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= 0025.0163.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 (... 390 e-110 gi|300311734|ref|YP_003775826.1| RNA polymerase sigma-E factor p... 96 2e-21 gi|300310115|ref|YP_003774207.1| RNA polymerase sigma-24 factor ... 84 1e-17 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 = 390 bits (1001), Expect = e-110, Method: Compositional matrix adjust. Identities = 192/200 (96%), Positives = 194/200 (97%) Query: 1 LTTEREIDQLLVERVQRGDKKAFELLVAKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAY 60 +TTEREIDQ LVERVQRGDKKAFELLV KYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAY Sbjct: 1 MTTEREIDQQLVERVQRGDKKAFELLVVKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAY 60 Query: 61 RALPQFRGDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAETFDDGEHLRDINT 120 RALPQFRGDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAETFDD +HLRDINT Sbjct: 61 RALPQFRGDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAETFDDADHLRDINT 120 Query: 121 PESMLATKQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIADAMGCPIGTVRSRIFRA 180 PESMLATKQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIADAM CPIGTVRSRIFRA Sbjct: 121 PESMLATKQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRA 180 Query: 181 REAIAEKLRPLLGTALDKRW 200 REAIAEKLRPLL TA DKRW Sbjct: 181 REAIAEKLRPLLDTAADKRW 200 >gi|300311734|ref|YP_003775826.1| RNA polymerase sigma-E factor protein [Herbaspirillum seropedicae SmR1] Length = 186 Score = 95.9 bits (237), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 56/174 (32%), Positives = 88/174 (50%), Gaps = 11/174 (6%) Query: 11 LVERVQRGDKKAFELLVAKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAYRALPQFRGDS 70 L+ER+ +GD+ AFE L Y +L + + RLV D +E+++ + + + G S Sbjct: 16 LIERIAQGDRGAFERLYRSYFPRLAQFLRRLVWDGPLSEEIINDTMFVVWTKAQTYNGQS 75 Query: 71 AFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAETFDDGEHLRDINTPESMLATKQI 130 TW++ I L R T E D E + ++ PE L+ Q+ Sbjct: 76 KVSTWIFAIAYKQGLKAL----SRVDTPVEMDMETMVS-------DELVEPEHQLSETQL 124 Query: 131 AQTVNVAMEALPEELRTAITLREIEGLSYDEIADAMGCPIGTVRSRIFRAREAI 184 + + A+E L E RT +TL G+SY+EIAD MGC I TV++R+F AR+ + Sbjct: 125 RRHIGGALERLSFEHRTVMTLTYFHGMSYEEIADTMGCSINTVKTRMFYARQKL 178 >gi|300310115|ref|YP_003774207.1| RNA polymerase sigma-24 factor protein [Herbaspirillum seropedicae SmR1] Length = 244 Score = 83.6 bits (205), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 58/160 (36%), Positives = 82/160 (51%), Gaps = 9/160 (5%) Query: 26 LVAKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAYRALPQFRGDSAFYTWLYRIGINTAK 85 L K++ L+R V R V + +AEDVVQ FI+A + +F G S TWL+ IG+N A+ Sbjct: 72 LYTKHRTHLLRFVLRYVGNHEDAEDVVQNTFIEAVKCAHRFSGLSKPSTWLFGIGLNLAR 131 Query: 86 NYLVTMGRRAPTSTEADAEEAETFDDGEHLRDINT-PESMLATKQIAQTVNVAMEALPEE 144 N + RR AD E + E L D + P + +QIAQ V+ + LP Sbjct: 132 NQV----RR----NSADRYEMVEENFMEQLVDASADPAMVYELRQIAQKVDDMLSELPPH 183 Query: 145 LRTAITLREIEGLSYDEIADAMGCPIGTVRSRIFRAREAI 184 +R +Y+E A + 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 = 47/161 (29%), Positives = 75/161 (46%), Gaps = 18/161 (11%) Query: 27 VAKYQRKLMRLVSRLVRDQAEAEDVVQEAF---IKAYRALPQFRGDSAFYTWLYRIGINT 83 V + + +L + R V D EAED++QE F ++AYR SA WL+R+ Sbjct: 21 VMRERSRLGGFIRRRVADAGEAEDILQEVFYEFVQAYRLPEPIEQVSA---WLFRV---- 73 Query: 84 AKNYLVTMGRRA---PTSTEADAEEAETFDDGEHL-----RDINTPESMLATKQIAQTVN 135 A+N ++ R+ P D E+ + DD L + PE+ A + + Sbjct: 74 ARNRIIDRFRKKKEEPLPEAHDIEQVDGADDAWRLDLALPASADGPEAAYARAALIDALQ 133 Query: 136 VAMEALPEELRTAITLREIEGLSYDEIADAMGCPIGTVRSR 176 A+ LPE R E++GLS+ E+A A G + T+ +R Sbjct: 134 EALGELPEAQREVFIAHELDGLSFKEMAAASGTSLNTLLAR 174 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 0.133 0.371 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: 485,021 Number of extensions: 15898 Number of successful extensions: 71 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 68 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)