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= 0007.0126.p         (177 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

PA0472 [K] COG1595 DNA-directed RNA polymerase specialized sigma...   134   1e-31
PA1912 [K] COG1595 DNA-directed RNA polymerase specialized sigma...   130   1e-30
fecI [K] COG1595 DNA-directed RNA polymerase specialized sigma s...   125   4e-29
PA3899 [K] COG1595 DNA-directed RNA polymerase specialized sigma...   124   9e-29
RSp0849 [K] COG1595 DNA-directed RNA polymerase specialized sigm...   108   5e-24

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

 Score =  134 bits (336), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 73/164 (44%), Positives = 97/164 (59%), Gaps = 11/164 (6%)

Query: 12  SFYSSHHGWLFGWLRKKLGCTHNAADVAQDTFVRIIAXADVAQDTFVRILLGVQEPRAYL 71
           S Y  H GWL  WL + LGC   A D++QDTFVR++   +         L G++EPRA+L
Sbjct: 14  SLYRDHRGWLLAWLNRNLGCRQRAEDLSQDTFVRLLGRPE---------LPGLREPRAFL 64

Query: 72  TATAKRLLVDRARRQMIEQSYLAELALTMEQTEGYPGPEEILLAVEALEQISAALQSVAA 131
              A+ L++D  RR  +EQ+YLAELAL  E  +  P  EE  L +E L +I   L +++ 
Sbjct: 65  AKVARGLMIDHFRRAALEQAYLAELALVPEAEQ--PSAEEQYLILEDLREIDRLLGTLSL 122

Query: 132 KAREAFLLHYLDGRTHAEVAAALGVSTRMVGKYLVQVLVKCRLA 175
           KAR AFL   LDG  HAE+A  LGVS   V +YL Q L +C +A
Sbjct: 123 KARSAFLYSRLDGMPHAEIAERLGVSVPRVRQYLAQGLRQCYIA 166


>PA1912 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 168

 Score =  130 bits (328), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 70/171 (40%), Positives = 103/171 (60%), Gaps = 11/171 (6%)

Query: 2   AESTLQPDMHSFYSSHHGWLFGWLRKKLGCTHNAADVAQDTFVRIIAXADVAQDTFVRIL 61
           A+++L   +   Y  HHGWL GWLR++LGC  NAAD+AQDTF R++A          R +
Sbjct: 4   ADASLHDAVSHLYQDHHGWLQGWLRRRLGCAENAADLAQDTFARLLAS---------RRV 54

Query: 62  LGVQEPRAYLTATAKRLLVDRARRQMIEQSYLAELALTMEQTEGYPGPEEILLAVEALEQ 121
           L  +EPRAYLT  AK L+++  +RQ +E++YL  LA   E     P PE+ L+ +E L +
Sbjct: 55  LDAREPRAYLTTVAKGLMINWFQRQSLERAYLDALANLPEDLA--PPPEQRLMVLETLHE 112

Query: 122 ISAALQSVAAKAREAFLLHYLDGRTHAEVAAALGVSTRMVGKYLVQVLVKC 172
           + A L S+  + R+AFLL  ++G  +  +A  LGVS   V +Y+ Q   +C
Sbjct: 113 VDALLGSLPDRVRQAFLLAQIEGLKYEAIAERLGVSLGSVKRYMQQAFRQC 163


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

 Score =  125 bits (315), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 68/173 (39%), Positives = 99/173 (57%), Gaps = 11/173 (6%)

Query: 2   AESTLQPDMHSFYSSHHGWLFGWLRKKLGCTHNAADVAQDTFVRIIAXADVAQDTFVRIL 61
           A +T      S Y +HHGWL  WL +KL    +A D+AQDTF+R++    ++        
Sbjct: 5   ATTTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLST------- 57

Query: 62  LGVQEPRAYLTATAKRLLVDRARRQMIEQSYLAELALTMEQTEGYPGPEEILLAVEALEQ 121
             +++PR++L   AKR++VD  RR  +E++YL  LAL  E   G P PEE    +E L+ 
Sbjct: 58  --IRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLALMPEG--GAPSPEERESQLETLQL 113

Query: 122 ISAALQSVAAKAREAFLLHYLDGRTHAEVAAALGVSTRMVGKYLVQVLVKCRL 174
           + + L  +  K REAFLL  LDG T++E+A  LGVS   V KY+ + +  C L
Sbjct: 114 LDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSISSVKKYVAKAVEHCLL 166


>PA3899 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 169

 Score =  124 bits (312), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 65/165 (39%), Positives = 97/165 (58%), Gaps = 11/165 (6%)

Query: 12  SFYSSHHGWLFGWLRKKLGCTHNAADVAQDTFVRIIAXADVAQDTFVRILLGVQEPRAYL 71
           + YS HH WL GWLR++LGC  NAAD+AQDTFV+++     A+         + EPRA+L
Sbjct: 14  TLYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAAR---------IDEPRAFL 64

Query: 72  TATAKRLLVDRARRQMIEQSYLAELALTMEQTEGYPGPEEILLAVEALEQISAALQSVAA 131
           T  A+R+L +  RRQ +E++YL  LA   E+    P  E   + +E L ++   L  +  
Sbjct: 65  TTIARRVLCNHYRRQDVERAYLEALASLPERE--VPSEETRAIVLETLVELDRLLDGLPP 122

Query: 132 KAREAFLLHYLDGRTHAEVAAALGVSTRMVGKYLVQVLVKCRLAQ 176
            A+E FLL  LDG  +AE+A  LG+S   V +Y+++   +C  A+
Sbjct: 123 LAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRCYFAE 167


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

 Score =  108 bits (270), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 66/164 (40%), Positives = 87/164 (53%), Gaps = 11/164 (6%)

Query: 12  SFYSSHHGWLFGWLRKKLGCTHNAADVAQDTFVRIIAXADVAQDTFVRILLGVQEPRAYL 71
            ++  H+ WL G + +K GC   A D+A + F +++   D           G +EPRA L
Sbjct: 14  DWFRQHYAWLAGRMGRKTGCRFGAEDLASEAFAQLLQMPDWQ---------GTREPRALL 64

Query: 72  TATAKRLLVDRARRQMIEQSYLAELALTMEQTEGYPGPEEILLAVEALEQISAALQSVAA 131
           T  A+RLL D  RR+ +E +Y A  A   E T   P PEE  L +EAL  I   L  +  
Sbjct: 65  TTIAQRLLYDIWRRRDLELAYQAWAAAQPEAT--LPSPEERALVLEALATIDRLLDGLPV 122

Query: 132 KAREAFLLHYLDGRTHAEVAAALGVSTRMVGKYLVQVLVKCRLA 175
           KAR AFL   LDG T+ E+A  L VS RMV KY+ Q +  C LA
Sbjct: 123 KARTAFLYSQLDGLTYPEIAGRLNVSVRMVQKYMTQAMRLCYLA 166