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= 0564.0010.p (180 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BH2026 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 80 2e-15 PM1789 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 65 4e-11 sll0856 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 64 9e-11 BH1615 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 64 1e-10 CAC3267 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 62 6e-10 >BH2026 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 179 Score = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 43/150 (28%), Positives = 82/150 (54%), Gaps = 5/150 (3%) Query: 8 IKKAQKGDHEAFIRLFRQLETQLYRLAKTILTQDEDCADALQETTLKVYKGLASLKQPKF 67 +K+A+KG+ EA ++L + + YRLA T + D DA+++ + +Y+ + L++ Sbjct: 7 VKRAKKGNKEALLQLVMAEKDRYYRLALTYMGNPHDAMDAMEDMIVTLYETIDQLQKEDA 66 Query: 68 FKTWVIRILINECNQLLRMRERTVAVAEIPEETAASYAHFEDS-----RNVDLQSCINRL 122 F +W IL+N C ++L +++ + E EE Y+ F D +++D+ ++ L Sbjct: 67 FYSWSNTILVNRCKRMLSKQQKLIHAKEWNEEETNRYSTFIDPFIQREQHLDIMRLLDHL 126 Query: 123 DESLRLAIVLFYYEDLSIKQIAGVLGISEG 152 +E + AI L Y+ DL + IA + +S G Sbjct: 127 NEQQKEAIQLKYFHDLDYQTIANMTNVSVG 156 >PM1789 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 191 Score = 65.5 bits (158), Expect = 4e-11, Method: Compositional matrix adjust. Identities = 48/179 (26%), Positives = 79/179 (44%), Gaps = 15/179 (8%) Query: 8 IKKAQKGDHEAFIRLFRQLETQLYRLAKTILTQDEDCADALQETTLKVYKGLASLKQPKF 67 +++ Q+GD +AF L + + ++ L ++Q+ D D +QE+ +K Y+ + S + Sbjct: 11 VERVQQGDKKAFNLLVSRYQNKVAGLLTRYVSQN-DIPDVVQESFIKAYRSIDSFRGDSA 69 Query: 68 FKTWVIRILINECNQLLRMRERTVAVAEIPEETAASYAHFEDSRNVDLQ----------- 116 F TW+ RI +N L + R +I E A SY + R+VD Sbjct: 70 FYTWLYRIAVNTAKNYLTAQGRRPPNEDILAEEAESYEMGSNLRDVDTPENEMLSSELKK 129 Query: 117 ---SCINRLDESLRLAIVLFYYEDLSIKQIAGVLGISEGXXXXXXXXXXXXXSEQIQPV 172 IN L E LR AI L E LS ++IA ++ G ++QP+ Sbjct: 130 IVFDTINGLQEDLRTAITLRELEGLSYEEIAEIMDCPVGTVRSRIFRAREIIESKVQPM 188 >sll0856 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 186 Score = 64.3 bits (155), Expect = 9e-11, Method: Compositional matrix adjust. Identities = 53/160 (33%), Positives = 80/160 (50%), Gaps = 16/160 (10%) Query: 8 IKKAQKGDHEAFIRLFRQLETQLYRLAKTILTQDEDCADALQETTLKVYKGLASLKQPKF 67 I+++Q+GD EAF +L+R+ + ++ + Q + D +QE KV+KGL L+ F Sbjct: 2 IQRSQQGDAEAFRQLYRRYQAKVRSTLYQLCGQHQ-LDDLVQEVFFKVWKGLPKLRNHNF 60 Query: 68 FKTWVIRILINEC----NQLLRMRER----TVAVAEIPEETAASYAHFEDSRNV------ 113 F TW+ RI N QL R R+R + A+A+ E + + EDS ++ Sbjct: 61 FATWLYRITWNVAQDARKQLGRSRQRIHQPSTALADNEGEISLQLSRPEDSPDLLQLHYQ 120 Query: 114 DL-QSCINRLDESLRLAIVLFYYEDLSIKQIAGVLGISEG 152 DL Q + L R +VL EDL K IA VL + G Sbjct: 121 DLVQQGLATLSFEHRTVLVLHDLEDLPQKTIAEVLNLPGG 160 >BH1615 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 176 Score = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust. Identities = 48/152 (31%), Positives = 76/152 (50%), Gaps = 6/152 (3%) Query: 5 ELDIKKAQKGDHEAFIRLFRQLETQLYRLAKTILTQDEDCADALQETTLKVYKGLASLKQ 64 EL + KA+KGD AF +L + + A + D QE +KVY+ L + Sbjct: 3 ELLLMKAKKGDEGAFEQLIELHLKTVEKFAFQLGVSPFAVEDISQEVFIKVYRFLHKHDR 62 Query: 65 PKFFKTWVIRILIN----ECNQLLRMRERTVAVAEIPEETAASYAHFEDSRNVDLQSCIN 120 KF TW+ I +N + R+R++ + + ETA HF++ L I Sbjct: 63 GKF-TTWLYSITLNVVRDHYRKEQRLRKKALELQHQSPETAYVEEHFDEEARA-LHEMIQ 120 Query: 121 RLDESLRLAIVLFYYEDLSIKQIAGVLGISEG 152 +LD+ ++ IVL Y+ D + ++IA VLGI+EG Sbjct: 121 QLDDKYKIPIVLHYFHDQTYQEIAQVLGITEG 152 >CAC3267 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 190 Score = 61.6 bits (148), Expect = 6e-10, Method: Compositional matrix adjust. Identities = 49/164 (29%), Positives = 74/164 (45%), Gaps = 14/164 (8%) Query: 2 LDNELDIKKAQKGDHEAFIRLFRQLETQLYRLAKTILTQDEDCADALQETTLKVYKGLAS 61 +D E+ +K+ +K D +F +LF E LY L D D +QE +KV+K + + Sbjct: 3 IDKEI-LKRCKKYDRASFSQLFHLYEKYLYNLCYGYTQNTSDAMDLVQEIYIKVFKNIKN 61 Query: 62 LKQPKFFKTWVIRILINECNQLLRMRERTVAV-------AEIPEET--AASYAHFEDS-- 110 + F WV +I +N C R V +E EE A Y ++ Sbjct: 62 FDENLPFHPWVRKISVNTCLNFKRDNRGNVMSLNSKYYDSEFEEEDRLAEDYNMEQEVVN 121 Query: 111 --RNVDLQSCINRLDESLRLAIVLFYYEDLSIKQIAGVLGISEG 152 N ++ I +L R+ I+L YYEDLS +IA VL + G Sbjct: 122 RINNEVVKESIKKLTYDYRMVIMLRYYEDLSYDEIASVLDMPIG 165 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.320 0.135 0.376 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 10,706,162 Number of extensions: 367192 Number of successful extensions: 622 Number of sequences better than 1.0e-05: 29 Number of HSP's gapped: 618 Number of HSP's successfully gapped: 29 Length of query: 180 Length of database: 38,378,431 Length adjustment: 100 Effective length of query: 80 Effective length of database: 26,845,031 Effective search space: 2147602480 Effective search space used: 2147602480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 112 (47.8 bits)