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= 0256.0020.p (229 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... 108 5e-24 VC2467 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 107 1e-23 BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigm... 102 4e-22 rpoE [K] COG1595 DNA-directed RNA polymerase specialized sigma s... 100 2e-21 PM1789 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 98 9e-21 >PA0762 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 193 Score = 108 bits (271), Expect = 5e-24, Method: Compositional matrix adjust. Identities = 66/191 (34%), Positives = 110/191 (57%), Gaps = 13/191 (6%) Query: 35 DSQLIQLIKQGNTEIYSELMRRYQRKILAFVYHMLKNSHMELLAEDLCSETFYKAFRSLH 94 D QL++ +++G+ + L+ +YQ KIL + + ++ A+D+ E F KA+R+L Sbjct: 7 DQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDAQE---AQDVAQEAFIKAYRALG 63 Query: 95 SFREVDASFSTWLYTIARNTVLSEL----RKNRAGNVSLEES----GYTPVAPIEVAPEQ 146 +FR D++F TWLY IA NT + L R+ +V+ E++ G + IE +PE+ Sbjct: 64 NFRG-DSAFYTWLYRIAINTAKNHLVARGRRPPDSDVTAEDAEFFEGDHALKDIE-SPER 121 Query: 147 AALRKERMNLVREAINNLPEKQRSALILREYDQMDYQEIAEILDQSVSSVKSLLFRARSS 206 A LR E V + I LPE R+AL LRE++ + Y++IA ++ V +V+S +FRAR + Sbjct: 122 AMLRDEIEATVHQTIQQLPEDLRTALTLREFEGLSYEDIATVMQCPVGTVRSRIFRAREA 181 Query: 207 VKLQLESYFYE 217 + L+ E Sbjct: 182 IDKALQPLLRE 192 >VC2467 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 190 Score = 107 bits (268), Expect = 1e-23, Method: Compositional matrix adjust. Identities = 65/187 (34%), Positives = 113/187 (60%), Gaps = 11/187 (5%) Query: 33 MTDSQLIQLIKQGNTEIYSELMRRYQRKILAFVYHMLKNSHMELLAEDLCSETFYKAFRS 92 +TD LI+ ++ G+ + ++ L+ RYQ K+ + + NS D+ E F KA+R+ Sbjct: 5 LTDQVLIERVQNGDKQAFNLLVLRYQNKVCNLISRYVSNSGD---VADVAQEAFIKAYRA 61 Query: 93 LHSFREVDASFSTWLYTIARNT----VLSELRKNRAGNVSLEESGY--TPVAPIEVA-PE 145 + +FR +++F TWLY IA NT ++++ R+ A +V EE+ + A E++ PE Sbjct: 62 IPTFRG-ESAFYTWLYRIAVNTAKNHIVAQSRRPPASDVDAEEAEFYEGGDALKELSNPE 120 Query: 146 QAALRKERMNLVREAINNLPEKQRSALILREYDQMDYQEIAEILDQSVSSVKSLLFRARS 205 L KE V +AI+ LP+ ++A+ LRE D + Y+EIAE++D V +V+S +FRAR Sbjct: 121 NITLSKELKKTVFDAIDALPDDLKTAMTLRELDGLSYEEIAEVMDCPVGTVRSRIFRARE 180 Query: 206 SVKLQLE 212 +V+ +++ Sbjct: 181 AVEKKIK 187 >BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 102 bits (255), Expect = 4e-22, Method: Compositional matrix adjust. Identities = 59/182 (32%), Positives = 102/182 (56%), Gaps = 15/182 (8%) Query: 39 IQLIKQGNTEIYSELMRRYQRKILAFVYHMLKNSHMELLAEDLCSETFYKAFRSLHSFRE 98 I+ +K+G+ + +++++ Y+ KI Y ML N H AED+ E F +A+ ++ SF + Sbjct: 9 IKQVKKGDQDAFADIVDIYKDKIYQLCYRMLGNVHE---AEDIAQEAFIRAYVNIDSF-D 64 Query: 99 VDASFSTWLYTIARNTVLSELRKNR---------AGNVSLEESGYTPVAPIEVAPEQAAL 149 ++ FSTWLY IA N + +RK + AG L + Y+ + V PE A + Sbjct: 65 INRKFSTWLYRIATNLTIDRIRKKKPDYYLDAEVAGTEGL--TMYSQIVADGVLPEDAVV 122 Query: 150 RKERMNLVREAINNLPEKQRSALILREYDQMDYQEIAEILDQSVSSVKSLLFRARSSVKL 209 E N +++ I LP+K R+ ++L+ D++ EI EIL+ V +VK+ + R R +++ Sbjct: 123 SLELSNTIQQKILKLPDKYRTVIVLKYIDELSLIEIGEILNIPVGTVKTRIHRGREALRK 182 Query: 210 QL 211 QL Sbjct: 183 QL 184 >rpoE [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 191 Score = 100 bits (248), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 62/182 (34%), Positives = 108/182 (59%), Gaps = 12/182 (6%) Query: 33 MTDSQLIQLIKQGNTEIYSELMRRYQRKILAFVYHMLKNSHMELLAEDLCSETFYKAFRS 92 +TD L++ +++G+ + ++ L+ RYQ K+ + V + + + D+ E F KA+R+ Sbjct: 5 LTDQVLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVPSGDVP----DVVQEAFIKAYRA 60 Query: 93 LHSFREVDASFSTWLYTIARNT----VLSELRKNRAGNV-SLEESGYTPVAPI-EVA-PE 145 L SFR D++F TWLY IA NT ++++ R+ + +V ++E + + E++ PE Sbjct: 61 LDSFRG-DSAFYTWLYRIAVNTAKNYLVAQGRRPPSSDVDAIEAENFESGGALKEISNPE 119 Query: 146 QAALRKERMNLVREAINNLPEKQRSALILREYDQMDYQEIAEILDQSVSSVKSLLFRARS 205 L +E +V I +LPE R A+ LRE D + Y+EIA I+D V +V+S +FRAR Sbjct: 120 NLMLSEELRQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRARE 179 Query: 206 SV 207 ++ Sbjct: 180 AI 181 >PM1789 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 191 Score = 98.2 bits (243), Expect = 9e-21, Method: Compositional matrix adjust. Identities = 62/187 (33%), Positives = 108/187 (57%), Gaps = 12/187 (6%) Query: 33 MTDSQLIQLIKQGNTEIYSELMRRYQRKILAFVYHMLKNSHMELLAEDLCSETFYKAFRS 92 +TD L++ ++QG+ + ++ L+ RYQ K+ + + + + D+ E+F KA+RS Sbjct: 5 LTDQALVERVQQGDKKAFNLLVSRYQNKVAGLLTRYVSQNDIP----DVVQESFIKAYRS 60 Query: 93 LHSFREVDASFSTWLYTIARNT----VLSELRKNRAGNVSLEES-GYTPVAPIEVA--PE 145 + SFR D++F TWLY IA NT + ++ R+ ++ EE+ Y + + PE Sbjct: 61 IDSFRG-DSAFYTWLYRIAVNTAKNYLTAQGRRPPNEDILAEEAESYEMGSNLRDVDTPE 119 Query: 146 QAALRKERMNLVREAINNLPEKQRSALILREYDQMDYQEIAEILDQSVSSVKSLLFRARS 205 L E +V + IN L E R+A+ LRE + + Y+EIAEI+D V +V+S +FRAR Sbjct: 120 NEMLSSELKKIVFDTINGLQEDLRTAITLRELEGLSYEEIAEIMDCPVGTVRSRIFRARE 179 Query: 206 SVKLQLE 212 ++ +++ Sbjct: 180 IIESKVQ 186 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 0.318 0.131 0.358 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: 15,144,196 Number of extensions: 538647 Number of successful extensions: 1331 Number of sequences better than 1.0e-05: 61 Number of HSP's gapped: 1277 Number of HSP's successfully gapped: 61 Length of query: 229 Length of database: 38,378,431 Length adjustment: 103 Effective length of query: 126 Effective length of database: 26,499,029 Effective search space: 3338877654 Effective search space used: 3338877654 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: 114 (48.5 bits)