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= 0557.0044.p (162 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value SMb20592 [K] COG1595 DNA-directed RNA polymerase specialized sig... 67 2e-11 lin0443 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 65 5e-11 PM1789 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 61 6e-10 BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigm... 60 2e-09 FN0479 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 59 3e-09 >SMb20592 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 227 Score = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 45/169 (26%), Positives = 79/169 (46%), Gaps = 12/169 (7%) Query: 1 VADVEQIYEQYFQDVYLFALSLSRDQQIAEEITQETFVKAVKNIDQFKGNCKISVWLCQI 60 +A I + + + +Y A S+ R+ AE++ QE +V+A + F+G+ I+ WL +I Sbjct: 19 LARFRAIMQAHNRKLYRIARSILRNDSDAEDVLQEAYVRAFTRFEDFRGDAAITTWLARI 78 Query: 61 AKNTYFKYMDKQKRDLGNPQEIMQGN-----SLSMEQKLID--KTEALR-----IHKLLH 108 N + K +R + + + Q + + + D KT A R + +L Sbjct: 79 VINEALGRLRKGRRQMRLAKYMRQSQEAEIIAFPLNSGISDPEKTMAQRQILDLVERLTD 138 Query: 109 GLKEPYKEVFTLRVFGELSFDHISEVFGRTESWARVTFHRARNIIQDLL 157 L + Y+ VF LRV L + + + G AR HRAR I+++ L Sbjct: 139 DLPDTYRTVFVLRVIEGLDNEEAAALLGLKPETARTRLHRARRILKEQL 187 >lin0443 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 301 Score = 65.1 bits (157), Expect = 5e-11, Method: Compositional matrix adjust. Identities = 4/161 (2%), Positives = 27/161 (16%), Gaps = 4/161 (2%) Query: 4 VEQIYEQYFQDVYLFALSLSRDQQIAEEITQETFVKAVKNIDQFKGNCKISVWLCQIAKN 63 + + ++ + +D + + + ++ Sbjct: 21 KSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYVDTPGLHMEEKRAINRLMNK 80 Query: 64 TYFKYMDK-QKRDLGNPQEI---MQGNSLSMEQKLIDKTEALRIHKLLHGLKEPYKEVFT 119 + + L+ ++ K Sbjct: 81 AASSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQEKADLLPHLQ 140 Query: 120 LRVFGELSFDHISEVFGRTESWARVTFHRARNIIQDLLMEE 160 D + + + +++ + Sbjct: 141 FLASQMNFLDIVPISAETGLNVDTIAAIVRKHLPEATHHFP 181 >PM1789 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 191 Score = 61.2 bits (147), Expect = 6e-10, Method: Compositional matrix adjust. Identities = 42/136 (30%), Positives = 67/136 (49%), Gaps = 13/136 (9%) Query: 31 EITQETFVKAVKNIDQFKGNCKISVWLCQIAKNTYFKYMDKQKRDLGNPQEIM--QGNSL 88 ++ QE+F+KA ++ID F+G+ WL +IA NT Y+ Q R N ++I+ + S Sbjct: 48 DVVQESFIKAYRSIDSFRGDSAFYTWLYRIAVNTAKNYLTAQGRRPPN-EDILAEEAESY 106 Query: 89 SMEQKLID----KTEALR------IHKLLHGLKEPYKEVFTLRVFGELSFDHISEVFGRT 138 M L D + E L + ++GL+E + TLR LS++ I+E+ Sbjct: 107 EMGSNLRDVDTPENEMLSSELKKIVFDTINGLQEDLRTAITLRELEGLSYEEIAEIMDCP 166 Query: 139 ESWARVTFHRARNIIQ 154 R RAR II+ Sbjct: 167 VGTVRSRIFRAREIIE 182 >BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 44/160 (27%), Positives = 68/160 (42%), Gaps = 14/160 (8%) Query: 2 ADVEQIYEQYFQDVYLFALSLSRDQQIAEEITQETFVKAVKNIDQFKGNCKISVWLCQIA 61 AD+ IY+ +Y + + AE+I QE F++A NID F N K S WL +IA Sbjct: 21 ADIVDIYKD---KIYQLCYRMLGNVHEAEDIAQEAFIRAYVNIDSFDINRKFSTWLYRIA 77 Query: 62 KNTYFKYMDKQKRDLGNPQEIMQGNSLSMEQKLI-------DKTEALRIHKLLH----GL 110 N + K+K D E+ L+M +++ D +L + + L Sbjct: 78 TNLTIDRIRKKKPDYYLDAEVAGTEGLTMYSQIVADGVLPEDAVVSLELSNTIQQKILKL 137 Query: 111 KEPYKEVFTLRVFGELSFDHISEVFGRTESWARVTFHRAR 150 + Y+ V L+ ELS I E+ + HR R Sbjct: 138 PDKYRTVIVLKYIDELSLIEIGEILNIPVGTVKTRIHRGR 177 >FN0479 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 149 Score = 58.9 bits (141), Expect = 3e-09, Method: Compositional matrix adjust. Identities = 36/119 (30%), Positives = 64/119 (53%), Gaps = 10/119 (8%) Query: 3 DVEQIYEQYFQDVYLFALSLSRDQQIAEEITQETFVKAVKNIDQFKGNCKISVWLCQIAK 62 D + IYE+YF VY LS+ ++ AE+I QETF+ KN+ +F+ I W+ +IA Sbjct: 2 DFDNIYEEYFDRVYYKVLSVVKNDDDAEDICQETFISVYKNLSKFREESNIYTWIYRIAI 61 Query: 63 NTYFKYMDKQKRD-------LGNPQEIMQGNSLSMEQKL---IDKTEALRIHKLLHGLK 111 N + + K+K + L P+++ + +E+KL +K + + + K ++G K Sbjct: 62 NKTYDFFKKRKLEFEINDDVLSLPEDVNFDTKVILEEKLKLISEKEKEIVVLKDIYGYK 120 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 0.322 0.136 0.391 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: 10,805,141 Number of extensions: 403489 Number of successful extensions: 2301 Number of sequences better than 1.0e-05: 31 Number of HSP's gapped: 2288 Number of HSP's successfully gapped: 31 Length of query: 162 Length of database: 38,378,431 Length adjustment: 98 Effective length of query: 64 Effective length of database: 27,075,699 Effective search space: 1732844736 Effective search space used: 1732844736 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: 111 (47.4 bits)