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= 0044.0003.p (197 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|ZP_00120022.1| COG1595: DNA-directed RNA polymerase speciali... 82 8e-15 ref|NP_792117.1| RNA polymerase sigma factor-70 sigW, putative [... 79 4e-14 gb|AAD34328.1| ECF sigma factor SigX [Pseudomonas syringae pv. s... 79 5e-14 ref|ZP_00082799.1| COG1595: DNA-directed RNA polymerase speciali... 79 5e-14 ref|ZP_00061824.1| COG1595: DNA-directed RNA polymerase speciali... 78 9e-14 >ref|ZP_00120022.1| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Cytophaga hutchinsonii] Length = 208 Score = 82.0 bits (201), Expect = 8e-15, Method: Compositional matrix adjust. Identities = 48/163 (29%), Positives = 76/163 (46%), Gaps = 11/163 (6%) Query: 16 GNIERFEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRALGKYNPDIPFGAWLY 75 G+ + F E+M Y+K + M+ + +AED E F KAF+ L K+NPD F WL+ Sbjct: 31 GDEKAFAELMSRYKKPVYHMILKMIRNVDDAEDLTIEAFAKAFKNLHKFNPDFTFSTWLF 90 Query: 76 TIAYNQCIDVIXXXXXXXXXXXXXXDERDNRHVDQQIEGKYLD-----------EAVQQA 124 IA N CID I + + H + I+ L E +Q Sbjct: 91 RIATNNCIDFIRRKKLVTTSISSTYKDDNGEHTEMDIKDSNLTPFEETIKSQKIEIIQAI 150 Query: 125 LSKLSIEERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERS 167 +SKL + + L+ LR EE SY+EI++ + ++ + R+ Sbjct: 151 VSKLPPKYQTLVRLRYFEEYSYEEIAVAIEAPLGTVKAQLHRA 193 >ref|NP_792117.1| RNA polymerase sigma factor-70 sigW, putative [Pseudomonas syringae pv. tomato str. DC3000] gb|AAO55812.1| RNA polymerase sigma factor-70 sigW, putative [Pseudomonas syringae pv. tomato str. DC3000] Length = 165 Score = 79.3 bits (194), Expect = 4e-14, Method: Compositional matrix adjust. Identities = 50/169 (29%), Positives = 79/169 (46%), Gaps = 26/169 (15%) Query: 21 FEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRALGKYNPDIPFGAWLYTIAYN 80 +EE+MR YQ+ + C LG+ +A+D QEV LK L + F WLY+I YN Sbjct: 5 YEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYN 64 Query: 81 QCIDVIXXXXXXXXXXXXXXDERDNRHVDQQIEGKYLDEAVQQALSK------------- 127 +CI ER R + + L+EA ++ K Sbjct: 65 ECI-------------TQYRKERRKRRLMDALSLDPLEEASEEKTPKPEERGGLDRWLVY 111 Query: 128 LSIEERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERSAKKFRRYYA 176 ++ +R +L+LR V E+ +QEI+ I+H S + +Y+R+ K R +A Sbjct: 112 VNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREKFA 160 >gb|AAD34328.1| ECF sigma factor SigX [Pseudomonas syringae pv. syringae] Length = 196 Score = 79.3 bits (194), Expect = 5e-14, Method: Compositional matrix adjust. Identities = 50/169 (29%), Positives = 79/169 (46%), Gaps = 26/169 (15%) Query: 21 FEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRALGKYNPDIPFGAWLYTIAYN 80 +EE+MR YQ+ + C LG+ +A+D QEV LK L + F WLY+I YN Sbjct: 36 YEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYN 95 Query: 81 QCIDVIXXXXXXXXXXXXXXDERDNRHVDQQIEGKYLDEAVQQALSK------------- 127 +CI ER R + + L+EA ++ K Sbjct: 96 ECI-------------TQYRKERRKRRLMDALSLDPLEEASEEKAPKPEEKGGPDRWLVY 142 Query: 128 LSIEERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERSAKKFRRYYA 176 ++ +R +L+LR V E+ +QEI+ I+H S + +Y+R+ K R +A Sbjct: 143 VNPIDRGILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREKFA 191 >ref|ZP_00082799.1| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Pseudomonas fluorescens PfO-1] Length = 165 Score = 79.0 bits (193), Expect = 5e-14, Method: Compositional matrix adjust. Identities = 50/169 (29%), Positives = 79/169 (46%), Gaps = 26/169 (15%) Query: 21 FEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRALGKYNPDIPFGAWLYTIAYN 80 +EE+MR YQ+ + C LG+ +A+D QEV LK L + F WLY+I YN Sbjct: 5 YEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYN 64 Query: 81 QCIDVIXXXXXXXXXXXXXXDERDNRHVDQQIEGKYLDEAVQQALSK------------- 127 +CI ER R + + L+EA ++ K Sbjct: 65 ECI-------------TQYRKERRKRRLMDALSLDPLEEASEEKAPKPEEKGGLDRWLVY 111 Query: 128 LSIEERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERSAKKFRRYYA 176 ++ +R +L+LR V E+ +QEI+ I+H S + +Y+R+ K R +A Sbjct: 112 VNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREKFA 160 >ref|ZP_00061824.1| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Clostridium thermocellum ATCC 27405] Length = 220 Score = 78.2 bits (191), Expect = 9e-14, Method: Compositional matrix adjust. Identities = 44/178 (24%), Positives = 85/178 (47%), Gaps = 11/178 (6%) Query: 7 RRIIADVLEGNIERFEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRALGKYNP 66 + +I +G++E FE+++ QK + MLG+Y +A + QEVFLKA++++ + Sbjct: 28 KELIKRAKKGDVEAFEQLIEGCQKKVFNIALRMLGNYDDASELAQEVFLKAYKSIKNFKG 87 Query: 67 DIPFGAWLYTIAYNQCIDVIXXXXXXXXXXXXXXDERDNRHVDQQI-----------EGK 115 D F W+Y + N C+D I E + +QI E Sbjct: 88 DSLFNTWIYKVTTNACLDEIRKRKNKKVVYLDEDIELGGNEIKRQIKDDSPGPELKAEDN 147 Query: 116 YLDEAVQQALSKLSIEERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERSAKKFRR 173 L AV +++ L E R +++LR ++ +Y+EI+ I+ ++ + R+ + ++ Sbjct: 148 ELKRAVMDSINMLPEEYRTVIVLRDIQGFTYEEIANIIKCPEGTVKSRINRARQALKK 205 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.320 0.136 0.393 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 252,077,340 Number of extensions: 8678973 Number of successful extensions: 24384 Number of sequences better than 1.0e-05: 167 Number of HSP's gapped: 24418 Number of HSP's successfully gapped: 167 Length of query: 197 Length of database: 757,237,578 Length adjustment: 119 Effective length of query: 78 Effective length of database: 434,140,797 Effective search space: 33862982166 Effective search space used: 33862982166 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: 122 (51.6 bits)