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: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value A0LYR6.1 A0LYR6_GRAFK RNA polymerase sigma factor 119 1e-25 C0ZJR5.1 C0ZJR5_BREBN RNA polymerase ECF-type sigma factor 117 3e-25 Q67T27.1 Q67T27_SYMTH RNA polymerase sigma factor 117 4e-25 Q8RBE8.1 Q8RBE8_THETN DNA-directed RNA polymerase specialized si... 115 1e-24 B7R6J3.1 B7R6J3_9THEO RNA polymerase sigma factor, sigma-70 family 115 1e-24 >A0LYR6.1 A0LYR6_GRAFK RNA polymerase sigma factor Length = 195 Score = 119 bits (297), Expect = 1e-25, Method: Compositional matrix adjust. Identities = 63/169 (37%), Positives = 97/169 (57%), Gaps = 12/169 (7%) Query: 1 VLGGQHQAFGHLVERYQGMVYRVCIKITGEAESAKDMAQEVFIKAYKALPSFRGQSSFST 60 VL G AFG LV+RYQ V+ + I+I E A+++AQ+ FIKAY +L SFRG S FST Sbjct: 13 VLNGDTNAFGELVDRYQNFVFTIAIRILKVTEEAEEVAQDSFIKAYDSLSSFRGDSKFST 72 Query: 61 WLYRIAYRTCLDWKRANDREWRHRSTADYTENDWVTSQTPEHV------LLRKEASEELG 114 WLYRI Y LD + N RHR+ Y N+ VT T H+ +L E ++ + Sbjct: 73 WLYRIVYHKSLDRIKMNK---RHRT---YEINEEVTEDTLNHIENGLEFMLSAERTQIIK 126 Query: 115 ENLNHLTEPYRSVVQMYYFQRHSYQEIAEQKGISVKTVESQLYRARQMM 163 ++ L E +++ +YY + S +EI + ++ ++ +LYR+R+ + Sbjct: 127 NCISQLPETEAAIISLYYLEEQSVKEIVKVTDLTEDNIKIKLYRSRKKL 175 >C0ZJR5.1 C0ZJR5_BREBN RNA polymerase ECF-type sigma factor Length = 188 Score = 117 bits (293), Expect = 3e-25, Method: Compositional matrix adjust. Identities = 63/166 (37%), Positives = 95/166 (57%), Gaps = 4/166 (2%) Query: 1 VLGGQHQAFGHLVERYQGMVYRVCIKITGEAESAKDMAQEVFIKAYKALPSFRGQSSFST 60 + G HQ + +++RY G + K+ G A+D+AQ+VF K + L +R + FS+ Sbjct: 11 IQAGNHQLYSQIIDRYNGKIVTYLYKMIGNMPDAQDLAQDVFTKTFYLLKDYRPEHKFSS 70 Query: 61 WLYRIAYRTCLDWKRANDREWRHRSTADYTENDWVTSQTPEHVLLRKEASEELGENLNHL 120 WLYRIA CLD R R R TA E V +TPE LL+KE +L ++ L Sbjct: 71 WLYRIASNHCLDEIR---RRKRTEQTA-IVEEQIVDPETPETALLKKERDAQLEHSIMLL 126 Query: 121 TEPYRSVVQMYYFQRHSYQEIAEQKGISVKTVESQLYRARQMMRKN 166 E YR V ++Y QR SY+EI+E+ ++ V+ +L+RAR+ M+K+ Sbjct: 127 DEEYREVFVLHYLQRLSYREISERLSLTESAVQMRLFRARKEMKKS 172 >Q67T27.1 Q67T27_SYMTH RNA polymerase sigma factor Length = 208 Score = 117 bits (292), Expect = 4e-25, Method: Compositional matrix adjust. Identities = 64/174 (36%), Positives = 104/174 (59%), Gaps = 7/174 (4%) Query: 4 GQHQAFGHLVERYQGMVYRVCIKITGEAESAKDMAQEVFIKAYKALPSFRGQSSFSTWLY 63 G AF LVER++G VYR ++ G+A A+D+AQEVF+K ++ L S+RG ++F+TWL+ Sbjct: 15 GDMDAFAALVERHKGRVYRTLYQVVGDAADAQDLAQEVFVKVFRNLGSYRGDAAFTTWLH 74 Query: 64 RIAYRTCLDWKRANDRE------WRHRSTADYTENDWVTSQT-PEHVLLRKEASEELGEN 116 R+ DW RA R ++ + D + + PE + LR+E L + Sbjct: 75 RVTLNVAFDWLRARKRRPLTVPLEPPPGEEEHRQADLPSPEAGPEELTLREERRRRLRDA 134 Query: 117 LNHLTEPYRSVVQMYYFQRHSYQEIAEQKGISVKTVESQLYRARQMMRKNGEEW 170 ++ L+ Y+ VV +Y+F SYQ+IA++ G+ V+TVE++LYRAR +++ W Sbjct: 135 IDRLSPDYKEVVLLYHFYHLSYQQIADRLGVPVRTVETRLYRARANLKRMLVSW 188 >Q8RBE8.1 Q8RBE8_THETN DNA-directed RNA polymerase specialized sigma subunits, sigma24 homologs Length = 191 Score = 115 bits (288), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 61/163 (37%), Positives = 97/163 (59%) Query: 3 GGQHQAFGHLVERYQGMVYRVCIKITGEAESAKDMAQEVFIKAYKALPSFRGQSSFSTWL 62 G +AF L+E Y+ VY V ++I E E AKD+AQE FIKAY ++ +FR SSF TW+ Sbjct: 12 NGDDEAFSLLIENYEKYVYNVILRIVEEKEEAKDIAQETFIKAYMSIKTFRKDSSFRTWI 71 Query: 63 YRIAYRTCLDWKRANDREWRHRSTADYTENDWVTSQTPEHVLLRKEASEELGENLNHLTE 122 YRIA T +D+ R R + TA E + + QTPE V+ +K E + ++ L Sbjct: 72 YRIAVNTAMDYLRKKVRSEVNLVTAAEDELEIKSFQTPEEVIEQKLTVEMVRREISKLPV 131 Query: 123 PYRSVVQMYYFQRHSYQEIAEQKGISVKTVESQLYRARQMMRK 165 Y+ + + + +Y+EIA +++ TV+S+++RAR ++R+ Sbjct: 132 DYKIALILRDIEGMNYEEIASILKVNLGTVKSRIWRARNLLRE 174 >B7R6J3.1 B7R6J3_9THEO RNA polymerase sigma factor, sigma-70 family Length = 191 Score = 115 bits (288), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 61/163 (37%), Positives = 97/163 (59%) Query: 3 GGQHQAFGHLVERYQGMVYRVCIKITGEAESAKDMAQEVFIKAYKALPSFRGQSSFSTWL 62 G +AF L+E Y+ VY V ++I E E AKD+AQE FIKAY ++ +FR SSF TW+ Sbjct: 12 NGDDEAFSLLIENYEKYVYNVILRIVEEKEEAKDIAQETFIKAYMSIKTFRKDSSFRTWI 71 Query: 63 YRIAYRTCLDWKRANDREWRHRSTADYTENDWVTSQTPEHVLLRKEASEELGENLNHLTE 122 YRIA T +D+ R R + TA E + + QTPE V+ +K E + ++ L Sbjct: 72 YRIAVNTAMDYLRKKVRSEVNLVTAAEDELEIKSFQTPEEVIEQKLTVEMVRREISKLPV 131 Query: 123 PYRSVVQMYYFQRHSYQEIAEQKGISVKTVESQLYRARQMMRK 165 Y+ + + + +Y+EIA +++ TV+S+++RAR ++R+ Sbjct: 132 DYKIALILRDIEGMNYEEIASILKVNLGTVKSRIWRARNLLRE 174 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 0.319 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: 9421015 Number of Hits to DB: 1,029,602,996 Number of extensions: 37747411 Number of successful extensions: 137493 Number of sequences better than 1.0e-05: 4003 Number of HSP's gapped: 136091 Number of HSP's successfully gapped: 4003 Length of query: 171 Length of database: 3,060,696,203 Length adjustment: 126 Effective length of query: 45 Effective length of database: 1,873,648,313 Effective search space: 84314174085 Effective search space used: 84314174085 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: 126 (53.1 bits)