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= 0231.0070.p (171 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... 101 5e-22 BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigm... 100 1e-21 VC2467 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 100 1e-21 RSc1055 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 100 1e-21 PM1789 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 93 2e-19 >PA0762 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 193 Score = 101 bits (252), Expect = 5e-22, Method: Compositional matrix adjust. Identities = 59/168 (35%), Positives = 92/168 (54%), Gaps = 6/168 (3%) Query: 4 GQHQAFGHLVERYQGMVYRVCIKITGEAESAKDMAQEVFIKAYKALPSFRGQSSFSTWLY 63 G +AF LV +YQ + + ++ +A+ A+D+AQE FIKAY+AL +FRG S+F TWLY Sbjct: 17 GDKRAFDLLVLKYQHKILGLIVRFVHDAQEAQDVAQEAFIKAYRALGNFRGDSAFYTWLY 76 Query: 64 RIAYRTCLDWKRANDREWRHRST----ADYTENDWVTS--QTPEHVLLRKEASEELGENL 117 RIA T + A R A++ E D ++PE +LR E + + + Sbjct: 77 RIAINTAKNHLVARGRRPPDSDVTAEDAEFFEGDHALKDIESPERAMLRDEIEATVHQTI 136 Query: 118 NHLTEPYRSVVQMYYFQRHSYQEIAEQKGISVKTVESQLYRARQMMRK 165 L E R+ + + F+ SY++IA V TV S+++RAR+ + K Sbjct: 137 QQLPEDLRTALTLREFEGLSYEDIATVMQCPVGTVRSRIFRAREAIDK 184 >BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 100 bits (249), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 55/168 (32%), Positives = 88/168 (52%), Gaps = 6/168 (3%) Query: 4 GQHQAFGHLVERYQGMVYRVCIKITGEAESAKDMAQEVFIKAYKALPSFRGQSSFSTWLY 63 G AF +V+ Y+ +Y++C ++ G A+D+AQE FI+AY + SF FSTWLY Sbjct: 15 GDQDAFADIVDIYKDKIYQLCYRMLGNVHEAEDIAQEAFIRAYVNIDSFDINRKFSTWLY 74 Query: 64 RIAYRTCLDWKRANDREWRHRSTADYTENDWVTSQT------PEHVLLRKEASEELGENL 117 RIA +D R ++ + TE + SQ PE ++ E S + + + Sbjct: 75 RIATNLTIDRIRKKKPDYYLDAEVAGTEGLTMYSQIVADGVLPEDAVVSLELSNTIQQKI 134 Query: 118 NHLTEPYRSVVQMYYFQRHSYQEIAEQKGISVKTVESQLYRARQMMRK 165 L + YR+V+ + Y S EI E I V TV+++++R R+ +RK Sbjct: 135 LKLPDKYRTVIVLKYIDELSLIEIGEILNIPVGTVKTRIHRGREALRK 182 >VC2467 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 190 Score = 100 bits (249), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 60/172 (34%), Positives = 90/172 (52%), Gaps = 8/172 (4%) Query: 1 VLGGQHQAFGHLVERYQGMVYRVCIKITGEAESAKDMAQEVFIKAYKALPSFRGQSSFST 60 V G QAF LV RYQ V + + + D+AQE FIKAY+A+P+FRG+S+F T Sbjct: 14 VQNGDKQAFNLLVLRYQNKVCNLISRYVSNSGDVADVAQEAFIKAYRAIPTFRGESAFYT 73 Query: 61 WLYRIAYRTCLDWKRANDREWRHRSTADYTENDWVTS-------QTPEHVLLRKEASEEL 113 WLYRIA T + A R S D E ++ PE++ L KE + + Sbjct: 74 WLYRIAVNTAKNHIVAQSRRP-PASDVDAEEAEFYEGGDALKELSNPENITLSKELKKTV 132 Query: 114 GENLNHLTEPYRSVVQMYYFQRHSYQEIAEQKGISVKTVESQLYRARQMMRK 165 + ++ L + ++ + + SY+EIAE V TV S+++RAR+ + K Sbjct: 133 FDAIDALPDDLKTAMTLRELDGLSYEEIAEVMDCPVGTVRSRIFRAREAVEK 184 >RSc1055 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 199 Score = 100 bits (249), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 55/167 (32%), Positives = 89/167 (53%), Gaps = 7/167 (4%) Query: 4 GQHQAFGHLVERYQGMVYRVCIKITGEAESAKDMAQEVFIKAYKALPSFRGQSSFSTWLY 63 G +AF LV +Y + R+ ++ +A +D+AQ+ FIKAY+ALP FRG+S+F TWLY Sbjct: 17 GDKRAFELLVVKYHRKIIRLISRLIRDAAEVEDVAQDAFIKAYRALPQFRGESAFYTWLY 76 Query: 64 RIAYRTCLDWKRANDREWRHRSTADYTENDWVTS-------QTPEHVLLRKEASEELGEN 116 RIA T ++ R + D E + TP+ +L K+ +E + Sbjct: 77 RIAVNTAKNYLATQGRRPESSTDIDTEEAETFADGEQLRDINTPDSMLHTKQVAETVNRA 136 Query: 117 LNHLTEPYRSVVQMYYFQRHSYQEIAEQKGISVKTVESQLYRARQMM 163 + L E R+ + + + SY+EIAE + TV S+++RAR+ + Sbjct: 137 MEALPEELRTAITLREIEGLSYEEIAEAMECPIGTVRSRIFRAREAI 183 >PM1789 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 191 Score = 93.2 bits (230), Expect = 2e-19, Method: Compositional matrix adjust. Identities = 58/166 (34%), Positives = 91/166 (54%), Gaps = 7/166 (4%) Query: 4 GQHQAFGHLVERYQGMVYRVCIKITGEAESAKDMAQEVFIKAYKALPSFRGQSSFSTWLY 63 G +AF LV RYQ V + + + + D+ QE FIKAY+++ SFRG S+F TWLY Sbjct: 17 GDKKAFNLLVSRYQNKVAGLLTRYVSQND-IPDVVQESFIKAYRSIDSFRGDSAFYTWLY 75 Query: 64 RIAYRTCLDWKRANDREWRHRST-ADYTENDWVTSQ-----TPEHVLLRKEASEELGENL 117 RIA T ++ A R + A+ E+ + S TPE+ +L E + + + + Sbjct: 76 RIAVNTAKNYLTAQGRRPPNEDILAEEAESYEMGSNLRDVDTPENEMLSSELKKIVFDTI 135 Query: 118 NHLTEPYRSVVQMYYFQRHSYQEIAEQKGISVKTVESQLYRARQMM 163 N L E R+ + + + SY+EIAE V TV S+++RAR+++ Sbjct: 136 NGLQEDLRTAITLRELEGLSYEEIAEIMDCPVGTVRSRIFRAREII 181 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 0.319 0.130 0.397 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: 12,655,719 Number of extensions: 444745 Number of successful extensions: 1043 Number of sequences better than 1.0e-05: 52 Number of HSP's gapped: 1009 Number of HSP's successfully gapped: 52 Length of query: 171 Length of database: 38,378,431 Length adjustment: 99 Effective length of query: 72 Effective length of database: 26,960,365 Effective search space: 1941146280 Effective search space used: 1941146280 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)