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= 0013.0028.p (228 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312431|ref|YP_003776523.1| two component LuxR family trans... 328 2e-91 gi|300312077|ref|YP_003776169.1| response regulator containing a... 105 3e-24 gi|300310532|ref|YP_003774624.1| virulence regulator protein [He... 94 9e-21 gi|300311885|ref|YP_003775977.1| LuxR family two component respo... 89 2e-19 gi|300310869|ref|YP_003774961.1| response regulator for colanic ... 89 4e-19 >gi|300312431|ref|YP_003776523.1| two component LuxR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 282 Score = 328 bits (842), Expect = 2e-91, Method: Compositional matrix adjust. Identities = 161/242 (66%), Positives = 196/242 (80%), Gaps = 17/242 (7%) Query: 4 WTATKAIRIALLDDHAVVRHGLAARLTEESDFEVVGAYAASKDMMSALRALPADILLIDY 63 WT +RIALLDDHAVVR+GLAARL EE D EVVG++A SK++M+ALRA PAD+LLIDY Sbjct: 41 WTLASRMRIALLDDHAVVRYGLAARLAEEPDLEVVGSFATSKELMTALRASPADLLLIDY 100 Query: 64 SLGANDIDGLNLIRALKVRFPDSKILVSSSHYNPATVALAMRAGARGFVGKEQELSELIA 123 SLG+NDIDGLNLIRAL+VRFP SKILV+S+H NPATVALAM+AGARGFVGK QEL EL+ Sbjct: 101 SLGSNDIDGLNLIRALRVRFPRSKILVTSAHNNPATVALAMKAGARGFVGKSQELGELVQ 160 Query: 124 AVRSVAVGRVHLNPFMAAEISSMLSSNGSD-----------------EESPNGDSLTDNV 166 A+R+V+VGR +LN MA E+++ML+S+ P+ DSL++ Sbjct: 161 AIRTVSVGREYLNAAMARELTAMLASDSPTPAPEGGPPQVRPPRRKRNSPPSSDSLSEMP 220 Query: 167 ELSPREREVLRCCLEGLSVTQIAEKFARSVKTISGQKQAAFRKLGVRNDNELFKIQHQLQ 226 LSPREREVLRCCL+GLSVT IA+KFARSVKTISGQKQ+AFRKLGVR+DNELFKI++Q++ Sbjct: 221 SLSPREREVLRCCLDGLSVTAIADKFARSVKTISGQKQSAFRKLGVRSDNELFKIEYQIK 280 Query: 227 DI 228 D+ Sbjct: 281 DL 282 >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 = 105 bits (263), Expect = 3e-24, Method: Compositional matrix adjust. Identities = 68/217 (31%), Positives = 117/217 (53%), Gaps = 11/217 (5%) Query: 2 MTWTATKAIRIALLDDHAVVRHGLAARLTEESDFEVVGAYAASKDMMSALRALPADILLI 61 M+ T AI++ + DDHA+VR GL D V G A + + R D+LL+ Sbjct: 1 MSKKVTAAIKVLIADDHAIVREGLRQICAGSKDIMVAGNAANGLEAIKLAREGNGDVLLL 60 Query: 62 DYSLGANDIDGLNLIRALKVRFPDSKILVSSSHYNPATVALAMRAGARGFVGKEQELSEL 121 D L D +G+++++ ++ P+ +L+ S H A++AGA GF+ K+ +EL Sbjct: 61 DIVL--PDRNGIDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQAAPAEL 118 Query: 122 IAAVRSVAVGRVHLNPFMAAEISSMLSSNGSDEESPNGDSLTDNVELSPREREVLRCCLE 181 +AA+R A GR +++P +A E+++ + G D E+P ++L+D RE + + Sbjct: 119 LAAIRQAASGRKYVSPSLAQELANQI---GFDHETPLHETLSD------REYQTMVMIAS 169 Query: 182 GLSVTQIAEKFARSVKTISGQKQAAFRKLGVRNDNEL 218 G +V+ IA + SVKTIS + K+ +R++ EL Sbjct: 170 GKTVSDIAAELTLSVKTISMYRSRVLSKMKMRHNAEL 206 >gi|300310532|ref|YP_003774624.1| virulence regulator protein [Herbaspirillum seropedicae SmR1] Length = 209 Score = 94.0 bits (232), Expect = 9e-21, Method: Compositional matrix adjust. Identities = 61/219 (27%), Positives = 119/219 (54%), Gaps = 14/219 (6%) Query: 11 RIALLDDHAVVRHGLAARLTEESDFEVVGAYAASKDMMSALRALPADILLIDYSLGANDI 70 +I ++DDHAVVR G+ ++E E+ G + +++ + +R DI+L+D ++ D Sbjct: 3 KILVVDDHAVVRAGVHHFISEIPSMEIGGEASTAEEAIRLVRTQDWDIVLLDIAMP--DK 60 Query: 71 DGLNLIRALKVRFPDSKILVSSSHYNPATVALAMRAGARGFVGKEQELSELIAAVRSVAV 130 G+ +++ +K P+ +L+ S H +R+GA G+V KE +EL+ A+ ++ Sbjct: 61 SGVEVLKQIKREKPELPVLMLSMHPESRYAVQVLRSGASGYVQKEALATELVNAINTILR 120 Query: 131 GRVHLNPFMAAEISSMLSSNGSDEESPNGDSLTDNVELSPREREVLRCCLEGLSVTQIAE 190 G + +++ ++ +L+S D E P ++ LS RE E+ +G VTQIA+ Sbjct: 121 G----HKYISYGVAELLTSEPVDSEKPLHET------LSQREYEIFYKLGQGQGVTQIAD 170 Query: 191 KFARSVKTISGQKQAAFRKLGVRNDNEL--FKIQHQLQD 227 + SVKT+S + +K+ + N+ ++ + I++ L D Sbjct: 171 ELCLSVKTVSTYRSRVLQKMSMTNNADIIYYAIKNNLID 209 >gi|300311885|ref|YP_003775977.1| LuxR family two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 216 Score = 89.4 bits (220), Expect = 2e-19, Method: Compositional matrix adjust. Identities = 62/208 (29%), Positives = 107/208 (51%), Gaps = 17/208 (8%) Query: 11 RIALLDDHAVVRHGLAARLTEESDFEVVGAYAASKDMMSALRALPADILLIDYSLGANDI 70 RI L DDHA+VR G+ A LT EVVG + +++ + L D++L+D ++ + Sbjct: 4 RIMLADDHALVRSGIKALLTAMPGVEVVGEASDGAEVIEMIPQLKPDLVLLDIAM--KGM 61 Query: 71 DGLNLIRALKVRFPDSKILVSSSHYNPATVALAMRAGARGFVGKEQELSELIAAVRSVAV 130 +GL +R L+ +P + L+ S + + V A+ AGA G++ K+ +EL A+ V Sbjct: 62 NGLEALRRLRGEYPTIRFLMLSMYGSEEYVMQALNAGANGYLFKDSAATELEKALYEVKH 121 Query: 131 GRVHLNPFMAAE----ISSMLSSNGSDEESPNGDSLTDNVELSPREREVLRCCLEGLSVT 186 GR +L+ ++ E ++ NG+ E L+PR+RE+L+ EG + Sbjct: 122 GRQYLDSHISREALDNYMKRVAQNGTPVEV-----------LTPRQREILQLIAEGNNTK 170 Query: 187 QIAEKFARSVKTISGQKQAAFRKLGVRN 214 +IA + S KTI + +L +R+ Sbjct: 171 EIAYQLNVSAKTIETHRAQLMERLDIRD 198 >gi|300310869|ref|YP_003774961.1| response regulator for colanic capsule biosynthesis protein [Herbaspirillum seropedicae SmR1] Length = 221 Score = 88.6 bits (218), Expect = 4e-19, Method: Compositional matrix adjust. Identities = 61/217 (28%), Positives = 106/217 (48%), Gaps = 13/217 (5%) Query: 8 KAIRIALLDDHAVVRHGLAARLTEESDFEVVGAYAASKDMMSALRALPADILLIDYSLG- 66 K + +A+ DDH +V L L + + +D+++AL+ P +I++ D+++ Sbjct: 5 KVLHVAIADDHPIVLGALRNELARLPEIRIDLEVDTGEDLINALKRTPCEIVITDFAMPN 64 Query: 67 --ANDIDGLNLIRALKVRFPDSKILVSSSHYNPATVALAMRAGARGFVGKEQELSELIAA 124 +++ DG L++ +K P +K++V ++ N A + R G + K ++ ELI A Sbjct: 65 EESDESDGFALVKRIKAEHPSTKLIVYTAMNNGAVIRRLYRMGVFAVINKREKPDELINA 124 Query: 125 VRSVAVGRVHLNPFMAAEISSMLSSNGSDEES-PNGDSLTDNVELSPREREVLRCCLEGL 183 + + P +S G E S GD EL+ E EV+R +EG Sbjct: 125 CLATQSSKQLYFP---------VSLRGELEMSWAQGDGFAATRELTQSELEVVRLFVEGQ 175 Query: 184 SVTQIAEKFARSVKTISGQKQAAFRKLGVRNDNELFK 220 S+ +I + +R+ TIS K A RKLG+ +D EL K Sbjct: 176 SLGEICVRLSRTPSTISTHKNNAMRKLGLSSDAELIK 212 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 0.131 0.360 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: 627,177 Number of extensions: 22925 Number of successful extensions: 116 Number of sequences better than 1.0e-08: 9 Number of HSP's gapped: 107 Number of HSP's successfully gapped: 9 Length of query: 228 Length of database: 1,619,870 Length adjustment: 82 Effective length of query: 146 Effective length of database: 1,231,600 Effective search space: 179813600 Effective search space used: 179813600 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: 129 (54.3 bits)