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= 0049.0090.p         (195 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

PA2896 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    73   3e-13
slr1545 [K] COG1595 DNA-directed RNA polymerase specialized sigm...    69   4e-12
PA1300 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    69   8e-12
alr3280 [K] COG1595 DNA-directed RNA polymerase specialized sigm...    67   2e-11
Rv3223c [K] COG1595 DNA-directed RNA polymerase specialized sigm...    61   1e-09

>PA2896 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 194

 Score = 73.2 bits (178), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 57/170 (33%), Positives = 86/170 (50%), Gaps = 16/170 (9%)

Query: 21  VMRERSRLGGFIRRPQADAGEAE---DILQEVFYEFVQAYRLPEPIEQVSAWLFRVARNR 77
           V+ +R R  G  R     AG+ E   +I QE +   +++   P+       WL+++ARNR
Sbjct: 31  VLYQRHR-QGLYRFLCGLAGQTELADEIYQETWLSLIRSESQPQGRASFRTWLYQIARNR 89

Query: 78  IIDRFRKKKE-EPLPEAHDIEQVDGADDAWRLDLALPASADGPEAAYARAALIDALQEAL 136
           +ID +RK  + +PL +++D EQ+           A P    GPE   + +   + LQ AL
Sbjct: 90  LIDHWRKHGQRQPLQDSYD-EQLH----------AQPDQGAGPEQQLSLSRDGERLQSAL 138

Query: 137 GELPEAQREVFIAHELDGLSFKEMAAASGTSLNTLLARKRYAVLHLRERL 186
             LPE QREVF+      L   E+A  + + L T+ +R RYAV  LR  L
Sbjct: 139 ETLPEEQREVFLMRAHGELELAEIATLTQSPLETVKSRFRYAVQKLRRLL 188


>slr1545 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Syn Synechocystis
          Length = 223

 Score = 69.3 bits (168), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 50/167 (29%), Positives = 84/167 (50%), Gaps = 7/167 (4%)

Query: 23  RERSRLGGFIRRPQADAGEAEDILQEVFYE-FVQAYRLPEPIEQVSAWLFRVARNRIIDR 81
           R +S +   +     D  +  D+ QEV+   +   +RL EP+ +   WL R+A N   D 
Sbjct: 57  RYQSHVDKILYHLAPDWQDRADLAQEVWIRVYRNIHRLNEPV-KFKGWLSRIATNLFYDE 115

Query: 82  FRKKKEEPLPEAHDI-EQVDGADDAWRLDLALPASADGPEAAYARAALIDALQEALGELP 140
            RK+K    P + D   ++D  +  W ++   P+    P+   + A   + L+ A+ +LP
Sbjct: 116 LRKRKRVSHPISLDAPRRMDDGEIDWDIESDYPS----PDETLSTAEFYECLRSAIKDLP 171

Query: 141 EAQREVFIAHELDGLSFKEMAAASGTSLNTLLARKRYAVLHLRERLQ 187
           EA R   I  E+DGL+++E+A  +G SL T+ +R   A   L+  LQ
Sbjct: 172 EAFRTTIILREIDGLAYEEIAEITGVSLGTVKSRIARARAKLQTFLQ 218


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

 Score = 68.6 bits (166), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 47/156 (30%), Positives = 83/156 (53%), Gaps = 9/156 (5%)

Query: 31  FIRRPQADAGEAEDILQEVFYEFVQAYRLPEPIEQVSAWLFRVARNRIIDRFRKKKEEPL 90
           F+R+    + +A D+ Q+ F ++++ +   + +EQ  A+LF++ARN + D +R+++    
Sbjct: 23  FLRKHLGSSADAADLAQDTFAQWLK-WPGRQSVEQPRAFLFQIARNLLRDHWRRQQSR-- 79

Query: 91  PEAHDIEQVDGADDAWRLDLALPASADGPEAAYARAALIDALQEALGELPEAQREVFIAH 150
               D+++    D+      AL   A GP   + +   +  L  AL ELP  +RE F+ H
Sbjct: 80  --GQDLDRPAANDEP----AALEGEAAGPGERFEQQQRLSHLAAALAELPPRRREAFVLH 133

Query: 151 ELDGLSFKEMAAASGTSLNTLLARKRYAVLHLRERL 186
           + DGLS  E+A   G SL+ +      A+LH + RL
Sbjct: 134 KFDGLSQVEVAERMGISLSMVEKHIASALLHCKRRL 169


>alr3280 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Nos Nostoc sp. PCC 7120
          Length = 218

 Score = 67.0 bits (162), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 47/155 (30%), Positives = 75/155 (48%), Gaps = 5/155 (3%)

Query: 38  DAGEAEDILQEVFYE-FVQAYRLPEPIEQVSAWLFRVARNRIIDRFRKKKEEPLPEAHDI 96
           D  +  D+ QEV+   +    RL EP  +   WL R+A N   D  RK+K    P + D 
Sbjct: 67  DWSDRADLAQEVWIRVYRNINRLQEP-SKFRGWLSRIATNLFYDELRKRKRVVSPLSLDA 125

Query: 97  EQVDGADDAWRLDLALPASADGPEAAYARAALIDALQEALGELPEAQREVFIAHELDGLS 156
            +    DD   +D  +     GPE         + L+EA+ +LPE  R   +  E++G++
Sbjct: 126 PR--SVDDG-EMDWEIAGDTPGPEEELTTREFYEQLREAIADLPEVFRTTIVLREIEGMA 182

Query: 157 FKEMAAASGTSLNTLLARKRYAVLHLRERLQAVYD 191
           ++E+A  +G SL T+ +R   A   L+ +LQ   D
Sbjct: 183 YEEIAEITGVSLGTVKSRIARARSRLQTQLQTYLD 217


>Rv3223c [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Mtu Mycobacterium tuberculosis H37Rv
          Length = 216

 Score = 61.2 bits (147), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 57/190 (30%), Positives = 89/190 (46%), Gaps = 15/190 (7%)

Query: 8   SPMSDQDREITATVMRERSRL-----GGFIRRPQADAGEAEDILQEVFYEFVQAYRLPEP 62
            P  + D E+TA   R+   L     GG +R  +  A +AED+LQE   +    +R    
Sbjct: 16  GPSEETDEELTARFERDAIPLLDQLYGGALRMTRNPA-DAEDLLQETMVKAYAGFRSFRH 74

Query: 63  IEQVSAWLFRVARNRIIDRFRKKKEEPLPEAHDIEQVDGADDAWRLDLALPASADGPEAA 122
              + AWL+R+  N  I+ +RKK+ +P    +  EQ+      W+L      S+ G  +A
Sbjct: 75  GTNLKAWLYRILTNTYINSYRKKQRQPA--EYPTEQITD----WQLASNAEHSSTGLRSA 128

Query: 123 YARA--ALIDA-LQEALGELPEAQREVFIAHELDGLSFKEMAAASGTSLNTLLARKRYAV 179
              A  AL D  ++EAL  LPE  R      +++G  +KE+A    T + T+++R     
Sbjct: 129 EVEALEALPDTEIKEALQALPEEFRMAVYYADVEGFPYKEIAEIMDTPIGTVMSRLHRGR 188

Query: 180 LHLRERLQAV 189
             LR  L  V
Sbjct: 189 RQLRGLLADV 198