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= 0502.0030.p (209 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value A9GTW4.1 A9GTW4_SORC5 ECF-family RNA polymerase sigma factor 141 4e-32 Q0S7H5.1 Q0S7H5_RHOSR Sigma factor, sigma 70 type, group 4 (ECF) 120 9e-26 A7HIP0.1 A7HIP0_ANADF RNA polymerase, sigma-24 subunit, ECF subf... 118 3e-25 Q5Z2K1.1 Q5Z2K1_NOCFA Putative sigma factor 118 4e-25 Q825N3.1 Q825N3_STRAW Putative RNA polymerase ECF-subfamily sigm... 115 2e-24 >A9GTW4.1 A9GTW4_SORC5 ECF-family RNA polymerase sigma factor Length = 297 Score = 141 bits (355), Expect = 4e-32, Method: Compositional matrix adjust. Identities = 82/199 (41%), Positives = 110/199 (55%), Gaps = 2/199 (1%) Query: 12 SDPECEALLADSVGLAMLVVLGSLNPAEQIAFVLHDVFALPFEEIAPIVGRSKEXXXXXX 71 +DPE EA+LADSVGLA+LVVL +L PAE++AFVLHD+FA+PFEEIA IVGRS Sbjct: 94 TDPEREAVLADSVGLALLVVLDTLTPAERLAFVLHDLFAVPFEEIASIVGRSPAAARQLA 153 Query: 72 XXXXXXVHGFDTARHADLARQRELVDAFLAATRAGNFXXXXXXXXXXXXXXXXXXXXSGA 131 V G + AD+ RQRE+VDAF+AA R G+F A Sbjct: 154 SRARRRVQGAPPSPDADVGRQREVVDAFIAAMRGGDFDALVAILDPDVVIHADATAEPPA 213 Query: 132 AQEIHXXXXXXXXX--XXXXXXXXXPILIDGDVGIVVAPRGELQFVIKVAITDGKIAGFH 189 E+ P L+DG VGIV+AP+G L V++ + GKIA Sbjct: 214 GGEVRGARAWAKQAIPAARGAKFARPALVDGTVGIVLAPKGRLFRVLRFTLAQGKIARID 273 Query: 190 IISDKERIREMDLAALSAG 208 ++ D+E++R++D+ L G Sbjct: 274 VVGDREQLRDLDVLVLDGG 292 >Q0S7H5.1 Q0S7H5_RHOSR Sigma factor, sigma 70 type, group 4 (ECF) Length = 310 Score = 120 bits (300), Expect = 9e-26, Method: Compositional matrix adjust. Identities = 76/201 (37%), Positives = 103/201 (51%), Gaps = 4/201 (1%) Query: 9 GDVSDPECEALLADSVGLAMLVVLGSLNPAEQIAFVLHDVFALPFEEIAPIVGRSKEXXX 68 GD DPE EA+LADSVGLA+LVVL +L P E++AFVLHD+F +PF+++AP+VGRS Sbjct: 108 GDGGDPEHEAMLADSVGLALLVVLDTLTPTERLAFVLHDMFDVPFDDVAPVVGRSSPAVR 167 Query: 69 XXXXXXXXXVHGFDTA-RHADLARQRELVDAFLAATRAGNFXXXXXXXXXXXXXXXXXXX 127 V G A ADL RQR +VDA+LAATR G+F Sbjct: 168 QLASRARRRVKGASPAPDTADLDRQRRVVDAYLAATRGGDFDALVALLDPDVVLRADPAV 227 Query: 128 XSGAAQEI---HXXXXXXXXXXXXXXXXXXPILIDGDVGIVVAPRGELQFVIKVAITDGK 184 A + L++G G+V+A G L V+ I DG+ Sbjct: 228 GPTPAPLLIRGARVVARGALASSERARSTQVALVNGAAGLVMALHGRLHLVLAFTIADGR 287 Query: 185 IAGFHIISDKERIREMDLAAL 205 I +I++ +R+R +DLA L Sbjct: 288 ITEIDVIAEPDRVRRLDLAVL 308 >A7HIP0.1 A7HIP0_ANADF RNA polymerase, sigma-24 subunit, ECF subfamily Length = 235 Score = 118 bits (296), Expect = 3e-25, Method: Compositional matrix adjust. Identities = 65/108 (60%), Positives = 75/108 (69%) Query: 1 VSELVSSGGDVSDPECEALLADSVGLAMLVVLGSLNPAEQIAFVLHDVFALPFEEIAPIV 60 V E + SG DPE EALLA SVGLA+LVVL +L PAE++AFVLHD+FA+PFEEIAPIV Sbjct: 25 VPEPIVSGEGGLDPEQEALLAGSVGLALLVVLDTLAPAERLAFVLHDMFAMPFEEIAPIV 84 Query: 61 GRSKEXXXXXXXXXXXXVHGFDTARHADLARQRELVDAFLAATRAGNF 108 GRS V G TA DL+RQRELVDAFL+A R G+F Sbjct: 85 GRSPAAARQLASRARRRVQGAPTAPDTDLSRQRELVDAFLSAARGGDF 132 >Q5Z2K1.1 Q5Z2K1_NOCFA Putative sigma factor Length = 293 Score = 118 bits (295), Expect = 4e-25, Method: Compositional matrix adjust. Identities = 76/202 (37%), Positives = 100/202 (49%), Gaps = 7/202 (3%) Query: 8 GGDVSDPECEALLADSVGLAMLVVLGSLNPAEQIAFVLHDVFALPFEEIAPIVGRSKEXX 67 G + SDPE EALLADSVGLA+LVVL SL+PAE++AFVLHD+FA+P+E+IAPIV R+ + Sbjct: 93 GENTSDPEHEALLADSVGLALLVVLESLSPAERLAFVLHDMFAMPYEQIAPIVDRTPQTA 152 Query: 68 XXXXXXXXXXVHGFDTARHADLARQRELVDAFLAATRAGNFXXXXXX----XXXXXXXXX 123 V G A DL RQR +VDAFL A R G+F Sbjct: 153 KKLASQARRRVQGLTPAPDPDLPRQRRVVDAFLTAARGGDFDELLQLLDPDVVLRADAGE 212 Query: 124 XXXXXSGAAQEIHXXXXXXXXXXXXXXXXXXPILIDGDVGIVVAPRGELQFVIKVAITDG 183 GAA P +++G G+V G VI + + Sbjct: 213 AMRVIRGAAA---VAGQAETFQRMATLCTVHPAVVNGGTGLVNTVEGAPFSVIGFTVAND 269 Query: 184 KIAGFHIISDKERIREMDLAAL 205 +I I+SD R+ +DL A+ Sbjct: 270 RITAIDILSDPTRLARLDLTAV 291 >Q825N3.1 Q825N3_STRAW Putative RNA polymerase ECF-subfamily sigma factor Length = 322 Score = 115 bits (289), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 73/197 (37%), Positives = 100/197 (50%), Gaps = 5/197 (2%) Query: 13 DPECEALLADSVGLAMLVVLGSLNPAEQIAFVLHDVFALPFEEIAPIVGRSKEXXXXXXX 72 DPE E LLADSVGLA+LVVL +L PAE++AFVLHD+FA+PF++IAPIV RS Sbjct: 125 DPEQEVLLADSVGLALLVVLETLEPAERLAFVLHDMFAVPFDDIAPIVDRSSAATRQLAS 184 Query: 73 XXXXXVHGFDTARHADLARQRELVDAFLAATRAGNFXXXXXXXXXXXXXXXXXXXXSGAA 132 V G A DL RQ++++DAFLAA+R G+F +G Sbjct: 185 RARRRVQGSAPAPDPDLGRQKQVLDAFLAASRGGDFEALLSVLDPDVVLRADAGALAGGV 244 Query: 133 QEIHXXXXXXXXXXXXXXXXXXP-----ILIDGDVGIVVAPRGELQFVIKVAITDGKIAG 187 +L++G VG+V G+ V+ V + DG+I Sbjct: 245 AVSKLVRGAAAVAEQALMFRQLAQFSRLVLVNGAVGVVTVLDGQPMGVMGVTVADGRIVD 304 Query: 188 FHIISDKERIREMDLAA 204 I+SD +R+ +DL A Sbjct: 305 ICILSDPDRLARLDLPA 321 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 0.321 0.139 0.387 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: 863,848,820 Number of extensions: 25753723 Number of successful extensions: 50467 Number of sequences better than 1.0e-05: 158 Number of HSP's gapped: 50438 Number of HSP's successfully gapped: 160 Length of query: 209 Length of database: 3,060,696,203 Length adjustment: 130 Effective length of query: 79 Effective length of database: 1,835,964,253 Effective search space: 145041175987 Effective search space used: 145041175987 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: 128 (53.9 bits)