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= 0101.0017.p (185 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value PA0762 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 82 3e-16 VC2467 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 80 2e-15 HI0628 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 79 3e-15 PM1789 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 78 7e-15 RSc1055 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 75 6e-14 >PA0762 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 193 Score = 82.4 bits (202), Expect = 3e-16, Method: Compositional matrix adjust. Identities = 55/179 (30%), Positives = 91/179 (50%), Gaps = 14/179 (7%) Query: 3 EDNELMARVQAGDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHR 62 +D +L+ RVQ GDK A++ LVLK++ K + FV D A+D+ QE F+ Y Sbjct: 6 QDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDAQEAQDVAQEAFI---KAYRAL 62 Query: 63 ETYQPSHAFNTYLFTIIRNSCIDYLRSRQASRSFSSEAVPE----------LSDHTTPEE 112 ++ AF T+L+ I N+ ++L +R R S+ E L D +PE Sbjct: 63 GNFRGDSAFYTWLYRIAINTAKNHLVAR-GRRPPDSDVTAEDAEFFEGDHALKDIESPER 121 Query: 113 ILASRENTKLIYEVLDDLQIDYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRARK 171 + E +++ + L D +TAL L SY+DIA++M+ V ++ ++RAR+ Sbjct: 122 AMLRDEIEATVHQTIQQLPEDLRTALTLREFEGLSYEDIATVMQCPVGTVRSRIFRARE 180 >VC2467 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 190 Score = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 55/188 (29%), Positives = 97/188 (51%), Gaps = 14/188 (7%) Query: 4 DNELMARVQAGDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHRE 63 D L+ RVQ GDK A+ LVL+++ K + +V + D+ QE F+ Y Sbjct: 7 DQVLIERVQNGDKQAFNLLVLRYQNKVCNLISRYVSNSGDVADVAQEAFIKA---YRAIP 63 Query: 64 TYQPSHAFNTYLFTIIRNSCIDYLRSRQASRSFSSEAVPE----------LSDHTTPEEI 113 T++ AF T+L+ I N+ +++ + Q+ R +S+ E L + + PE I Sbjct: 64 TFRGESAFYTWLYRIAVNTAKNHIVA-QSRRPPASDVDAEEAEFYEGGDALKELSNPENI 122 Query: 114 LASRENTKLIYEVLDDLQIDYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRARKKF 173 S+E K +++ +D L D KTA+ L + SY++IA +M V ++ ++RAR+ Sbjct: 123 TLSKELKKTVFDAIDALPDDLKTAMTLRELDGLSYEEIAEVMDCPVGTVRSRIFRAREAV 182 Query: 174 KLQYKELM 181 + + K L+ Sbjct: 183 EKKIKPLL 190 >HI0628 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 189 Score = 79.3 bits (194), Expect = 3e-15, Method: Compositional matrix adjust. Identities = 57/188 (30%), Positives = 95/188 (50%), Gaps = 15/188 (7%) Query: 4 DNELMARVQAGDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHRE 63 D L+ RVQ GDK A+ LV +++ K +V D+VQE F+ Y E Sbjct: 7 DQALVERVQQGDKKAFNLLVSRYQNKVAGLLTRYVS-RNDIPDVVQESFIKA---YRSIE 62 Query: 64 TYQPSHAFNTYLFTIIRNSCIDYLRSRQASRSFSSEAVPE----------LSDHTTPEEI 113 +++ AF T+L+ I N+ +YL + Q R + + + E L D TPE Sbjct: 63 SFRGESAFYTWLYRIAVNTAKNYLTA-QGRRPPNEDILAEDAENYDVGTHLRDVDTPENE 121 Query: 114 LASRENTKLIYEVLDDLQIDYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRARKKF 173 + S E +++++ + +L D KTA+ L + SY+DIA IM V ++ ++RAR+ Sbjct: 122 MLSSELERIVFDTIHNLPEDLKTAITLRELEGLSYEDIAEIMDCPVGTVRSRIFRAREMI 181 Query: 174 KLQYKELM 181 + + + LM Sbjct: 182 ENKIQPLM 189 >PM1789 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 191 Score = 78.2 bits (191), Expect = 7e-15, Method: Compositional matrix adjust. Identities = 54/177 (30%), Positives = 90/177 (50%), Gaps = 13/177 (7%) Query: 4 DNELMARVQAGDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHRE 63 D L+ RVQ GDK A+ LV +++ K +V D+VQE F+ Y + Sbjct: 7 DQALVERVQQGDKKAFNLLVSRYQNKVAGLLTRYVSQ-NDIPDVVQESFIKA---YRSID 62 Query: 64 TYQPSHAFNTYLFTIIRNSCIDYLRSRQ---------ASRSFSSEAVPELSDHTTPEEIL 114 +++ AF T+L+ I N+ +YL ++ A + S E L D TPE + Sbjct: 63 SFRGDSAFYTWLYRIAVNTAKNYLTAQGRRPPNEDILAEEAESYEMGSNLRDVDTPENEM 122 Query: 115 ASRENTKLIYEVLDDLQIDYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRARK 171 S E K++++ ++ LQ D +TA+ L + SY++IA IM V ++ ++RAR+ Sbjct: 123 LSSELKKIVFDTINGLQEDLRTAITLRELEGLSYEEIAEIMDCPVGTVRSRIFRARE 179 >RSc1055 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 199 Score = 75.1 bits (183), Expect = 6e-14, Method: Compositional matrix adjust. Identities = 52/193 (26%), Positives = 95/193 (49%), Gaps = 15/193 (7%) Query: 4 DNELMARVQAGDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHRE 63 D L+ RVQ GDK A+E LV+K+ K I + + D ED+ Q+ F+ Y Sbjct: 7 DQILVERVQQGDKRAFELLVVKYHRKIIRLISRLIRDAAEVEDVAQDAFI---KAYRALP 63 Query: 64 TYQPSHAFNTYLFTIIRNSCIDYLRSRQASRSFSSEAV-----------PELSDHTTPEE 112 ++ AF T+L+ I N+ +YL + Q R SS + +L D TP+ Sbjct: 64 QFRGESAFYTWLYRIAVNTAKNYL-ATQGRRPESSTDIDTEEAETFADGEQLRDINTPDS 122 Query: 113 ILASRENTKLIYEVLDDLQIDYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRARKK 172 +L +++ + + ++ L + +TA+ L + SY++IA M+ + ++ ++RAR+ Sbjct: 123 MLHTKQVAETVNRAMEALPEELRTAITLREIEGLSYEEIAEAMECPIGTVRSRIFRAREA 182 Query: 173 FKLQYKELMVNEE 185 + + L+ E Sbjct: 183 IAEKLRPLLGTAE 195 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 0.321 0.134 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: 11,503,808 Number of extensions: 387267 Number of successful extensions: 820 Number of sequences better than 1.0e-05: 29 Number of HSP's gapped: 828 Number of HSP's successfully gapped: 29 Length of query: 185 Length of database: 38,378,431 Length adjustment: 100 Effective length of query: 85 Effective length of database: 26,845,031 Effective search space: 2281827635 Effective search space used: 2281827635 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 (21.9 bits) S2: 112 (47.8 bits)