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= 0001.2218.p         (236 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

PA2426 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    99   1e-20
SMc04203 [K] COG1595 DNA-directed RNA polymerase specialized sig...    86   6e-17
PA1300 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    69   8e-12
PA0149 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    66   7e-11
fecI [K] COG1595 DNA-directed RNA polymerase specialized sigma s...    59   8e-09

>PA2426 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 187

 Score = 98.6 bits (244), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 64/173 (36%), Positives = 91/173 (52%), Gaps = 21/173 (12%)

Query: 65  CASPARQALIEVYLSRRSELRGVAAKIIARPEEVDDVLQDVYLRLASS-TCASEVQNPFG 123
           C +P    L++ ++  R+ L  +AA+I       +DV+QD + RL S+    S  +    
Sbjct: 10  CDTP----LLQAFVDNRTILVKIAARITGCRSRAEDVVQDAFFRLQSAPQITSSFKAQLS 65

Query: 124 YCCQVVRNTAVNYCRRRMVEANHLVTTADGEMPEVEG------GRAAEVGIDERRLLERI 177
           Y  Q+VRN A+++ R++ +E  +         PE EG      G + E        LE I
Sbjct: 66  YLFQIVRNLAIDHYRKQALEQKY-------SGPEEEGLNVVIQGASPETSHINYATLEHI 118

Query: 178 EAALATLPPRTRRVFELYRLEGRTQRDIAQCLGVSATLVNFMLKDVMAALASC 230
             AL  LP RTR  FE+YRL G  Q+DIA+ LGVS TLVNFM++D   AL  C
Sbjct: 119 ADALTELPKRTRYAFEMYRLHGVPQKDIAKELGVSPTLVNFMIRD---ALVHC 168


>SMc04203 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Sme Sinorhizobium meliloti
          Length = 159

 Score = 86.3 bits (212), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 56/160 (35%), Positives = 85/160 (53%), Gaps = 7/160 (4%)

Query: 76  VYLSRRSELRGVAAKIIARPEEVDDVLQDVYLRLASSTCASEVQNPFGYCCQVVRNTAVN 135
           +YL  R  L   AA ++   ++ +D++QD YLR    T A E   P  Y  ++VRN + N
Sbjct: 1   MYLRHRRSLIDYAAPLLGSKDDAEDIVQDAYLRFVRET-ADEHMPPKTYLFRIVRNLSFN 59

Query: 136 YCRRRMVEANHLVTTAD---GEMPEVEGGRAAEVGIDERRLLERIEAALATLPPRTRRVF 192
              RR +E N++V +AD     +P+      A+  + E    +R+  AL  LP R RR F
Sbjct: 60  KRSRRKLE-NNVVESADIPWWALPQAVETPEAQFLMSE--AADRVAQALGALPDRMRRAF 116

Query: 193 ELYRLEGRTQRDIAQCLGVSATLVNFMLKDVMAALASCGD 232
           ELYR EG T +DIA+ L +S    + +++D M  L +  D
Sbjct: 117 ELYRFEGSTLKDIAEELSISIPTAHRLVRDAMEHLKAGLD 156


>PA1300 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 175

 Score = 68.9 bits (167), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 46/168 (27%), Positives = 79/168 (47%), Gaps = 5/168 (2%)

Query: 70  RQALIEVYLSRRSELRGVAAKIIARPEEVDDVLQDVYLRLASSTCASEVQNPFGYCCQVV 129
           R ++   Y +   EL     K +    +  D+ QD + +         V+ P  +  Q+ 
Sbjct: 6   RGSVSHAYQAFHGELLRFLRKHLGSSADAADLAQDTFAQWLKWPGRQSVEQPRAFLFQIA 65

Query: 130 RNTAVNYCRRRMVEANHLVTTADGEMPEVEGGRAAEVG--IDERRLLERIEAALATLPPR 187
           RN   ++ RR+      L   A  + P    G AA  G   ++++ L  + AALA LPPR
Sbjct: 66  RNLLRDHWRRQQSRGQDLDRPAANDEPAALEGEAAGPGERFEQQQRLSHLAAALAELPPR 125

Query: 188 TRRVFELYRLEGRTQRDIAQCLGVSATLVNFMLKDVMAALASCGDLLG 235
            R  F L++ +G +Q ++A+ +G+S ++V    K + +AL  C   LG
Sbjct: 126 RREAFVLHKFDGLSQVEVAERMGISLSMVE---KHIASALLHCKRRLG 170


>PA0149 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 181

 Score = 65.9 bits (159), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 51/167 (30%), Positives = 82/167 (49%), Gaps = 18/167 (10%)

Query: 70  RQALIEVYLSRRSELRGVAAKIIARPEEVDDVLQDVYLRLASSTCASEVQNPFGYCCQVV 129
           R  L++ +L++R  +  + ++ +       D++Q+++LR      A  V+    Y  +  
Sbjct: 10  RADLLKAFLAQRQRMESLVSRWVGCRATAADLVQELFLRFWRRPAAP-VEELGSYLLRSA 68

Query: 130 RNTAVNYCRRRMVEANHLVTTADGEMPEVEGG------RAAEVGIDERRLLERIEAALAT 183
           RN A+++ R        L    D  +PE   G      +A E G   RR    +EAAL  
Sbjct: 69  RNLAIDHLRGEGSRQRQL----DDWLPEQRQGEPVGPEQALEAGDQWRR----VEAALRG 120

Query: 184 LPPRTRRVFELYRLEGRTQRDIAQCLGVSATLVNFMLKDVMAALASC 230
           LP RTRR+F L R+ GRT  +IAQ + +S + V    K +M AL +C
Sbjct: 121 LPERTRRIFLLNRIHGRTYAEIAQAMQLSQSAVE---KHMMRALDAC 164


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

 Score = 59.3 bits (142), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 44/155 (28%), Positives = 74/155 (47%), Gaps = 6/155 (3%)

Query: 76  VYLSRRSELRGVAAKIIARPEEVDDVLQDVYLRLASSTCASEVQNPFGYCCQVVRNTAVN 135
           +Y +    L+    + +    + DD+ QD +LR+  S   S +++P  + C + +   V+
Sbjct: 16  LYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVD 75

Query: 136 YCRRRMVEANHLVTTADGEMPEVEGGRAAEVGIDERRLLERIEAALATLPPRTRRVFELY 195
             RR  +E  +L   A   MPE  G  + E    +   L+ +++ L  L  +TR  F L 
Sbjct: 76  LFRRNALEKAYLEMLA--LMPE-GGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLS 132

Query: 196 RLEGRTQRDIAQCLGVSATLVNFMLKDVMAALASC 230
           +L+G T  +IA  LGVS + V    K V  A+  C
Sbjct: 133 QLDGLTYSEIAHKLGVSISSVK---KYVAKAVEHC 164