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= 0001.2739.p (164 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312008|ref|YP_003776100.1| RNA polymerase sigma-E factor [... 211 3e-56 gi|300311734|ref|YP_003775826.1| RNA polymerase sigma-E factor p... 66 1e-12 gi|300310115|ref|YP_003774207.1| RNA polymerase sigma-24 factor ... 60 6e-11 gi|300311253|ref|YP_003775345.1| RNA polymerase sigma-E factor (... 57 1e-09 >gi|300312008|ref|YP_003776100.1| RNA polymerase sigma-E factor [Herbaspirillum seropedicae SmR1] Length = 163 Score = 211 bits (537), Expect = 3e-56, Method: Compositional matrix adjust. Identities = 121/164 (73%), Positives = 136/164 (82%), Gaps = 1/164 (0%) Query: 1 MLACLPRLRRYARALTGARDSADDLVQDTLERAWQRLDSYQRGSDMRPWLFAIMHNLHAD 60 MLACLPRLRRYARALTGAR++ADDLVQDTLERAWQ+LDS+QRGS MRPWLF+IMHNLHAD Sbjct: 1 MLACLPRLRRYARALTGAREAADDLVQDTLERAWQKLDSWQRGSPMRPWLFSIMHNLHAD 60 Query: 61 QRRKPALATVELEQADEASATPLLPDQGLALDMEAALQRLPAEQREVLLLVVLEEMRYED 120 RR+ + ATV L++ E + D G+ LD+E ALQ LP EQREVLLLVVLEEMRYE+ Sbjct: 61 ARRRASPATVALDEYGEIDQAQVALDPGVLLDLETALQLLPPEQREVLLLVVLEEMRYEE 120 Query: 121 VAVTLGIPVGTVMSRLSRARERLRQSMDGPGGRGEAGSTLKVVK 164 VAVTLGIP GTVMSRLSRARERLR+ M G G GS+LKVVK Sbjct: 121 VAVTLGIPTGTVMSRLSRARERLRRVMQG-QGESSPGSSLKVVK 163 >gi|300311734|ref|YP_003775826.1| RNA polymerase sigma-E factor protein [Herbaspirillum seropedicae SmR1] Length = 186 Score = 66.2 bits (160), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 43/146 (29%), Positives = 72/146 (49%), Gaps = 4/146 (2%) Query: 3 ACLPRLRRYARALTGARDSADDLVQDTLERAWQRLDSYQRGSDMRPWLFAIMHN--LHAD 60 + PRL ++ R L +++++ DT+ W + +Y S + W+FAI + L A Sbjct: 34 SYFPRLAQFLRRLVWDGPLSEEIINDTMFVVWTKAQTYNGQSKVSTWIFAIAYKQGLKAL 93 Query: 61 QR-RKPALATVELEQADE-ASATPLLPDQGLALDMEAALQRLPAEQREVLLLVVLEEMRY 118 R P +E +DE L + L + AL+RL E R V+ L M Y Sbjct: 94 SRVDTPVEMDMETMVSDELVEPEHQLSETQLRRHIGGALERLSFEHRTVMTLTYFHGMSY 153 Query: 119 EDVAVTLGIPVGTVMSRLSRARERLR 144 E++A T+G + TV +R+ AR++L+ Sbjct: 154 EEIADTMGCSINTVKTRMFYARQKLK 179 >gi|300310115|ref|YP_003774207.1| RNA polymerase sigma-24 factor protein [Herbaspirillum seropedicae SmR1] Length = 244 Score = 60.5 bits (145), Expect = 6e-11, Method: Compositional matrix adjust. Identities = 47/147 (31%), Positives = 70/147 (47%), Gaps = 8/147 (5%) Query: 7 RLRRYARALTGARDSADDLVQDTLERAWQRLDSYQRGSDMRPWLFAIMHNLHADQRRKPA 66 L R+ G + A+D+VQ+T A + + S WLF I NL +Q R+ + Sbjct: 79 HLLRFVLRYVGNHEDAEDVVQNTFIEAVKCAHRFSGLSKPSTWLFGIGLNLARNQVRRNS 138 Query: 67 LATVEL------EQADEASATPLLPDQ--GLALDMEAALQRLPAEQREVLLLVVLEEMRY 118 E+ EQ +ASA P + + +A ++ L LP R V+ + Y Sbjct: 139 ADRYEMVEENFMEQLVDASADPAMVYELRQIAQKVDDMLSELPPHIRHTFEAVLDGDATY 198 Query: 119 EDVAVTLGIPVGTVMSRLSRARERLRQ 145 E+ A L IP+GTV SR+SR R +RQ Sbjct: 199 EEAAQHLNIPIGTVRSRVSRVRAAVRQ 225 >gi|300311253|ref|YP_003775345.1| RNA polymerase sigma-E factor (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 200 Score = 56.6 bits (135), Expect = 1e-09, Method: Compositional matrix adjust. Identities = 41/141 (29%), Positives = 72/141 (51%), Gaps = 15/141 (10%) Query: 22 ADDLVQDTLERAWQRLDSYQRGSDMRPWLFAIMHNLHADQ-----RRKPALATVELEQA- 75 A+D+VQ+ +A++ L ++ S WL+ I N + RR P + E+A Sbjct: 48 AEDVVQEAFIKAYRALPQFRGDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAE 107 Query: 76 --DEAS-----ATP--LLPDQGLALDMEAALQRLPAEQREVLLLVVLEEMRYEDVAVTLG 126 D+A TP +L + +A + A++ LP E R + L +E + Y+++A + Sbjct: 108 TFDDADHLRDINTPESMLATKQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIADAMN 167 Query: 127 IPVGTVMSRLSRARERLRQSM 147 P+GTV SR+ RARE + + + Sbjct: 168 CPIGTVRSRIFRAREAIAEKL 188 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.320 0.134 0.381 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 509,486 Number of extensions: 19257 Number of successful extensions: 100 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 99 Number of HSP's successfully gapped: 4 Length of query: 164 Length of database: 1,619,870 Length adjustment: 78 Effective length of query: 86 Effective length of database: 1,250,540 Effective search space: 107546440 Effective search space used: 107546440 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: 127 (53.5 bits)