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= 0003.0063.p (310 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312870|ref|YP_003776962.1| transcription regulator protein... 493 e-141 gi|300311849|ref|YP_003775941.1| LysR family transcription regul... 94 2e-20 gi|300313839|ref|YP_003777931.1| MetE/MetH family transcription ... 65 5e-12 gi|300313602|ref|YP_003777694.1| LysR family transcription regul... 65 7e-12 gi|300313922|ref|YP_003778014.1| LysR family transcription regul... 64 1e-11 >gi|300312870|ref|YP_003776962.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 312 Score = 493 bits (1269), Expect = e-141, Method: Compositional matrix adjust. Identities = 239/307 (77%), Positives = 271/307 (88%) Query: 1 MNLTLESLQILDMIDRKGSFAAAAVVLDRVPSALTYSVRKLEDDLDVLLFDRRGHRAKLT 60 MNLTLESL ILDMIDRKGSFAAAAV LDRVPSALTYSVRKLEDDLDVLLFDRRGHRA+LT Sbjct: 1 MNLTLESLLILDMIDRKGSFAAAAVALDRVPSALTYSVRKLEDDLDVLLFDRRGHRAQLT 60 Query: 61 PAGRELLTEGRHLLAAADDLEQRVKRTATGRETELRIVLNSIIPFANMLPLIAAFDREGG 120 PAG +LL EGRHLL AA+DLEQRVKRTATGRETEL IVLNS+IPF MLP+IAAFDRE Sbjct: 61 PAGLQLLQEGRHLLLAANDLEQRVKRTATGRETELHIVLNSLIPFDKMLPIIAAFDREQS 120 Query: 121 GTRLRFTPGVLSGTWDDMLAGRADLVIGATLDGPEIVRTSGRFQTRQLGTIDWIFAVAPD 180 GTRLRFTPGVL+G W+ ++ GRA+LVIG TLDGPE+VRTSGRFQ ++LG +DW+F VAP Sbjct: 121 GTRLRFTPGVLTGAWEKLIEGRANLVIGVTLDGPEVVRTSGRFQMQELGAVDWVFVVAPQ 180 Query: 181 HPLADAPEPLSPELVRRHRAVAVGDSSRNHPGLTMGLLAGQETLTVPTVAAKLQAQLAGL 240 HPLA EPLS ELVR HRA+AVGD+S++ P LTMGLL+GQETLTV TVA KLQAQLAGL Sbjct: 181 HPLAGVEEPLSAELVRSHRAIAVGDNSQSLPTLTMGLLSGQETLTVATVADKLQAQLAGL 240 Query: 241 GCGHLPRYWAAPYLASGALIEKQTQMSKPHENFLIAWPKAEQGKSLKWFLQHLSLPEVQR 300 GCGHLPR WA PYLASGAL+EKQT +KP++NF++AWPKAEQGKSLKWF+QHL+ P V++ Sbjct: 241 GCGHLPRIWAEPYLASGALVEKQTLAAKPNDNFMVAWPKAEQGKSLKWFIQHLAQPHVRQ 300 Query: 301 ALLSGAP 307 +L+ P Sbjct: 301 SLIGPVP 307 >gi|300311849|ref|YP_003775941.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 309 Score = 93.6 bits (231), Expect = 2e-20, Method: Compositional matrix adjust. Identities = 85/305 (27%), Positives = 140/305 (45%), Gaps = 28/305 (9%) Query: 3 LTLESLQILDMIDRKGSFAAAAVVLDRVPSALTYSVRKLEDDLDVLLFDRRGHRAKLTPA 62 L+L+ L++ + GSF AAA L R SA++Y++ LE+ L +LLFDR G+R +LT Sbjct: 6 LSLDQLRVFVQVADSGSFLAAARKLARAQSAVSYAIASLEEQLGLLLFDRSGYRPQLTAP 65 Query: 63 GRELLTEGRHLLAAADDLEQRVKRTATGRETELRIVLNSIIPFANMLPLIAAFDREGGGT 122 G LL + R +L D L+ R A G+E E+ + ++ P ++ L+ F Sbjct: 66 GEALLADARQVLDHVDSLQVRASSYARGQELEMALAVDVFFPLDCLVDLLQRFRAAFPAV 125 Query: 123 RLRFTPGVLSGTWDDMLAGRADLVIGATLDG--PEIVRTSGRFQTRQLGTIDWIFAVAPD 180 +R L + ++ GRA L I TL P ++R + L ++ + VAP Sbjct: 126 TVRLEVEALGAVAERVIDGRAMLGILGTLPTTPPNLMRIT-------LPSVRLVAVVAPH 178 Query: 181 HPLADAPEPLSPELVRRHRAVAVGDSSRNHPGLTMGLLAGQE-------TLTVPTVAAKL 233 HPLA ++ +++ + + + D S L A Q+ T + + K Sbjct: 179 HPLAKVKGRIAEKMLLQQTQLVLSDRSE--------LTARQDFSVHSRLTWRMSDLGTKH 230 Query: 234 QAQLAGLGCGHLPRYWAAPYLASGALIEKQTQMSKPHENFL----IAWPKAEQGKSLKWF 289 AG+G G++P + LA+G L+ T P L + P G +L W+ Sbjct: 231 ALLRAGMGWGNMPLHVVKEDLAAGRLVSISTIHHPPQGAELPIQCVYKPDHRAGPALSWW 290 Query: 290 LQHLS 294 L L+ Sbjct: 291 LDALA 295 >gi|300313839|ref|YP_003777931.1| MetE/MetH family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 295 Score = 65.5 bits (158), Expect = 5e-12, Method: Compositional matrix adjust. Identities = 73/255 (28%), Positives = 111/255 (43%), Gaps = 21/255 (8%) Query: 8 LQILDMIDRKGSFAAAAVVLDRVPSALTYSVRKLEDDLDVLLFDRRGHRAKLTPAGRELL 67 L I+ ++R+GS AAA VL SAL++S++KLE L ++ R G +LT AG+ LL Sbjct: 7 LSIVQEVERQGSLTAAAGVLHVTQSALSHSMKKLEQQLGTDIWLREGRHLRLTQAGQYLL 66 Query: 68 TEGRHLLAAADDLEQRVKRTATGRETELRIVLNSIIPFANML----PLIAAFDREGGGTR 123 +L E+R+++ A G LRI + + +L P +AA+ + Sbjct: 67 AVANRVLPQLSLAEERLRQFAQGERGALRIGMECHPCYQWLLKVVSPYLAAWPDVDVDVK 126 Query: 124 LRFTPGVLSGTWDDMLAGRADLVIGAT-LDGPEIVRTSGRFQTRQLGTIDWIFAVAPDHP 182 +F G + + DL++ LD P +V F Q + VA DHP Sbjct: 127 QKFQFGGIGA----LFGYEIDLLVTPDPLDKPGLV-FEPVFDYEQ------VLVVASDHP 175 Query: 183 LADA----PEPLSPELVRRHRAVAVGDSSRNHPGLTMGLLAGQETLTVPTVAAKLQAQLA 238 LAD P LS E++ + V V L + + T+ T LQ + Sbjct: 176 LADVDYVKPRQLSNEVLVTY-PVPVDRLDIYTQFLAPAGIVPRRHKTIETTDIMLQMVAS 234 Query: 239 GLGCGHLPRYWAAPY 253 G G LPR+ Y Sbjct: 235 GRGVAALPRWLVLEY 249 >gi|300313602|ref|YP_003777694.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 65.1 bits (157), Expect = 7e-12, Method: Compositional matrix adjust. Identities = 63/202 (31%), Positives = 100/202 (49%), Gaps = 20/202 (9%) Query: 1 MNLTLESLQILDMIDRKGSFAAAAVVLDRVPSALTYSVRKLEDDLDVLLFDRRGHRAKLT 60 M +TL LQI + + GS AAA ++ SA + ++ +LE L V LFDR G R L Sbjct: 1 MKITLRQLQIFLAVAQSGSTTAAADLVALSQSAASAALNELEHLLGVQLFDRVGKRLVLN 60 Query: 61 PAGRELLTEGRHLLAAADDLEQRVKRTATGRETELRIVLNSIIPFANMLP-LIAAFDREG 119 +GR+LL + RH+L AA +E++ G +EL I ++ I + MLP +IAA+ ++ Sbjct: 61 DSGRQLLPQARHMLDAAQTIERQFSDPEAG--SELHIGASTTIG-SYMLPAMIAAYRKDH 117 Query: 120 GGTRLRFTPGVLSGTWDDMLAGRADLVIGATLDGPEIVRTSGRFQTRQLGTIDW-----I 174 G R+R +++ T D + D V+ +D I G + W I Sbjct: 118 AGARVR---ALVANTADIV-----DAVVNFEVDAGLI---EGPCHADDVEVEPWMMDELI 166 Query: 175 FAVAPDHPLADAPEPLSPELVR 196 AP HPL + ++ + +R Sbjct: 167 VVAAPRHPLVKSGRKITLKRLR 188 >gi|300313922|ref|YP_003778014.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 308 Score = 64.3 bits (155), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 73/272 (26%), Positives = 107/272 (39%), Gaps = 24/272 (8%) Query: 5 LESLQILDMIDRKGSFAAAAVVLDRVPSALTYSVRKLEDDLDVLLFDRRGHRAKLTPAGR 64 L ++Q+ + GS +AAA LD ++ V +LED + L R R LTPAG Sbjct: 4 LMAMQVFVTVVDSGSLSAAAEQLDLSRPVVSRYVAELEDWVGARLLHRTTRRLSLTPAGN 63 Query: 65 ELLTEGRHLLAAADDLEQRVKRTATGRETELRIVLNSIIPFANMLPLIAAFDREGGGTRL 124 ELL R +L ++D+ + LRI ++ ++ + + R G + Sbjct: 64 ELLPRCRQMLEYSEDMRHALDAPDETPRGLLRITASTSFAQTQLIQAVVEYGRRYPGVAV 123 Query: 125 RFTPGVLSGTWDDMLAGRADLVIGATLDGPEIVRTSGRFQTRQLGTIDWIFAVAPD---- 180 L T +++ R DL I T R R LG I PD Sbjct: 124 DLL--ALDRTV-NLVEERIDLAIRMT------NRLEPNLIARPLGVCRSIICATPDYLAR 174 Query: 181 HPLADAPEPLSPELVRRHRAVA-----------VGDSSRNHPGLTMGLLAGQETLTVPTV 229 H L E L+ H V S R +A +++ V Sbjct: 175 HGLPRKVEDLALHNCLTHSYVGRSLWQFDPKKKKARSGRGASAAKPQSVAVGGSISANEV 234 Query: 230 AAKLQAQLAGLGCGHLPRYWAAPYLASGALIE 261 LQA LAG+G GH+P Y AP +ASG L++ Sbjct: 235 TVLLQAVLAGVGIGHMPAYTVAPLVASGQLVQ 266 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 0.136 0.406 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: 1,013,510 Number of extensions: 44293 Number of successful extensions: 220 Number of sequences better than 1.0e-08: 10 Number of HSP's gapped: 224 Number of HSP's successfully gapped: 10 Length of query: 310 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 225 Effective length of database: 1,217,395 Effective search space: 273913875 Effective search space used: 273913875 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: 130 (54.7 bits)