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= 0001.3563.p (216 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312940|ref|YP_003777032.1| nitrate/nitrite response regula... 367 e-103 gi|300311885|ref|YP_003775977.1| LuxR family two component respo... 129 2e-31 gi|300311281|ref|YP_003775373.1| LuxR family response regulator ... 123 1e-29 gi|300312077|ref|YP_003776169.1| response regulator containing a... 111 6e-26 gi|300310532|ref|YP_003774624.1| virulence regulator protein [He... 106 2e-24 >gi|300312940|ref|YP_003777032.1| nitrate/nitrite response regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 219 Score = 367 bits (941), Expect = e-103, Method: Compositional matrix adjust. Identities = 185/218 (84%), Positives = 201/218 (92%), Gaps = 3/218 (1%) Query: 1 MSIRILLVDDHTLFRSGIRLLLQRHPEFEVVGEAVDGLDGVKRARQLRPDVVLMDLNMPG 60 M+IRILLVDDHTLFRSGIRLLLQRHP+ +VVGEAVDGLDGVKRA QLRPDVVLMDLNMPG Sbjct: 1 MAIRILLVDDHTLFRSGIRLLLQRHPDIDVVGEAVDGLDGVKRALQLRPDVVLMDLNMPG 60 Query: 61 LSGLEAMQLIVEDLPETAVLMLSVSEEAEDLSTALHNGAAGYLLKNIEADYLVQAIKRAA 120 LSGLEAMQLIV+DLPETAVLMLSVSEEA+DL+TALHNGA GYLLKNIEADYLVQ+IKRAA Sbjct: 61 LSGLEAMQLIVQDLPETAVLMLSVSEEADDLTTALHNGARGYLLKNIEADYLVQSIKRAA 120 Query: 121 AGEPVISEAMTAKLVMQFR--AARPGV-AGDMKEKLTARERETMRCVAQGQSNKEIARSL 177 AGEPVISE+MTAKLVMQ R A P A + +KLTARER TM C+A+GQSNKEIARSL Sbjct: 121 AGEPVISESMTAKLVMQLRAGAGNPAASAAEPTDKLTARERATMVCIARGQSNKEIARSL 180 Query: 178 DVAESTVKIHVQNILKKLNLSSRVQIAVYAVEHGLDKT 215 +VAESTVKIHVQN+L+KL LSSRVQIAVYAVEHGLDK+ Sbjct: 181 EVAESTVKIHVQNLLRKLQLSSRVQIAVYAVEHGLDKS 218 >gi|300311885|ref|YP_003775977.1| LuxR family two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 216 Score = 129 bits (324), Expect = 2e-31, Method: Compositional matrix adjust. Identities = 78/216 (36%), Positives = 124/216 (57%), Gaps = 2/216 (0%) Query: 1 MSIRILLVDDHTLFRSGIRLLLQRHPEFEVVGEAVDGLDGVKRARQLRPDVVLMDLNMPG 60 M RI+L DDH L RSGI+ LL P EVVGEA DG + ++ QL+PD+VL+D+ M G Sbjct: 1 MLTRIMLADDHALVRSGIKALLTAMPGVEVVGEASDGAEVIEMIPQLKPDLVLLDIAMKG 60 Query: 61 LSGLEAMQLIVEDLPETAVLMLSVSEEAEDLSTALHNGAAGYLLKNIEADYLVQAIKRAA 120 ++GLEA++ + + P LMLS+ E + AL+ GA GYL K+ A L +A+ Sbjct: 61 MNGLEALRRLRGEYPTIRFLMLSMYGSEEYVMQALNAGANGYLFKDSAATELEKALYEVK 120 Query: 121 AGEPVISEAMTAKLVMQFRAARPGVAGDMKEKLTARERETMRCVAQGQSNKEIARSLDVA 180 G + ++ + + + R G E LT R+RE ++ +A+G + KEIA L+V+ Sbjct: 121 HGRQYLDSHISREALDNY-MKRVAQNGTPVEVLTPRQREILQLIAEGNNTKEIAYQLNVS 179 Query: 181 ESTVKIHVQNILKKLNLSSRVQIAVYAVEHGLDKTP 216 T++ H ++++L++ + YA+ G+ TP Sbjct: 180 AKTIETHRAQLMERLDIRDVPGLVRYAIRTGI-ATP 214 >gi|300311281|ref|YP_003775373.1| LuxR family response regulator protein [Herbaspirillum seropedicae SmR1] Length = 217 Score = 123 bits (308), Expect = 1e-29, Method: Compositional matrix adjust. Identities = 77/205 (37%), Positives = 117/205 (57%), Gaps = 9/205 (4%) Query: 5 ILLVDDHTLFRSGIRLLLQRHPEFEVVGEAVDGLDGVKRARQLRPDVVLMDLNMPGLSGL 64 I+L+DDH L R G+R L+ P EVV EA + + A D+ LMD+NM G++G+ Sbjct: 14 IMLIDDHPLVRDGLRARLETVPGLEVVAEAGHADEALAAAAAQEIDLTLMDINMRGINGI 73 Query: 65 EAMQLIVEDLPETAVLMLSVSEEAEDLSTALHNGAAGYLLKNIEADYLVQAIKRAAAGEP 124 E L PE AVL+LS+ ++AE + ++ GA GY+LK+ + +V AI+ +G Sbjct: 74 ELTALFHARHPEIAVLILSMHDKAEYVMQSIQAGARGYVLKDAPSQDIVHAIETVRSGGI 133 Query: 125 VISEAMTAKLVMQFRAARPGVAGDMKEKLTARERETMRCVAQGQSNKEIARSLDVAESTV 184 S A+ +L +E LT RERE + +A G+SNK+IAR LD++ TV Sbjct: 134 YYSAALARQLTQPLPP---------RELLTQREREVLMHIANGESNKQIARELDLSVRTV 184 Query: 185 KIHVQNILKKLNLSSRVQIAVYAVE 209 + H NI +KLN+ + ++ +AVE Sbjct: 185 ETHRLNIKRKLNIDGQAELIKFAVE 209 >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 = 111 bits (277), Expect = 6e-26, Method: Compositional matrix adjust. Identities = 66/213 (30%), Positives = 121/213 (56%), Gaps = 7/213 (3%) Query: 2 SIRILLVDDHTLFRSGIRLLLQRHPEFEVVGEAVDGLDGVKRARQLRPDVVLMDLNMPGL 61 +I++L+ DDH + R G+R + + V G A +GL+ +K AR+ DV+L+D+ +P Sbjct: 8 AIKVLIADDHAIVREGLRQICAGSKDIMVAGNAANGLEAIKLAREGNGDVLLLDIVLPDR 67 Query: 62 SGLEAMQLIVEDLPETAVLMLSVSEEAEDLSTALHNGAAGYLLKNIEADYLVQAIKRAAA 121 +G++ ++ I ++ PE VL+LS+ E + AL GAAG+L K L+ AI++AA+ Sbjct: 68 NGIDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQAAPAELLAAIRQAAS 127 Query: 122 GEPVISEAMTAKLVMQ--FRAARPGVAGDMKEKLTARERETMRCVAQGQSNKEIARSLDV 179 G +S ++ +L Q F P + E L+ RE +TM +A G++ +IA L + Sbjct: 128 GRKYVSPSLAQELANQIGFDHETP-----LHETLSDREYQTMVMIASGKTVSDIAAELTL 182 Query: 180 AESTVKIHVQNILKKLNLSSRVQIAVYAVEHGL 212 + T+ ++ +L K+ + ++ YA+++ L Sbjct: 183 SVKTISMYRSRVLSKMKMRHNAELTHYALKNAL 215 >gi|300310532|ref|YP_003774624.1| virulence regulator protein [Herbaspirillum seropedicae SmR1] Length = 209 Score = 106 bits (264), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 67/210 (31%), Positives = 110/210 (52%), Gaps = 6/210 (2%) Query: 4 RILLVDDHTLFRSGIRLLLQRHPEFEVVGEAVDGLDGVKRARQLRPDVVLMDLNMPGLSG 63 +IL+VDDH + R+G+ + P E+ GEA + ++ R D+VL+D+ MP SG Sbjct: 3 KILVVDDHAVVRAGVHHFISEIPSMEIGGEASTAEEAIRLVRTQDWDIVLLDIAMPDKSG 62 Query: 64 LEAMQLIVEDLPETAVLMLSVSEEAEDLSTALHNGAAGYLLKNIEADYLVQAIKRAAAGE 123 +E ++ I + PE VLMLS+ E+ L +GA+GY+ K A LV AI G Sbjct: 63 VEVLKQIKREKPELPVLMLSMHPESRYAVQVLRSGASGYVQKEALATELVNAINTILRGH 122 Query: 124 PVISEAMTAKLVMQ-FRAARPGVAGDMKEKLTARERETMRCVAQGQSNKEIARSLDVAES 182 IS + L + + +P + E L+ RE E + QGQ +IA L ++ Sbjct: 123 KYISYGVAELLTSEPVDSEKP-----LHETLSQREYEIFYKLGQGQGVTQIADELCLSVK 177 Query: 183 TVKIHVQNILKKLNLSSRVQIAVYAVEHGL 212 TV + +L+K+++++ I YA+++ L Sbjct: 178 TVSTYRSRVLQKMSMTNNADIIYYAIKNNL 207 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 0.133 0.357 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: 584,849 Number of extensions: 21020 Number of successful extensions: 226 Number of sequences better than 1.0e-08: 21 Number of HSP's gapped: 230 Number of HSP's successfully gapped: 21 Length of query: 216 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 135 Effective length of database: 1,236,335 Effective search space: 166905225 Effective search space used: 166905225 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)