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= 0002.0589.p         (159 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

PA3899 [K] COG1595 DNA-directed RNA polymerase specialized sigma...   172   3e-43
PA1912 [K] COG1595 DNA-directed RNA polymerase specialized sigma...   167   1e-41
fecI [K] COG1595 DNA-directed RNA polymerase specialized sigma s...   155   3e-38
PA0472 [K] COG1595 DNA-directed RNA polymerase specialized sigma...   142   4e-34
PA2468 [K] COG1595 DNA-directed RNA polymerase specialized sigma...   131   5e-31

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

 Score =  172 bits (436), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 85/150 (56%), Positives = 109/150 (72%)

Query: 4   LYTGHHHWLLGWLRRRTGNPELAADLAQDTFLRIMVSRRDFYLDEARALLATIARGLVID 63
           LY+ HHHWL GWLRRR G P+ AADLAQDTF++++VSR+   +DE RA L TIAR ++ +
Sbjct: 15  LYSDHHHWLTGWLRRRLGCPQNAADLAQDTFVKVLVSRQAARIDEPRAFLTTIARRVLCN 74

Query: 64  HFRRCALEAAFLEMLAQLPPEHVPSPEARLAVLETLNQIDAMLAALPAKVRSAFLLSQLD 123
           H+RR  +E A+LE LA LP   VPS E R  VLETL ++D +L  LP   +  FLL+QLD
Sbjct: 75  HYRRQDVERAYLEALASLPEREVPSEETRAIVLETLVELDRLLDGLPPLAKETFLLAQLD 134

Query: 124 GLSYAEIAVRLEVSLSSVQQYMKRAFMACY 153
           GL YAEIA +L +SLSSV++YM +A   CY
Sbjct: 135 GLGYAEIATQLGISLSSVKRYMLKAAQRCY 164


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

 Score =  167 bits (422), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 85/149 (57%), Positives = 109/149 (73%)

Query: 4   LYTGHHHWLLGWLRRRTGNPELAADLAQDTFLRIMVSRRDFYLDEARALLATIARGLVID 63
           LY  HH WL GWLRRR G  E AADLAQDTF R++ SRR     E RA L T+A+GL+I+
Sbjct: 15  LYQDHHGWLQGWLRRRLGCAENAADLAQDTFARLLASRRVLDAREPRAYLTTVAKGLMIN 74

Query: 64  HFRRCALEAAFLEMLAQLPPEHVPSPEARLAVLETLNQIDAMLAALPAKVRSAFLLSQLD 123
            F+R +LE A+L+ LA LP +  P PE RL VLETL+++DA+L +LP +VR AFLL+Q++
Sbjct: 75  WFQRQSLERAYLDALANLPEDLAPPPEQRLMVLETLHEVDALLGSLPDRVRQAFLLAQIE 134

Query: 124 GLSYAEIAVRLEVSLSSVQQYMKRAFMAC 152
           GL Y  IA RL VSL SV++YM++AF  C
Sbjct: 135 GLKYEAIAERLGVSLGSVKRYMQQAFRQC 163


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

 Score =  155 bits (393), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 81/157 (51%), Positives = 108/157 (68%), Gaps = 2/157 (1%)

Query: 4   LYTGHHHWLLGWLRRRTGNPELAADLAQDTFLRIMVSRRDFYLDEARALLATIARGLVID 63
           LY  HH WL  WL R+  +   A D+AQDTFLR+MVS     + + R+ L TIA+ +++D
Sbjct: 16  LYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVD 75

Query: 64  HFRRCALEAAFLEMLAQLPPEHVPSPEARLAVLETLNQIDAMLAALPAKVRSAFLLSQLD 123
            FRR ALE A+LEMLA +P    PSPE R + LETL  +D+ML  L  K R AFLLSQLD
Sbjct: 76  LFRRNALEKAYLEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLD 135

Query: 124 GLSYAEIAVRLEVSLSSVQQYMKRAFMAC--YRVQYG 158
           GL+Y+EIA +L VS+SSV++Y+ +A   C  +R++YG
Sbjct: 136 GLTYSEIAHKLGVSISSVKKYVAKAVEHCLLFRLEYG 172


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

 Score =  142 bits (357), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 77/159 (48%), Positives = 99/159 (62%)

Query: 1   MAGLYTGHHHWLLGWLRRRTGNPELAADLAQDTFLRIMVSRRDFYLDEARALLATIARGL 60
           +  LY  H  WLL WL R  G  + A DL+QDTF+R++       L E RA LA +ARGL
Sbjct: 12  VGSLYRDHRGWLLAWLNRNLGCRQRAEDLSQDTFVRLLGRPELPGLREPRAFLAKVARGL 71

Query: 61  VIDHFRRCALEAAFLEMLAQLPPEHVPSPEARLAVLETLNQIDAMLAALPAKVRSAFLLS 120
           +IDHFRR ALE A+L  LA +P    PS E +  +LE L +ID +L  L  K RSAFL S
Sbjct: 72  MIDHFRRAALEQAYLAELALVPEAEQPSAEEQYLILEDLREIDRLLGTLSLKARSAFLYS 131

Query: 121 QLDGLSYAEIAVRLEVSLSSVQQYMKRAFMACYRVQYGD 159
           +LDG+ +AEIA RL VS+  V+QY+ +    CY   YG+
Sbjct: 132 RLDGMPHAEIAERLGVSVPRVRQYLAQGLRQCYIALYGE 170


>PA2468 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 172

 Score =  131 bits (330), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 83/159 (52%), Positives = 105/159 (66%)

Query: 1   MAGLYTGHHHWLLGWLRRRTGNPELAADLAQDTFLRIMVSRRDFYLDEARALLATIARGL 60
           M  LY+ HH WL  WLR + G    AADLAQDTFLRI++ R    +   RA L TIARGL
Sbjct: 14  MHALYSEHHGWLQNWLRGKLGCAADAADLAQDTFLRILLKRELREIGMPRAFLRTIARGL 73

Query: 61  VIDHFRRCALEAAFLEMLAQLPPEHVPSPEARLAVLETLNQIDAMLAALPAKVRSAFLLS 120
           VIDH+RR  L+ A+LE +A LP    PSPEAR  VLE L +I  ML  L  KVR+AFLL+
Sbjct: 74  VIDHWRREELQRAYLESIAHLPEAQAPSPEARELVLELLEEISRMLDGLKPKVRTAFLLA 133

Query: 121 QLDGLSYAEIAVRLEVSLSSVQQYMKRAFMACYRVQYGD 159
           Q + LS+ +IA R+ VS  SV++Y+  A   CY ++YG+
Sbjct: 134 QCEDLSHRQIAERMGVSQRSVERYVAEALYHCYLLRYGE 172