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= 0001.1796.p (200 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311253|ref|YP_003775345.1| RNA polymerase sigma-E factor (... 405 e-114 gi|300311734|ref|YP_003775826.1| RNA polymerase sigma-E factor p... 95 4e-21 gi|300310115|ref|YP_003774207.1| RNA polymerase sigma-24 factor ... 86 2e-18 gi|300312377|ref|YP_003776469.1| RNA polymerase sigma-70 factor,... 57 1e-09 >gi|300311253|ref|YP_003775345.1| RNA polymerase sigma-E factor (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 200 Score = 405 bits (1040), Expect = e-114, Method: Compositional matrix adjust. Identities = 199/200 (99%), Positives = 200/200 (100%) Query: 1 LTTEREIDQQLVERVQRGDKKAFELLVVKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAY 60 +TTEREIDQQLVERVQRGDKKAFELLVVKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAY Sbjct: 1 MTTEREIDQQLVERVQRGDKKAFELLVVKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAY 60 Query: 61 RALPQFRGDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAETFDDADHLRDINT 120 RALPQFRGDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAETFDDADHLRDINT Sbjct: 61 RALPQFRGDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAETFDDADHLRDINT 120 Query: 121 PESMLATKQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRA 180 PESMLATKQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRA Sbjct: 121 PESMLATKQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRA 180 Query: 181 REAIAEKLRPLLDTAADKRW 200 REAIAEKLRPLLDTAADKRW Sbjct: 181 REAIAEKLRPLLDTAADKRW 200 >gi|300311734|ref|YP_003775826.1| RNA polymerase sigma-E factor protein [Herbaspirillum seropedicae SmR1] Length = 186 Score = 94.7 bits (234), Expect = 4e-21, Method: Compositional matrix adjust. Identities = 62/189 (32%), Positives = 93/189 (49%), Gaps = 15/189 (7%) Query: 8 DQQLVERVQRGDKKAFELLVVKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAYRALPQFR 67 D L+ER+ +GD+ AFE L Y +L + + RLV D +E+++ + + + Sbjct: 13 DIDLIERIAQGDRGAFERLYRSYFPRLAQFLRRLVWDGPLSEEIINDTMFVVWTKAQTYN 72 Query: 68 GDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAETFDDADHLRDINTPESMLAT 127 G S TW++ I L R T E D E + D L + PE L+ Sbjct: 73 GQSKVSTWIFAIAYKQGLKAL----SRVDTPVEMDMETMVS----DELVE---PEHQLSE 121 Query: 128 KQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRAREAIAEK 187 Q+ + + A+E L E RT +TL G+SY+EIAD M C I TV++R+F AR +K Sbjct: 122 TQLRRHIGGALERLSFEHRTVMTLTYFHGMSYEEIADTMGCSINTVKTRMFYAR----QK 177 Query: 188 LRPLLDTAA 196 L+ L A Sbjct: 178 LKVFLSAYA 186 >gi|300310115|ref|YP_003774207.1| RNA polymerase sigma-24 factor protein [Herbaspirillum seropedicae SmR1] Length = 244 Score = 85.9 bits (211), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 58/160 (36%), Positives = 83/160 (51%), Gaps = 9/160 (5%) Query: 26 LVVKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAYRALPQFRGDSAFYTWLYRIGINTAK 85 L K++ L+R V R V + +AEDVVQ FI+A + +F G S TWL+ IG+N A+ Sbjct: 72 LYTKHRTHLLRFVLRYVGNHEDAEDVVQNTFIEAVKCAHRFSGLSKPSTWLFGIGLNLAR 131 Query: 86 NYLVTMGRRAPTSTEADAEEAETFDDADHLRDINT-PESMLATKQIAQTVNVAMEALPEE 144 N + RR AD E + + L D + P + +QIAQ V+ + LP Sbjct: 132 NQV----RR----NSADRYEMVEENFMEQLVDASADPAMVYELRQIAQKVDDMLSELPPH 183 Query: 145 LRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRAREAI 184 +R +Y+E A +N PIGTVRSR+ R R A+ Sbjct: 184 IRHTFEAVLDGDATYEEAAQHLNIPIGTVRSRVSRVRAAV 223 >gi|300312377|ref|YP_003776469.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 195 Score = 56.6 bits (135), Expect = 1e-09, Method: Compositional matrix adjust. Identities = 51/178 (28%), Positives = 84/178 (47%), Gaps = 18/178 (10%) Query: 27 VVKYQRKLMRLVSRLVRDQAEAEDVVQEAF---IKAYRALPQFRGDSAFYTWLYRIGINT 83 V++ + +L + R V D EAED++QE F ++AYR SA WL+R+ Sbjct: 21 VMRERSRLGGFIRRRVADAGEAEDILQEVFYEFVQAYRLPEPIEQVSA---WLFRV---- 73 Query: 84 AKNYLVTMGRRA---PTSTEADAEEAETFDDADHL-----RDINTPESMLATKQIAQTVN 135 A+N ++ R+ P D E+ + DDA L + PE+ A + + Sbjct: 74 ARNRIIDRFRKKKEEPLPEAHDIEQVDGADDAWRLDLALPASADGPEAAYARAALIDALQ 133 Query: 136 VAMEALPEELRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRAREAIAEKLRPLLD 193 A+ LPE R E++GLS+ E+A A + T+ +R A + E+L+ + D Sbjct: 134 EALGELPEAQREVFIAHELDGLSFKEMAAASGTSLNTLLARKRYAVLHLRERLQAVYD 191 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 0.319 0.132 0.366 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: 482,498 Number of extensions: 15689 Number of successful extensions: 74 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 71 Number of HSP's successfully gapped: 6 Length of query: 200 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 119 Effective length of database: 1,236,335 Effective search space: 147123865 Effective search space used: 147123865 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)