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= 0004.0094.p         (237 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...    74   4e-13
slr1545 [K] COG1595 DNA-directed RNA polymerase specialized sigm...    72   1e-12
PA1300 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    71   3e-12
Rv1221 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    65   2e-10
MT1259 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    65   2e-10

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

 Score = 73.6 bits (179), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 55/170 (32%), Positives = 87/170 (51%), Gaps = 16/170 (9%)

Query: 63  VMRERSRLGGFIRRRVADAGE---AEDILQEVFYEFVQAYRLPEPIEQVSAWLFRVARNR 119
           V+ +R R  G  R     AG+   A++I QE +   +++   P+       WL+++ARNR
Sbjct: 31  VLYQRHR-QGLYRFLCGLAGQTELADEIYQETWLSLIRSESQPQGRASFRTWLYQIARNR 89

Query: 120 IIDRFRKK-KEEPLPEAHDIEQVEGGEDSWRLDLVLPASDGGPEAAYARAALIEALQAAL 178
           +ID +RK  + +PL +++D EQ+             P    GPE   + +   E LQ+AL
Sbjct: 90  LIDHWRKHGQRQPLQDSYD-EQLHAQ----------PDQGAGPEQQLSLSRDGERLQSAL 138

Query: 179 DELPPAQREVFIAHELDGLSFKEMSAASGTSLNTLLARKRYAVLHLRERL 228
           + LP  QREVF+      L   E++  + + 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 = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 50/167 (29%), Positives = 85/167 (50%), Gaps = 7/167 (4%)

Query: 65  RERSRLGGFIRRRVADAGEAEDILQEVFYE-FVQAYRLPEPIEQVSAWLFRVARNRIIDR 123
           R +S +   +     D  +  D+ QEV+   +   +RL EP+ +   WL R+A N   D 
Sbjct: 57  RYQSHVDKILYHLAPDWQDRADLAQEVWIRVYRNIHRLNEPV-KFKGWLSRIATNLFYDE 115

Query: 124 FRKKKEEPLPEAHDI-EQVEGGEDSWRLDLVLPASDGGPEAAYARAALIEALQAALDELP 182
            RK+K    P + D   +++ GE  W ++   P+    P+   + A   E L++A+ +LP
Sbjct: 116 LRKRKRVSHPISLDAPRRMDDGEIDWDIESDYPS----PDETLSTAEFYECLRSAIKDLP 171

Query: 183 PAQREVFIAHELDGLSFKEMSAASGTSLNTLLARKRYAVLHLRERLQ 229
            A R   I  E+DGL+++E++  +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 = 70.9 bits (172), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 45/156 (28%), Positives = 84/156 (53%), Gaps = 9/156 (5%)

Query: 73  FIRRRVADAGEAEDILQEVFYEFVQAYRLPEPIEQVSAWLFRVARNRIIDRFRKKKEEPL 132
           F+R+ +  + +A D+ Q+ F ++++ +   + +EQ  A+LF++ARN + D +R+++    
Sbjct: 23  FLRKHLGSSADAADLAQDTFAQWLK-WPGRQSVEQPRAFLFQIARNLLRDHWRRQQ---- 77

Query: 133 PEAHDIEQVEGGEDSWRLDLVLPASDGGPEAAYARAALIEALQAALDELPPAQREVFIAH 192
               D+++    ++       L     GP   + +   +  L AAL ELPP +RE F+ H
Sbjct: 78  SRGQDLDRPAANDEP----AALEGEAAGPGERFEQQQRLSHLAAALAELPPRRREAFVLH 133

Query: 193 ELDGLSFKEMSAASGTSLNTLLARKRYAVLHLRERL 228
           + DGLS  E++   G SL+ +      A+LH + RL
Sbjct: 134 KFDGLSQVEVAERMGISLSMVEKHIASALLHCKRRL 169


>Rv1221 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Mtu Mycobacterium tuberculosis H37Rv
          Length = 257

 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 52/161 (32%), Positives = 75/161 (46%), Gaps = 25/161 (15%)

Query: 76  RRVADAGEAEDILQEVF---YEFVQAYRLPEPIEQVSAWLFRVARNRIIDRFRKK---KE 129
           R   +  +AED+ QE F   +  VQ Y+ P   E    WL R+  N  +D  R++   + 
Sbjct: 101 RLSGNQHDAEDLTQETFIRVFRSVQNYQ-PGTFE---GWLHRITTNLFLDMVRRRARIRM 156

Query: 130 EPLPEAHDIEQVEGGEDSWRLDLVLPASDGGPEAAYARAALIEALQAALDELPPAQREVF 189
           E LPE +D                +PA +  PE  Y  A L   LQAAL  LPP  R   
Sbjct: 157 EALPEDYD---------------RVPADEPNPEQIYHDARLGPDLQAALASLPPEFRAAV 201

Query: 190 IAHELDGLSFKEMSAASGTSLNTLLARKRYAVLHLRERLQA 230
           +  +++GLS++E+ A  G  L T+ +R       LR+ L A
Sbjct: 202 VLCDIEGLSYEEIGATLGVKLGTVRSRIHRGRQALRDYLAA 242


>MT1259 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog MtC Mycobacterium tuberculosis CDC1551
          Length = 257

 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 52/161 (32%), Positives = 75/161 (46%), Gaps = 25/161 (15%)

Query: 76  RRVADAGEAEDILQEVF---YEFVQAYRLPEPIEQVSAWLFRVARNRIIDRFRKK---KE 129
           R   +  +AED+ QE F   +  VQ Y+ P   E    WL R+  N  +D  R++   + 
Sbjct: 101 RLSGNQHDAEDLTQETFIRVFRSVQNYQ-PGTFE---GWLHRITTNLFLDMVRRRARIRM 156

Query: 130 EPLPEAHDIEQVEGGEDSWRLDLVLPASDGGPEAAYARAALIEALQAALDELPPAQREVF 189
           E LPE +D                +PA +  PE  Y  A L   LQAAL  LPP  R   
Sbjct: 157 EALPEDYD---------------RVPADEPNPEQIYHDARLGPDLQAALASLPPEFRAAV 201

Query: 190 IAHELDGLSFKEMSAASGTSLNTLLARKRYAVLHLRERLQA 230
           +  +++GLS++E+ A  G  L T+ +R       LR+ L A
Sbjct: 202 VLCDIEGLSYEEIGATLGVKLGTVRSRIHRGRQALRDYLAA 242