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= 0584.0019.p (178 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value lin0443 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 91 1e-18 SMb20592 [K] COG1595 DNA-directed RNA polymerase specialized sig... 77 1e-14 Rv1221 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 75 4e-14 MT1259 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 75 4e-14 VC1045 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 70 2e-12 >lin0443 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 301 Score = 90.5 bits (223), Expect = 1e-18, Method: Compositional matrix adjust. Identities = 9/166 (5%), Positives = 33/166 (19%), Gaps = 2/166 (1%) Query: 12 TAGALQTLMENYGDDVWNYAYYLTRSRSAADDIAQETFIRAYKYMNTFRGEAAVRTWLLQ 71 TL+ + ++ Y++T + + + Sbjct: 17 PNVGKSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYVDTPGLHMEEKRAINR 76 Query: 72 ITRNRWLSYRSSSFIRRVTLQESAGG--KSFSPSAEEVYMQQSLSSEVWKIVLQLPRKHR 129 + S + ++ + + + + +Q Sbjct: 77 LMNKAASSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQEKADLL 136 Query: 130 EVLMLYAHYGLSMEELAGLLDISLPAAKSRLHRARQKAKEGWEKEL 175 L A ++ + + L + + Sbjct: 137 PHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHLPEATHHFPE 182 >SMb20592 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 227 Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 51/171 (29%), Positives = 86/171 (50%), Gaps = 10/171 (5%) Query: 16 LQTLMENYGDDVWNYAYYLTRSRSAADDIAQETFIRAYKYMNTFRGEAAVRTWLLQITRN 75 + +M+ + ++ A + R+ S A+D+ QE ++RA+ FRG+AA+ TWL +I N Sbjct: 22 FRAIMQAHNRKLYRIARSILRNDSDAEDVLQEAYVRAFTRFEDFRGDAAITTWLARIVIN 81 Query: 76 RWLS--------YRSSSFIRRVTLQE--SAGGKSFSPSAEEVYMQQSLSSEVWKIVLQLP 125 L R + ++R+ E + S E+ Q+ + V ++ LP Sbjct: 82 EALGRLRKGRRQMRLAKYMRQSQEAEIIAFPLNSGISDPEKTMAQRQILDLVERLTDDLP 141 Query: 126 RKHREVLMLYAHYGLSMEELAGLLDISLPAAKSRLHRARQKAKEGWEKELG 176 +R V +L GL EE A LL + A++RLHRAR+ KE E+++G Sbjct: 142 DTYRTVFVLRVIEGLDNEEAAALLGLKPETARTRLHRARRILKEQLERQIG 192 >Rv1221 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 257 Score = 75.5 bits (184), Expect = 4e-14, Method: Compositional matrix adjust. Identities = 50/167 (29%), Positives = 84/167 (50%), Gaps = 5/167 (2%) Query: 5 TNEAATMTAGALQTLMENYGDDVWNYAYYLTRSRSAADDIAQETFIRAYKYMNTFRGEAA 64 T + ATM + L+ + D V+ AY L+ ++ A+D+ QETFIR ++ + ++ Sbjct: 75 TGDKATMPS--WDELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSVQNYQ-PGT 131 Query: 65 VRTWLLQITRNRWLS-YRSSSFIRRVTLQESAGG-KSFSPSAEEVYMQQSLSSEVWKIVL 122 WL +IT N +L R + IR L E + P+ E++Y L ++ + Sbjct: 132 FEGWLHRITTNLFLDMVRRRARIRMEALPEDYDRVPADEPNPEQIYHDARLGPDLQAALA 191 Query: 123 QLPRKHREVLMLYAHYGLSMEELAGLLDISLPAAKSRLHRARQKAKE 169 LP + R ++L GLS EE+ L + L +SR+HR RQ ++ Sbjct: 192 SLPPEFRAAVVLCDIEGLSYEEIGATLGVKLGTVRSRIHRGRQALRD 238 >MT1259 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 257 Score = 75.5 bits (184), Expect = 4e-14, Method: Compositional matrix adjust. Identities = 50/167 (29%), Positives = 84/167 (50%), Gaps = 5/167 (2%) Query: 5 TNEAATMTAGALQTLMENYGDDVWNYAYYLTRSRSAADDIAQETFIRAYKYMNTFRGEAA 64 T + ATM + L+ + D V+ AY L+ ++ A+D+ QETFIR ++ + ++ Sbjct: 75 TGDKATMPS--WDELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSVQNYQ-PGT 131 Query: 65 VRTWLLQITRNRWLS-YRSSSFIRRVTLQESAGG-KSFSPSAEEVYMQQSLSSEVWKIVL 122 WL +IT N +L R + IR L E + P+ E++Y L ++ + Sbjct: 132 FEGWLHRITTNLFLDMVRRRARIRMEALPEDYDRVPADEPNPEQIYHDARLGPDLQAALA 191 Query: 123 QLPRKHREVLMLYAHYGLSMEELAGLLDISLPAAKSRLHRARQKAKE 169 LP + R ++L GLS EE+ L + L +SR+HR RQ ++ Sbjct: 192 SLPPEFRAAVVLCDIEGLSYEEIGATLGVKLGTVRSRIHRGRQALRD 238 >VC1045 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 188 Score = 69.7 bits (169), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 48/155 (30%), Positives = 79/155 (50%), Gaps = 10/155 (6%) Query: 17 QTLMENYGDDVWNYAYYLTRSRSAADDIAQETFIRAYKYMNTFRGEAAVRTWLLQITRNR 76 + L+ Y D++ YAY+L + RS A+D+ QET +RA+K +++ E A + WL+ I R Sbjct: 28 EALVRAYHRDLYRYAYWLCKDRSIAEDLVQETCLRAWKSLDSLLDEKAAKAWLITILR-- 85 Query: 77 WLSYRSSSFIRRVTLQESAGGKSFSPSAEEVYMQQSLSSEVW--KIVLQLPRKHREVLML 134 R ++ RR ++ E Y W + +L+L ++RE+L L Sbjct: 86 ----RENA--RRFERKQFDLVDIDDHDYEAKYSDDEHHQNEWLQRQILKLDVEYRELLFL 139 Query: 135 YAHYGLSMEELAGLLDISLPAAKSRLHRARQKAKE 169 G S EE+A +L ++ +RL RAR + KE Sbjct: 140 QVVGGFSGEEIADILSLNKNTVMTRLFRARNQLKE 174 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 0.317 0.128 0.369 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: 11,731,779 Number of extensions: 393377 Number of successful extensions: 1220 Number of sequences better than 1.0e-05: 55 Number of HSP's gapped: 1185 Number of HSP's successfully gapped: 55 Length of query: 178 Length of database: 38,378,431 Length adjustment: 99 Effective length of query: 79 Effective length of database: 26,960,365 Effective search space: 2129868835 Effective search space used: 2129868835 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: 41 (21.7 bits) S2: 112 (47.8 bits)