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= 0001.3720.p (300 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313102|ref|YP_003777194.1| LysR family transcription regul... 560 e-161 gi|300312961|ref|YP_003777053.1| transcription regulator protein... 178 5e-46 gi|300310436|ref|YP_003774528.1| LysR family transcription regul... 155 6e-39 gi|300309864|ref|YP_003773956.1| LysR family transcription regul... 146 2e-36 gi|300312750|ref|YP_003776842.1| LysR family transcription regul... 140 1e-34 >gi|300313102|ref|YP_003777194.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 560 bits (1442), Expect = e-161, Method: Compositional matrix adjust. Identities = 264/297 (88%), Positives = 285/297 (95%) Query: 1 MIELRHLLYFRTVAETLHFGRAAALLHISQPPLTRQIAALEKELDAQLFDRSKRAIQLTA 60 MIELRHL YFRTVAETLHFGRAA LLHISQPPLTRQIAALEKEL AQLFDRSKRAIQLTA Sbjct: 1 MIELRHLTYFRTVAETLHFGRAAELLHISQPPLTRQIAALEKELGAQLFDRSKRAIQLTA 60 Query: 61 AGKHFYRDSTEIFKALERAKRNVASSSSGTLGALKVGFMMSSAYNILPAVTRHYSAAYPD 120 AGK+FYRD+TEIFKALERAKRNV+SSS+G GALKVGFMMS+AYNILP+VTRHYSAAYP+ Sbjct: 61 AGKYFYRDTTEIFKALERAKRNVSSSSTGKSGALKVGFMMSTAYNILPSVTRHYSAAYPE 120 Query: 121 VDLRMSEYLPNLLATDLEDEKVDVGIMYRPEDCRRLDSHTIYAEPLLAVLPRAHRLAGKP 180 VD+R++EY+PNLLATD+EDEK+DVGIMYRPEDCRRLDSHTIYAEPLLAVLPR HRLAG+ Sbjct: 121 VDMRLTEYVPNLLATDIEDEKIDVGIMYRPEDCRRLDSHTIYAEPLLAVLPRDHRLAGRQ 180 Query: 181 AISAAELAEDAFISIPRAIAPVVFDLILQHCQLHGFRPRIVLETNLQQTIVNLVGEGLGV 240 +ISAAELAEDAFISIPR IAPVV+DLI QHCQLHGFRPRIVLETNLQQTIVNLVGEGLGV Sbjct: 181 SISAAELAEDAFISIPRMIAPVVYDLIQQHCQLHGFRPRIVLETNLQQTIVNLVGEGLGV 240 Query: 241 ALVPTSMQAMHLESTVFKPLIGAPMVEVAVVWNKDNSNPCIGTFVQTAVEVWSRMQP 297 ALVPTSMQAMHL++TVFKPLIGAPMVEVAV+WNKDN+NPCI TF +TAVEVW RMQP Sbjct: 241 ALVPTSMQAMHLDTTVFKPLIGAPMVEVAVIWNKDNTNPCIRTFAETAVEVWGRMQP 297 >gi|300312961|ref|YP_003777053.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 178 bits (451), Expect = 5e-46, Method: Compositional matrix adjust. Identities = 104/283 (36%), Positives = 145/283 (51%), Gaps = 11/283 (3%) Query: 2 IELRHLLYFRTVAETLHFGRAAALLHISQPPLTRQIAALEKELDAQLFDRSKRAIQLTAA 61 +ELRHL YF VA TL F RAA LLHI+QPPL+RQI LE+ L +L DR+ R I LT A Sbjct: 1 MELRHLKYFNAVASTLSFSRAAELLHIAQPPLSRQIRQLEEMLGVELIDRASRPIALTMA 60 Query: 62 GKHFYRDSTEIFKALERAKRNVASSSSGTLGALKVGFMMSSAYNILPAVTRHYSAAYPDV 121 GK FY + ++ LE+ + + G +GF+ S+ Y +LP + + + P++ Sbjct: 61 GKFFYEQTLQVLSRLEQIEEGTRVIARGRQHWFNIGFVPSALYGLLPEMIKRFRTEMPEI 120 Query: 122 DLRMSEYLPNLLATDLEDEKVDVGIMYRPEDCRRLDSHTIYAEPLLAVLPRAHRLAGKPA 181 ++ SE + L+ ++DVG P + TI EPL+AV P H L + Sbjct: 121 EIGFSEIVTMEQVEALKSGRIDVGFGRLPISDPDIVCETIVEEPLVAVFPLGHPLLARNK 180 Query: 182 ISAAELAEDAFISIPRAIAPVVFDLILQHCQLHGFRPRIVLETNLQQTIVNLVGEGLGVA 241 ++ A+LA FI P P D +L RP IV E N QT + LV G+GV Sbjct: 181 VTLAQLAAQRFILYPARPRPSYADQVLDIFSSRALRPSIVKEANEMQTAIGLVAAGVGVT 240 Query: 242 LVPTSMQAMHLESTVFKPLIGAPMVEVAVVWNKDNSNPCIGTF 284 LVP S+Q +H V++PL NK +P I F Sbjct: 241 LVPRSVQGLHRSDVVYRPL-----------SNKGVHSPVIMNF 272 >gi|300310436|ref|YP_003774528.1| LysR family transcription regulator [Herbaspirillum seropedicae SmR1] Length = 300 Score = 155 bits (391), Expect = 6e-39, Method: Compositional matrix adjust. Identities = 102/289 (35%), Positives = 155/289 (53%), Gaps = 5/289 (1%) Query: 2 IELRHLLYFRTVAETLHFGRAAALLHISQPPLTRQIAALEKELDAQLFDRSKRAIQLTAA 61 +ELR L YF VAE +HFGRAAA LH++QPPL++ IAALE+ L LF R+KR++ LTAA Sbjct: 7 LELRQLRYFAAVAEEMHFGRAAARLHMTQPPLSQTIAALEELLGTPLFQRTKRSVALTAA 66 Query: 62 GKHFYRDSTEIFKALERAKRNVASSSSGTLGALKVGFMMSSAYNILPAVTRHYSAAYPDV 121 G ++ + + V ++SG G L + F+ S+ Y+ILP + + + A YP V Sbjct: 67 GAALLPEAQRLLQQAAALPDLVRRAASGASGLLSLSFISSADYSILPPLLQRFRAHYPQV 126 Query: 122 DLRMSEYLPNLLATDLEDEKVDVGIMYRP---EDCRRLDSHTIYAEPLLAVLPRAHRLAG 178 + + E ++ DL K+D G++ P + L+ + +EPL+A LP Sbjct: 127 QIELREATTDVQLEDLLQGKIDAGLLLPPLPEKAAALLEVRPVLSEPLIAALPEGAVRKR 186 Query: 179 KPAISAAELAEDAFISIPRAIAPVVFDLILQHCQLHGFRPRIVLETNLQQTIVNLVGEGL 238 P +S L E I PR IAP D IL + G P I E QTIV LV G+ Sbjct: 187 GP-VSLKSLRELPLIIFPRRIAPAFHDTILSCFRDAGVTPHIGQEAIQMQTIVGLVSAGM 245 Query: 239 GVALVPTSMQAMHLESTVFKPLIG-APMVEVAVVWNKDNSNPCIGTFVQ 286 G+ALVP S+ + ++ L AP ++ ++ W +D+ + + ++ Sbjct: 246 GMALVPQSVSNLKRPGVDYRRLSDPAPAIQTSLAWRRDSPSSVLRALLE 294 >gi|300309864|ref|YP_003773956.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 306 Score = 146 bits (369), Expect = 2e-36, Method: Compositional matrix adjust. Identities = 87/286 (30%), Positives = 145/286 (50%), Gaps = 3/286 (1%) Query: 1 MIELRHLLYFRTVAETLHFGRAAALLHISQPPLTRQIAALEKELDAQLFDRSKRAIQLTA 60 M++L + F A L+F RAAALL+++QPPL+RQI LE L QLF+R R ++LT Sbjct: 1 MLDLAQVRCFVVAATELNFRRAAALLNMTQPPLSRQIHLLEHRLGVQLFERVGRTVRLTT 60 Query: 61 AGKHFYRDSTEIFKALERAKRNVASSSSGTLGALKVGFMMSSAYNILPAVTRHYSAAYPD 120 G+ F D++ + + E+A+ V +S G G ++VGF ++ Y ++P + + P+ Sbjct: 61 EGRVFLADASRLLQLSEQAESTVRRASQGKTGRVRVGFTGAAGYELIPELLMQARTSLPE 120 Query: 121 VDLRMSEYLPNLLATDLEDEKVDVGIMYRPEDCRR-LDSHTIYAEPLLAVLPRAHRLAGK 179 +D+ + E + +D+G + RP R+ L+ + E L+ +P+ H LA Sbjct: 121 IDVVLFELISVAQLEAFTANTIDIGFL-RPVASRQPLELQLVDEEALVLAMPQGHALAAY 179 Query: 180 PAISAAELAEDAFISIPRAIAPVVFDLILQHCQLHGFRPRIVLETNLQQTIVNLVGEGLG 239 I+ +L FI ++ I+ +P + TI++LV GLG Sbjct: 180 DRIATTQLDGQPFIMHSPTHGKYFYERIMAMLGAADVKPDFTQYIDQSHTILSLVRAGLG 239 Query: 240 VALVPTSMQAMHLESTVFKPLIG-APMVEVAVVWNKDNSNPCIGTF 284 V ++P S Q H + F+PL AP E+++ W D NP + F Sbjct: 240 VGILPASAQRFHYDRVEFRPLADEAPRAEMSMAWRPDQDNPAVTAF 285 >gi|300312750|ref|YP_003776842.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 322 Score = 140 bits (353), Expect = 1e-34, Method: Compositional matrix adjust. Identities = 91/268 (33%), Positives = 143/268 (53%), Gaps = 5/268 (1%) Query: 2 IELRHLLYFRTVAETLHFGRAAALLHISQPPLTRQIAALEKELDAQLFDRSKRAIQLTAA 61 I+LR L YF VAE H +AA + I QPPL++QI LE+EL LF+R R ++LT + Sbjct: 19 IDLRLLRYFIAVAEEGHLTKAAERIGIQQPPLSQQIRVLERELGVTLFNRLPRGMELTDS 78 Query: 62 GKHFYRDSTEIFKALERAKRNVASSSSGTLGALKVGFMMSSAYN-ILPAVTRHYSAAYPD 120 G D+ + L+ +V + G +G + VGF S++ + + +V R + A PD Sbjct: 79 GAALLIDARALLAQLDTTVASVRRIAQGKMGRIAVGFTESASLHPFVHSVIRAFRADAPD 138 Query: 121 VDLRMSEYLPNLLATDLEDEKVDVGIMYRP-EDCRRLDSHTIYAEPLLAVLPRAHRL--A 177 V + + E N L L +++D+ + P D L T+ E ++A LP H L Sbjct: 139 VAMTVEESNTNELIEALRGKRLDLAFVRSPVGDSGGLTIETMLEEDMVAALPIDHPLVDG 198 Query: 178 GK-PAISAAELAEDAFISIPRAIAPVVFDLILQHCQLHGFRPRIVLETNLQQTIVNLVGE 236 GK +I+ LAE++FI R P ++D I+ C GF P+++ E + ++LV Sbjct: 199 GKRKSIALHALAEESFIMTRRPNGPGLYDTIIAACHAAGFSPQVIQEARKNLSTLSLVAA 258 Query: 237 GLGVALVPTSMQAMHLESTVFKPLIGAP 264 G+GV ++P SM ++ E V+ L GAP Sbjct: 259 GVGVTVIPASMTRVNAEGVVYLKLTGAP 286 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 0.322 0.135 0.394 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: 915,204 Number of extensions: 38187 Number of successful extensions: 231 Number of sequences better than 1.0e-08: 49 Number of HSP's gapped: 205 Number of HSP's successfully gapped: 49 Length of query: 300 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 215 Effective length of database: 1,217,395 Effective search space: 261739925 Effective search space used: 261739925 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 (22.0 bits) S2: 130 (54.7 bits)