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: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KKT7.1 B3KKT7_9BACI RNA polymerase sigma factor, sigma-70 family 340 7e-92 B1DMF9.1 B1DMF9_9BACL RNA polymerase, sigma-24 subunit, ECF subf... 299 1e-79 C0ZCF1.1 C0ZCF1_BREBN RNA polymerase ECF-type sigma factor 258 4e-67 A9U7Y0.1 A9U7Y0_PHYPA Predicted protein 196 1e-48 Q1IS06.1 Q1IS06_ACIBL RNA polymerase sigma factor 121 5e-26 >B3KKT7.1 B3KKT7_9BACI RNA polymerase sigma factor, sigma-70 family Length = 197 Score = 340 bits (871), Expect = 7e-92, Method: Compositional matrix adjust. Identities = 164/190 (86%), Positives = 178/190 (93%) Query: 33 MTDSQLIQLIKQGNTEIYSELMRRYQRKILAFVYHMLKNSHMELLAEDLCSETFYKAFRS 92 MTDSQLIQ IKQGNTE+YSELMRRYQRKILAFVYHMLK+SHMEL+AEDLCSETFYKAFRS Sbjct: 1 MTDSQLIQEIKQGNTELYSELMRRYQRKILAFVYHMLKSSHMELMAEDLCSETFYKAFRS 60 Query: 93 LHSFREVDASFSTWLYTIARNTVLSELRKNRAGNVSLEESGYTPVAPIEVAPEQAALRKE 152 LHSFREVDASFSTWLYTIARNTVLSELRK+R+G + LEESG PVAP+EVAPEQA LR E Sbjct: 61 LHSFREVDASFSTWLYTIARNTVLSELRKHRSGTLPLEESGVVPVAPLEVAPEQAILRSE 120 Query: 153 RMNLVREAINNLPEKQRSALILREYDQMDYQEIAEILDQSVSSVKSLLFRARSSVKLQLE 212 R+++VREAINNLPEKQRSALILREYDQ+DYQEIA+IL QSVSSVKSLLFRAR SVK+QLE Sbjct: 121 RVHMVREAINNLPEKQRSALILREYDQLDYQEIADILGQSVSSVKSLLFRARGSVKIQLE 180 Query: 213 SYFYEPEIEE 222 YFYEP E+ Sbjct: 181 PYFYEPVFED 190 >B1DMF9.1 B1DMF9_9BACL RNA polymerase, sigma-24 subunit, ECF subfamily Length = 198 Score = 299 bits (766), Expect = 1e-79, Method: Compositional matrix adjust. Identities = 149/191 (78%), Positives = 166/191 (86%), Gaps = 1/191 (0%) Query: 33 MTDSQLIQLIKQGNTEIYSELMRRYQRKILAFVYHMLKNSHMELLAEDLCSETFYKAFRS 92 MTDSQLI+ IK GN E+YSELMRRYQRKILAF+YHMLK++ +ELLAEDLCSETFYKA+RS Sbjct: 1 MTDSQLIREIKDGNIELYSELMRRYQRKILAFIYHMLKSAKLELLAEDLCSETFYKAYRS 60 Query: 93 LHSFREVDASFSTWLYTIARNTVLSELRKNRAGNVSLEESGYTPVAPIEVAPEQAALRKE 152 LHSFREVDASFSTWLYTIARNTVLSELRK ++ +V L+ES P AP + PEQ LR E Sbjct: 61 LHSFREVDASFSTWLYTIARNTVLSELRKQKSAHVPLDESNMMPAAPPDQVPEQHVLRNE 120 Query: 153 RMNLVREAINNLPEKQRSALILREYDQMDYQEIAEILDQSVSSVKSLLFRARSSVKLQLE 212 RM +VREAINNLPEKQRSALILREYDQ+DYQEIA IL Q+VSSVKSLLFRAR+SVK QLE Sbjct: 121 RMAMVREAINNLPEKQRSALILREYDQLDYQEIANILGQTVSSVKSLLFRARASVKSQLE 180 Query: 213 SYFYE-PEIEE 222 YF E P +EE Sbjct: 181 PYFGETPMMEE 191 >C0ZCF1.1 C0ZCF1_BREBN RNA polymerase ECF-type sigma factor Length = 196 Score = 258 bits (658), Expect = 4e-67, Method: Compositional matrix adjust. Identities = 123/196 (62%), Positives = 162/196 (82%) Query: 33 MTDSQLIQLIKQGNTEIYSELMRRYQRKILAFVYHMLKNSHMELLAEDLCSETFYKAFRS 92 MTDSQLI+ IK+GN E Y+EL+RRY++KIL+FV H+L+ +H+E +AED+C ETFYKA++S Sbjct: 1 MTDSQLIREIKEGNLECYAELIRRYEKKILSFVTHLLRQAHLEHIAEDICQETFYKAYKS 60 Query: 93 LHSFREVDASFSTWLYTIARNTVLSELRKNRAGNVSLEESGYTPVAPIEVAPEQAALRKE 152 +HSFR+V+A+FSTWLYTIARN+VLSELRK+R +V L+++ P+A + PEQ LR E Sbjct: 61 IHSFRDVEATFSTWLYTIARNSVLSELRKSRNSDVYLDDTLQVPMASPKTLPEQVLLRNE 120 Query: 153 RMNLVREAINNLPEKQRSALILREYDQMDYQEIAEILDQSVSSVKSLLFRARSSVKLQLE 212 R ++VR AIN+LPEKQRSALILREY+QMDY EIA ILD +VSSVKSLLFRAR S++ QLE Sbjct: 121 RESMVRLAINSLPEKQRSALILREYEQMDYTEIATILDLTVSSVKSLLFRARQSIRGQLE 180 Query: 213 SYFYEPEIEEDQQAER 228 +Y +P ++E + R Sbjct: 181 NYILDPHLDEAEGMNR 196 >A9U7Y0.1 A9U7Y0_PHYPA Predicted protein Length = 351 Score = 196 bits (498), Expect = 1e-48, Method: Compositional matrix adjust. Identities = 95/147 (64%), Positives = 122/147 (82%), Gaps = 2/147 (1%) Query: 62 LAFVYHMLKNSHMELLAEDLCSETFYKAFRSLHSFREVDASFSTWLYTIARNTVLSELRK 121 L+ +Y L+ +H+E +AED+C ETFYKA++S+HSFR+V+A+FSTWLYTIARN+VLSELRK Sbjct: 8 LSLIY--LRQAHLEHIAEDICQETFYKAYKSIHSFRDVEATFSTWLYTIARNSVLSELRK 65 Query: 122 NRAGNVSLEESGYTPVAPIEVAPEQAALRKERMNLVREAINNLPEKQRSALILREYDQMD 181 +R +V L+++ PVA + PEQ LR ER +VR+AIN+LPEKQRSALILREY+QMD Sbjct: 66 SRNSDVYLDDTLQVPVASAKALPEQVLLRNERELMVRQAINSLPEKQRSALILREYEQMD 125 Query: 182 YQEIAEILDQSVSSVKSLLFRARSSVK 208 Y EIA ILD +VSSVKSLLFRAR S++ Sbjct: 126 YTEIATILDLTVSSVKSLLFRARQSIR 152 >Q1IS06.1 Q1IS06_ACIBL RNA polymerase sigma factor Length = 198 Score = 121 bits (303), Expect = 5e-26, Method: Compositional matrix adjust. Identities = 72/192 (37%), Positives = 113/192 (58%), Gaps = 13/192 (6%) Query: 33 MTDSQLIQLIKQGNTEIYSELMRRYQRKILAFVYHMLKNSHMELLAEDLCSETFYKAFRS 92 ++D++++ + QG+ + L+ +++R I++F+Y + +H + AE+L E F + +RS Sbjct: 11 LSDAEVMLRVAQGDDAAFDYLVDKFRRPIISFMY---RTTHNQATAEELAQEVFLRVYRS 67 Query: 93 LHSFREVDASFSTWLYTIARNTVLSELRKNR----AGNVSL----EESGYT-PVAPIEVA 143 S+ E A F+TWLY IA N ++ R + VSL EESG T VA Sbjct: 68 RESY-EASAKFTTWLYRIATNLAVNNARDTKHERAEAQVSLDEPDEESGSTMDVADSRPT 126 Query: 144 PEQAALRKERMNLVREAINNLPEKQRSALILREYDQMDYQEIAEILDQSVSSVKSLLFRA 203 EQ LR ERM +R+ + LPE+QR A+++ +Y MDY+EIA +L S S+ KSLLFRA Sbjct: 127 VEQEILRNERMTAIRKVVEGLPERQRMAVLMHKYQNMDYKEIAAVLKLSESATKSLLFRA 186 Query: 204 RSSVKLQLESYF 215 S++ L+ Y Sbjct: 187 YESLRESLKQYL 198 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 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: 9421015 Number of Hits to DB: 1,208,589,541 Number of extensions: 43234150 Number of successful extensions: 152053 Number of sequences better than 1.0e-05: 4000 Number of HSP's gapped: 149374 Number of HSP's successfully gapped: 4000 Length of query: 229 Length of database: 3,060,696,203 Length adjustment: 131 Effective length of query: 98 Effective length of database: 1,826,543,238 Effective search space: 179001237324 Effective search space used: 179001237324 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: 129 (54.3 bits)