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= 0004.0088.p (307 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309859|ref|YP_003773951.1| LysR family transcription regul... 87 2e-18 gi|300311165|ref|YP_003775257.1| transcription regulator protein... 84 1e-17 gi|300313217|ref|YP_003777309.1| LysR family transcription regul... 76 4e-15 gi|300312961|ref|YP_003777053.1| transcription regulator protein... 75 5e-15 gi|300309864|ref|YP_003773956.1| LysR family transcription regul... 74 1e-14 >gi|300309859|ref|YP_003773951.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 297 Score = 87.0 bits (214), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 51/139 (36%), Positives = 75/139 (53%) Query: 4 YLKTFIAAARLGSFSTAGARLGLTQSAVSMQIRRLEDELNCELFTRVGKTVAVSEHGKQL 63 +L+TF AA SF+ AG +LGLTQS VS IRRLE+ L LF R ++A++ G+ L Sbjct: 21 WLQTFSTAASSASFTEAGRQLGLTQSTVSDHIRRLEESLGRRLFVRDTHSLALTADGESL 80 Query: 64 FVTAEEIVRLFESMKGQTDVAATRGKIDIGAISTVQLGLLPAVLADFCKELPLVEVNVVP 123 V A I++ + Q RG++ G + +G LP +LA F + P VE+ + Sbjct: 81 LVHARLILQAHARAEAQFSAPRLRGRVRFGTSDDLAMGPLPDMLAAFRSQHPEVELEITI 140 Query: 124 GTSVQLMSQIDSNDLSLAV 142 G + L + +D L L V Sbjct: 141 GLTSDLYASLDQGKLDLLV 159 >gi|300311165|ref|YP_003775257.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 311 Score = 84.0 bits (206), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 68/249 (27%), Positives = 116/249 (46%), Gaps = 24/249 (9%) Query: 2 IRYLKTFIAAARLGSFSTAGARLGLTQSAVSMQIRRLEDELNCELFTRVGKTVAVSEHGK 61 IR+L+TF+ ARL +F RL TQ+AVS +I LE + LF R + VA++ G Sbjct: 3 IRFLETFVWLARLRNFRLTAERLHTTQAAVSSRIASLEQDFGVRLFDRSAREVALTADGS 62 Query: 62 QLFVTAEEIVRLFESMK-GQTDVAATRGKIDIGAISTVQLGLLPAVLADFCKELPLVEVN 120 + V AE +V+L MK +D G I IG I ++ P L K P +++ Sbjct: 63 KALVHAERMVKLMREMKEDMSDREVYAGVIRIGVIESIVHSWFPDFLGRLHKTFPRLQIE 122 Query: 121 VVPGTSVQLMSQIDSNDLSLAV----MIRP---NLKMTK-GLKWTTMLRETYVVIAP--T 170 +V T++ L Q +L L + +I P NL + + ++W V +P Sbjct: 123 IVSDTTIHLHEQFSKGNLDLVLQAEAVIGPQVSNLALCEFPMRW---------VGSPKLD 173 Query: 171 SARETSIKSLLESHPFLRYSRRSYGGQLVDRYLKRTRLQVNDTMELDEPMVIIEMVR--- 227 ET + L + P + ++R S +++R ++ + T+ ++ + M+R Sbjct: 174 IGSETLSLADLAAFPIISFARNSGPHAVIERLFSDSQ-RSERTLHINCIASVATMIRLAT 232 Query: 228 KGLGVAIIP 236 G G+ +P Sbjct: 233 DGFGITAVP 241 >gi|300313217|ref|YP_003777309.1| LysR family transcription regulator [Herbaspirillum seropedicae SmR1] Length = 296 Score = 75.9 bits (185), Expect = 4e-15, Method: Compositional matrix adjust. Identities = 64/253 (25%), Positives = 112/253 (44%), Gaps = 27/253 (10%) Query: 15 GSFSTAGARLGLTQSAVSMQIRRLEDELNCELFTRVGKTVAVSEHGKQLFVTAEEIVRLF 74 G + A RL QS V+ +I++LE + LF R + + ++ G+ L AE I+ L Sbjct: 25 GGVTRAAERLNRVQSNVTTRIKQLEQSMGVPLFVRDRRRMVLTAAGEALLDYAERILDLA 84 Query: 75 ESMKGQTDVAATRGKIDIGAISTVQLGLLPAVLADFCKELPLVEVNVVPGTSVQLMSQID 134 + + + RG++ IG++ + LP LA+F + P V + + + LM+Q+ Sbjct: 85 QEARQAVAPQSPRGRLRIGSMESAAASRLPGPLAEFHQRWPEVRLELSTAPTDVLMAQVR 144 Query: 135 SNDLSLAVMIRPNLKMTKGLKWTTMLRETYVVIAPTSAR------ETSIKSLL---ESHP 185 + L A++ P T + RE +++ P S R E + +L+ + Sbjct: 145 ACKLDAALVAGP--VSDPAFDATPLFREELLLVTPRSHRRVRAPEEVMLDTLIVFEQGCA 202 Query: 186 FLRYSRRSYGGQLVDRYLKRTRLQVNDTMELDEPMVIIEMVRKGLGVAIIPYDLAAGASI 245 + R++ + G R L R T+EL I+ V G GVA++P Sbjct: 203 YRRHAEAWFAGHGAGRQLPR-------TLELASYHAILACVSAGAGVAVVP--------- 246 Query: 246 RKVRVLPLEGGGF 258 R V + +E GF Sbjct: 247 RSVIAMQMEPHGF 259 >gi|300312961|ref|YP_003777053.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 75.5 bits (184), Expect = 5e-15, Method: Compositional matrix adjust. Identities = 67/245 (27%), Positives = 116/245 (47%), Gaps = 14/245 (5%) Query: 2 IRYLKTFIAAARLGSFSTAGARLGLTQSAVSMQIRRLEDELNCELFTRVGKTVAVSEHGK 61 +R+LK F A A SFS A L + Q +S QIR+LE+ L EL R + +A++ GK Sbjct: 3 LRHLKYFNAVASTLSFSRAAELLHIAQPPLSRQIRQLEEMLGVELIDRASRPIALTMAGK 62 Query: 62 QLFVTAEEIVRLFESMKGQTDVAATRGK---IDIGAISTVQLGLLPAVLADFCKELPLVE 118 + +++ E ++ T V A RG+ +IG + + GLLP ++ F E+P +E Sbjct: 63 FFYEQTLQVLSRLEQIEEGTRVIA-RGRQHWFNIGFVPSALYGLLPEMIKRFRTEMPEIE 121 Query: 119 VNVVPGTSVQLMSQIDSNDLSLAVMIRPNLKMTKGLKWTTMLRETYVVIAPTS----ARE 174 + +++ + + S + + P + T++ E V + P AR Sbjct: 122 IGFSEIVTMEQVEALKSGRIDVGFGRLP--ISDPDIVCETIVEEPLVAVFPLGHPLLARN 179 Query: 175 TSIKSLLESHPFLRY---SRRSYGGQLVDRYLKRTRLQVNDTMELDEPMVIIEMVRKGLG 231 + L + F+ Y R SY Q++D + R L+ + E +E I +V G+G Sbjct: 180 KVTLAQLAAQRFILYPARPRPSYADQVLDIFSSRA-LRPSIVKEANEMQTAIGLVAAGVG 238 Query: 232 VAIIP 236 V ++P Sbjct: 239 VTLVP 243 >gi|300309864|ref|YP_003773956.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 306 Score = 73.9 bits (180), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 63/241 (26%), Positives = 114/241 (47%), Gaps = 12/241 (4%) Query: 5 LKTFIAAARLGSFSTAGARLGLTQSAVSMQIRRLEDELNCELFTRVGKTVAVSEHGKQLF 64 ++ F+ AA +F A A L +TQ +S QI LE L +LF RVG+TV ++ G+ Sbjct: 7 VRCFVVAATELNFRRAAALLNMTQPPLSRQIHLLEHRLGVQLFERVGRTVRLTTEGRVFL 66 Query: 65 VTAEEIVRLFESMKGQTDVAAT--RGKIDIGAISTVQLGLLPAVLADFCKELPLVEVNVV 122 A +++L E + A+ G++ +G L+P +L LP ++V + Sbjct: 67 ADASRLLQLSEQAESTVRRASQGKTGRVRVGFTGAAGYELIPELLMQARTSLPEIDVVLF 126 Query: 123 PGTSVQLMSQIDSNDLSLAVMIRPNLKMTKGLKWTTMLRETYVVIAPT----SARETSIK 178 SV + +N + + +RP + + L+ + E V+ P +A + Sbjct: 127 ELISVAQLEAFTANTIDIG-FLRP-VASRQPLELQLVDEEALVLAMPQGHALAAYDRIAT 184 Query: 179 SLLESHPFLRYSRRSYGGQLVDR---YLKRTRLQVNDTMELDEPMVIIEMVRKGLGVAII 235 + L+ PF+ +S ++G +R L ++ + T +D+ I+ +VR GLGV I+ Sbjct: 185 TQLDGQPFIMHS-PTHGKYFYERIMAMLGAADVKPDFTQYIDQSHTILSLVRAGLGVGIL 243 Query: 236 P 236 P Sbjct: 244 P 244 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 0.367 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: 793,772 Number of extensions: 29348 Number of successful extensions: 236 Number of sequences better than 1.0e-08: 38 Number of HSP's gapped: 230 Number of HSP's successfully gapped: 38 Length of query: 307 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 222 Effective length of database: 1,217,395 Effective search space: 270261690 Effective search space used: 270261690 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 (21.9 bits) S2: 130 (54.7 bits)