNARQAFL 135
            L+ D +RR  LE AYLA LA   EA  PS E    +++ L  IDRLL  LS  AR AFL
Sbjct: 70  GLMIDHFRRAALEQAYLAELALVPEAEQPSAEEQYLILEDLREIDRLLGTLSLKARSAFL 129

Query: 136 YSQLDGLTYREIAELLGVSVSMVRKYIAQALAKCY 170
           YS+LDG+ + EIAE LGVSV  VR+Y+AQ L +CY
Sbjct: 130 YSRLDGMPHAEIAERLGVSVPRVRQYLAQGLRQCY 164