BLASTP 2.2.18 [Mar-02-2008] 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= 0188.0037.p (314 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B1DJU5.1 B1DJU5_9BACL DNA-directed RNA polymerase, alpha subunit 531 e-149 C0ZIK7.1 RPOA_BREBN DNA-directed RNA polymerase subunit alpha EC... 496 e-139 C3J6R5.1 C3J6R5_9BACI DNA-directed RNA polymerase, alpha subunit 477 e-133 Q5L3R2.1 RPOA_GEOKA DNA-directed RNA polymerase subunit alpha EC... 477 e-133 B4BSP7.1 B4BSP7_9BACI DNA-directed RNA polymerase, alpha subunit 476 e-133 >B1DJU5.1 B1DJU5_9BACL DNA-directed RNA polymerase, alpha subunit Length = 314 Score = 531 bits (1367), Expect = e-149, Method: Compositional matrix adjust. Identities = 262/295 (88%), Positives = 276/295 (93%) Query: 1 VIEIEKPKIETVEANDEGTYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60 +IEIEKPKIETV+ N++GTYG+FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG Sbjct: 1 MIEIEKPKIETVDLNEDGTYGRFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60 Query: 61 VLHEFSTVPGVMEDVTEIILNLKALSLKIHSDEEKVFEIDAEGEGIVTAGDIRADSDVEI 120 VLHEFSTVPGV+EDVTEIILNLK LSLKIHSDEEKV EIDAEGEGIVTAGDIRADSDVEI Sbjct: 61 VLHEFSTVPGVIEDVTEIILNLKGLSLKIHSDEEKVLEIDAEGEGIVTAGDIRADSDVEI 120 Query: 121 LNPDLHIATLGPGARLHMRIFAGRGRGYVQADRNKREDQPIGVIPVDSIYTPISRVNYGI 180 LNPDLHIATL GARLH+RIFA RGRGYVQADRNKR+DQPIGVIPVDSIYTPI+RVNY + Sbjct: 121 LNPDLHIATLASGARLHLRIFANRGRGYVQADRNKRDDQPIGVIPVDSIYTPITRVNYSV 180 Query: 181 DNTRVGQVTNYDKLTMEIWTDGSIRPEEAVSLGAKILNEHLVLFVGLTDEAKDAEIMVXX 240 +NTRVGQVTNYDKLT+E+WTDGSIRPEEAVSLGAKIL EHL LFVGLTDEAKDAEIMV Sbjct: 181 ENTRVGQVTNYDKLTLEVWTDGSIRPEEAVSLGAKILTEHLDLFVGLTDEAKDAEIMVEK 240 Query: 241 XXXXXXXVLEMTIEELDLSVRSYNCLKRAGINTVQELTTKTEEDMMKVRNLGRKS 295 VLEMTIEELDLSVRSYNCLKRAGINTVQEL TK+EEDMMKVRNLGRKS Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELITKSEEDMMKVRNLGRKS 295 >C0ZIK7.1 RPOA_BREBN DNA-directed RNA polymerase subunit alpha EC=2.7.7.6 Length = 314 Score = 496 bits (1278), Expect = e-139, Method: Compositional matrix adjust. Identities = 244/295 (82%), Positives = 265/295 (89%) Query: 1 VIEIEKPKIETVEANDEGTYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60 +IEIEKPKIE VE +D+ +YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAV +VQIDG Sbjct: 1 MIEIEKPKIEVVEVSDDNSYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVRTVQIDG 60 Query: 61 VLHEFSTVPGVMEDVTEIILNLKALSLKIHSDEEKVFEIDAEGEGIVTAGDIRADSDVEI 120 VLHEFSTV GV+EDVTEIILN+K L+LKIHSDEEKV EIDAEGEG+V AGDIRADSDVE+ Sbjct: 61 VLHEFSTVEGVVEDVTEIILNIKGLALKIHSDEEKVIEIDAEGEGVVKAGDIRADSDVEV 120 Query: 121 LNPDLHIATLGPGARLHMRIFAGRGRGYVQADRNKREDQPIGVIPVDSIYTPISRVNYGI 180 LNPDLHIATL G RLH+R+ AGRGRGYVQ+D NK ED PIGVIP+DSIYTPI RVNY + Sbjct: 121 LNPDLHIATLANGGRLHIRMTAGRGRGYVQSDGNKSEDLPIGVIPIDSIYTPIKRVNYQV 180 Query: 181 DNTRVGQVTNYDKLTMEIWTDGSIRPEEAVSLGAKILNEHLVLFVGLTDEAKDAEIMVXX 240 +NTRVGQ+TNYDKLT+E+WT+GSI PEEAVSLGAKI+ EHL LFVGLTDEAKDAEIMV Sbjct: 181 ENTRVGQMTNYDKLTLEVWTNGSISPEEAVSLGAKIMTEHLNLFVGLTDEAKDAEIMVEK 240 Query: 241 XXXXXXXVLEMTIEELDLSVRSYNCLKRAGINTVQELTTKTEEDMMKVRNLGRKS 295 VLEMTIEELDLSVRSYNCLKRAGINTVQELT KTEEDMMKVRNLGRKS Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEDMMKVRNLGRKS 295 >C3J6R5.1 C3J6R5_9BACI DNA-directed RNA polymerase, alpha subunit Length = 314 Score = 477 bits (1228), Expect = e-133, Method: Compositional matrix adjust. Identities = 234/295 (79%), Positives = 261/295 (88%) Query: 1 VIEIEKPKIETVEANDEGTYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60 +IEIEKPKIETVE +++ YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG Sbjct: 1 MIEIEKPKIETVELSEDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60 Query: 61 VLHEFSTVPGVMEDVTEIILNLKALSLKIHSDEEKVFEIDAEGEGIVTAGDIRADSDVEI 120 VLHEFST+ GV+EDVT IILN+K L+LKI+SDEEK EID +GEG+VTA DI DSDVEI Sbjct: 61 VLHEFSTIDGVVEDVTAIILNIKKLALKIYSDEEKTLEIDVQGEGVVTAADITHDSDVEI 120 Query: 121 LNPDLHIATLGPGARLHMRIFAGRGRGYVQADRNKREDQPIGVIPVDSIYTPISRVNYGI 180 LNPDLHIATL G RL MR+ A RGRGYV A+ NKREDQPIGVIP+DSIYTP+SRV+Y + Sbjct: 121 LNPDLHIATLAEGGRLRMRMTAKRGRGYVPAEANKREDQPIGVIPIDSIYTPVSRVSYQV 180 Query: 181 DNTRVGQVTNYDKLTMEIWTDGSIRPEEAVSLGAKILNEHLVLFVGLTDEAKDAEIMVXX 240 +NTRVGQVT+YDKLT+++WTDGSI P+EA+SLGAKIL EHL +FVGLTDEA++AEIMV Sbjct: 181 ENTRVGQVTDYDKLTIDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240 Query: 241 XXXXXXXVLEMTIEELDLSVRSYNCLKRAGINTVQELTTKTEEDMMKVRNLGRKS 295 VLEMTIEELDLSVRSYNCLKRAGINTVQELT KTEEDMMKVRNLGRKS Sbjct: 241 EDDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEDMMKVRNLGRKS 295 >Q5L3R2.1 RPOA_GEOKA DNA-directed RNA polymerase subunit alpha EC=2.7.7.6 Length = 314 Score = 477 bits (1228), Expect = e-133, Method: Compositional matrix adjust. Identities = 234/295 (79%), Positives = 261/295 (88%) Query: 1 VIEIEKPKIETVEANDEGTYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60 +IEIEKPKIETVE +++ YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG Sbjct: 1 MIEIEKPKIETVELSEDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60 Query: 61 VLHEFSTVPGVMEDVTEIILNLKALSLKIHSDEEKVFEIDAEGEGIVTAGDIRADSDVEI 120 VLHEFST+ GV+EDVT IILN+K L+LKI+SDEEK EID +GEG+VTA DI DSDVEI Sbjct: 61 VLHEFSTIDGVVEDVTAIILNIKKLALKIYSDEEKTLEIDVQGEGVVTAADITHDSDVEI 120 Query: 121 LNPDLHIATLGPGARLHMRIFAGRGRGYVQADRNKREDQPIGVIPVDSIYTPISRVNYGI 180 LNPDLHIATL G RL MR+ A RGRGYV A+ NKREDQPIGVIP+DSIYTP+SRV+Y + Sbjct: 121 LNPDLHIATLAEGGRLRMRMTAKRGRGYVPAEANKREDQPIGVIPIDSIYTPVSRVSYQV 180 Query: 181 DNTRVGQVTNYDKLTMEIWTDGSIRPEEAVSLGAKILNEHLVLFVGLTDEAKDAEIMVXX 240 +NTRVGQVT+YDKLT+++WTDGSI P+EA+SLGAKIL EHL +FVGLTDEA++AEIMV Sbjct: 181 ENTRVGQVTDYDKLTIDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240 Query: 241 XXXXXXXVLEMTIEELDLSVRSYNCLKRAGINTVQELTTKTEEDMMKVRNLGRKS 295 VLEMTIEELDLSVRSYNCLKRAGINTVQELT KTEEDMMKVRNLGRKS Sbjct: 241 EDDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEDMMKVRNLGRKS 295 >B4BSP7.1 B4BSP7_9BACI DNA-directed RNA polymerase, alpha subunit Length = 314 Score = 476 bits (1226), Expect = e-133, Method: Compositional matrix adjust. Identities = 234/295 (79%), Positives = 261/295 (88%) Query: 1 VIEIEKPKIETVEANDEGTYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60 +IEIEKPKIETVE +++ YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG Sbjct: 1 MIEIEKPKIETVELSEDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60 Query: 61 VLHEFSTVPGVMEDVTEIILNLKALSLKIHSDEEKVFEIDAEGEGIVTAGDIRADSDVEI 120 VLHEFST+ GV+EDVT IILN+K L+LKI+SDEEK EID +GEG+VTA DI DSDVEI Sbjct: 61 VLHEFSTIEGVVEDVTAIILNVKKLALKIYSDEEKTLEIDVQGEGVVTAADITHDSDVEI 120 Query: 121 LNPDLHIATLGPGARLHMRIFAGRGRGYVQADRNKREDQPIGVIPVDSIYTPISRVNYGI 180 LNPDLHIATL G RL MR+ A RGRGYV A+ NKREDQPIGVIP+DSIYTP+SRV+Y + Sbjct: 121 LNPDLHIATLAEGGRLRMRMTARRGRGYVPAEANKREDQPIGVIPIDSIYTPVSRVSYQV 180 Query: 181 DNTRVGQVTNYDKLTMEIWTDGSIRPEEAVSLGAKILNEHLVLFVGLTDEAKDAEIMVXX 240 +NTRVGQVT+YDKLT+++WTDGSI P+EA+SLGAKIL EHL +FVGLTDEA++AEIMV Sbjct: 181 ENTRVGQVTDYDKLTIDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240 Query: 241 XXXXXXXVLEMTIEELDLSVRSYNCLKRAGINTVQELTTKTEEDMMKVRNLGRKS 295 VLEMTIEELDLSVRSYNCLKRAGINTVQELT KTEEDMMKVRNLGRKS Sbjct: 241 EDDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEDMMKVRNLGRKS 295 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.315 0.136 0.376 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9421015 Number of Hits to DB: 1,639,244,478 Number of extensions: 66679368 Number of successful extensions: 124232 Number of sequences better than 1.0e-05: 2736 Number of HSP's gapped: 119868 Number of HSP's successfully gapped: 2739 Length of query: 314 Length of database: 3,060,696,203 Length adjustment: 135 Effective length of query: 179 Effective length of database: 1,788,859,178 Effective search space: 320205792862 Effective search space used: 320205792862 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 131 (55.1 bits)