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= 0001.2773.p (217 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312077|ref|YP_003776169.1| response regulator containing a... 415 e-117 gi|300310532|ref|YP_003774624.1| virulence regulator protein [He... 207 5e-55 gi|300311885|ref|YP_003775977.1| LuxR family two component respo... 120 7e-29 gi|300312940|ref|YP_003777032.1| nitrate/nitrite response regula... 107 5e-25 gi|300311281|ref|YP_003775373.1| LuxR family response regulator ... 103 1e-23 >gi|300312077|ref|YP_003776169.1| response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 217 Score = 415 bits (1066), Expect = e-117, Method: Compositional matrix adjust. Identities = 203/217 (93%), Positives = 213/217 (98%) Query: 1 MSKKATAAIKVLIADDHAIVREGLRQICAVSKDIVVAGNAANGLEAIKLAREGDGDVMLL 60 MSKK TAAIKVLIADDHAIVREGLRQICA SKDI+VAGNAANGLEAIKLAREG+GDV+LL Sbjct: 1 MSKKVTAAIKVLIADDHAIVREGLRQICAGSKDIMVAGNAANGLEAIKLAREGNGDVLLL 60 Query: 61 DIVLPDRNGIDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQASPSEVIA 120 DIVLPDRNGIDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQA+P+E++A Sbjct: 61 DIVLPDRNGIDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQAAPAELLA 120 Query: 121 AIRQAAAGRKYVSPSLAQELANQIGFDHDTPLHETLSDREYQTMVMIASGKTVSDIAAEL 180 AIRQAA+GRKYVSPSLAQELANQIGFDH+TPLHETLSDREYQTMVMIASGKTVSDIAAEL Sbjct: 121 AIRQAASGRKYVSPSLAQELANQIGFDHETPLHETLSDREYQTMVMIASGKTVSDIAAEL 180 Query: 181 LLSVKTISMYRSRVLAKMKMRHNAELTHYALKNDLVE 217 LSVKTISMYRSRVL+KMKMRHNAELTHYALKN LVE Sbjct: 181 TLSVKTISMYRSRVLSKMKMRHNAELTHYALKNALVE 217 >gi|300310532|ref|YP_003774624.1| virulence regulator protein [Herbaspirillum seropedicae SmR1] Length = 209 Score = 207 bits (528), Expect = 5e-55, Method: Compositional matrix adjust. Identities = 96/208 (46%), Positives = 149/208 (71%), Gaps = 1/208 (0%) Query: 10 KVLIADDHAIVREGLRQICAVSKDIVVAGNAANGLEAIKLAREGDGDVMLLDIVLPDRNG 69 K+L+ DDHA+VR G+ + + + G A+ EAI+L R D D++LLDI +PD++G Sbjct: 3 KILVVDDHAVVRAGVHHFISEIPSMEIGGEASTAEEAIRLVRTQDWDIVLLDIAMPDKSG 62 Query: 70 IDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQASPSEVIAAIRQAAAGR 129 +++LKQI++E+PELPVL+LS+H E +YA++ L++GA+G++ K+A +E++ AI G Sbjct: 63 VEVLKQIKREKPELPVLMLSMHPESRYAVQVLRSGASGYVQKEALATELVNAINTILRGH 122 Query: 130 KYVSPSLAQELANQIGFDHDTPLHETLSDREYQTMVMIASGKTVSDIAAELLLSVKTISM 189 KY+S +A+ L ++ D + PLHETLS REY+ + G+ V+ IA EL LSVKT+S Sbjct: 123 KYISYGVAELLTSE-PVDSEKPLHETLSQREYEIFYKLGQGQGVTQIADELCLSVKTVST 181 Query: 190 YRSRVLAKMKMRHNAELTHYALKNDLVE 217 YRSRVL KM M +NA++ +YA+KN+L++ Sbjct: 182 YRSRVLQKMSMTNNADIIYYAIKNNLID 209 >gi|300311885|ref|YP_003775977.1| LuxR family two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 216 Score = 120 bits (302), Expect = 7e-29, Method: Compositional matrix adjust. Identities = 65/209 (31%), Positives = 129/209 (61%), Gaps = 4/209 (1%) Query: 10 KVLIADDHAIVREGLRQICAVSKDIVVAGNAANGLEAIKLAREGDGDVMLLDIVLPDRNG 69 ++++ADDHA+VR G++ + + V G A++G E I++ + D++LLDI + NG Sbjct: 4 RIMLADDHALVRSGIKALLTAMPGVEVVGEASDGAEVIEMIPQLKPDLVLLDIAMKGMNG 63 Query: 70 IDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQASPSEVIAAIRQAAAGR 129 ++ L+++R E P + L+LS++ ++Y ++AL AGA G+L K ++ +E+ A+ + GR Sbjct: 64 LEALRRLRGEYPTIRFLMLSMYGSEEYVMQALNAGANGYLFKDSAATELEKALYEVKHGR 123 Query: 130 KYVSPSLAQE-LANQIG--FDHDTPLHETLSDREYQTMVMIASGKTVSDIAAELLLSVKT 186 +Y+ +++E L N + + TP+ E L+ R+ + + +IA G +IA +L +S KT Sbjct: 124 QYLDSHISREALDNYMKRVAQNGTPV-EVLTPRQREILQLIAEGNNTKEIAYQLNVSAKT 182 Query: 187 ISMYRSRVLAKMKMRHNAELTHYALKNDL 215 I +R++++ ++ +R L YA++ + Sbjct: 183 IETHRAQLMERLDIRDVPGLVRYAIRTGI 211 >gi|300312940|ref|YP_003777032.1| nitrate/nitrite response regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 219 Score = 107 bits (268), Expect = 5e-25, Method: Compositional matrix adjust. Identities = 67/214 (31%), Positives = 119/214 (55%), Gaps = 6/214 (2%) Query: 8 AIKVLIADDHAIVREGLRQICAVSKDIVVAGNAANGLEAIKLAREGDGDVMLLDIVLPDR 67 AI++L+ DDH + R G+R + DI V G A +GL+ +K A + DV+L+D+ +P Sbjct: 2 AIRILLVDDHTLFRSGIRLLLQRHPDIDVVGEAVDGLDGVKRALQLRPDVVLMDLNMPGL 61 Query: 68 NGIDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQASPSEVIAAIRQAAA 127 +G++ ++ I ++ PE VL+LS+ E AL GA G+L K ++ +I++AAA Sbjct: 62 SGLEAMQLIVQDLPETAVLMLSVSEEADDLTTALHNGARGYLLKNIEADYLVQSIKRAAA 121 Query: 128 GRKYVSPSLAQELANQIGFDHDTPL------HETLSDREYQTMVMIASGKTVSDIAAELL 181 G +S S+ +L Q+ P + L+ RE TMV IA G++ +IA L Sbjct: 122 GEPVISESMTAKLVMQLRAGAGNPAASAAEPTDKLTARERATMVCIARGQSNKEIARSLE 181 Query: 182 LSVKTISMYRSRVLAKMKMRHNAELTHYALKNDL 215 ++ T+ ++ +L K+++ ++ YA+++ L Sbjct: 182 VAESTVKIHVQNLLRKLQLSSRVQIAVYAVEHGL 215 >gi|300311281|ref|YP_003775373.1| LuxR family response regulator protein [Herbaspirillum seropedicae SmR1] Length = 217 Score = 103 bits (258), Expect = 1e-23, Method: Compositional matrix adjust. Identities = 65/203 (32%), Positives = 115/203 (56%), Gaps = 6/203 (2%) Query: 11 VLIADDHAIVREGLRQICAVSKDIVVAGNAANGLEAIKLAREGDGDVMLLDIVLPDRNGI 70 +++ DDH +VR+GLR + V A + EA+ A + D+ L+DI + NGI Sbjct: 14 IMLIDDHPLVRDGLRARLETVPGLEVVAEAGHADEALAAAAAQEIDLTLMDINMRGINGI 73 Query: 71 DILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQASPSEVIAAIRQAAAGRK 130 ++ PE+ VLILS+H + +Y +++++AGA G++ K A +++ AI +G Sbjct: 74 ELTALFHARHPEIAVLILSMHDKAEYVMQSIQAGARGYVLKDAPSQDIVHAIETVRSGGI 133 Query: 131 YVSPSLAQELANQIGFDHDTPLHETLSDREYQTMVMIASGKTVSDIAAELLLSVKTISMY 190 Y S +LA++L + P E L+ RE + ++ IA+G++ IA EL LSV+T+ + Sbjct: 134 YYSAALARQLTQPL------PPRELLTQREREVLMHIANGESNKQIARELDLSVRTVETH 187 Query: 191 RSRVLAKMKMRHNAELTHYALKN 213 R + K+ + AEL +A+++ Sbjct: 188 RLNIKRKLNIDGQAELIKFAVES 210 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 0.318 0.132 0.354 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: 611,372 Number of extensions: 24605 Number of successful extensions: 179 Number of sequences better than 1.0e-08: 19 Number of HSP's gapped: 197 Number of HSP's successfully gapped: 19 Length of query: 217 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 136 Effective length of database: 1,236,335 Effective search space: 168141560 Effective search space used: 168141560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 128 (53.9 bits)