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= 0001.3646.p (448 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313028|ref|YP_003777120.1| two component response regulato... 807 0.0 gi|300310565|ref|YP_003774657.1| response regulator containing a... 115 6e-27 gi|300314016|ref|YP_003778108.1| two component transcription reg... 74 2e-14 gi|300313282|ref|YP_003777374.1| HD-GYP domain-containing protei... 74 3e-14 gi|300313916|ref|YP_003778008.1| two component response regulato... 72 1e-13 >gi|300313028|ref|YP_003777120.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 807 bits (2084), Expect = 0.0, Method: Compositional matrix adjust. Identities = 391/448 (87%), Positives = 431/448 (96%) Query: 1 MSAIHSQEIQTLQQADPFALPPPCVLLVDDEQSILSALKRTFRPQGYQLLTATSAEAGLD 60 MSAIHS EI TLQQADPFALPPPCVLLVDDEQSILSALKRTFRPQGY+L+ ATSAEA L+ Sbjct: 1 MSAIHSHEIDTLQQADPFALPPPCVLLVDDEQSILSALKRTFRPQGYRLIMATSAEAALE 60 Query: 61 ILASAEVDLVISDMRMPGMNGAQFLAQVRQRWPATMRILLTGYSEIGSTISAINDGGINH 120 ++A++EVDLVISDMRMPGMNGAQFLA+VRQ+WP+TMRILLTGYSEIGSTISAINDGGINH Sbjct: 61 MMAASEVDLVISDMRMPGMNGAQFLAKVRQQWPSTMRILLTGYSEIGSTISAINDGGINH 120 Query: 121 YLAKPWDDRELLMTVTHALEEQQLRKQKMALERKVREQNLQLADFNRQLERQVQARTEEL 180 YL+KPWDDRELL+ V HALEEQQLRKQKMALERKVREQNLQLADFNRQLERQVQ+RTEEL Sbjct: 121 YLSKPWDDRELLLIVAHALEEQQLRKQKMALERKVREQNLQLADFNRQLERQVQSRTEEL 180 Query: 181 RQTVMFLESGQEEEQKAFLAMMQVFSDISELRAGLATGQSARVARWCEQLSLRMGMTSHH 240 RQTVMFLES QEEEQK+FL+M++VFSDISELRAGLATGQSARVARWCEQL+LRMGMT+HH Sbjct: 181 RQTVMFLESAQEEEQKSFLSMLRVFSDISELRAGLATGQSARVARWCEQLALRMGMTTHH 240 Query: 241 AKDAMMAGMLHGIGKLDLSDELVRKPIEKMSSEELQRFLWHPVKGQMLLTPIPTLAEAGE 300 A+D MMAGMLHGIGKL+L DELVRKPIEKM+S+E+QRFLWHPV+GQMLLTPIP+LAE+GE Sbjct: 241 ARDTMMAGMLHGIGKLELPDELVRKPIEKMNSDEVQRFLWHPVRGQMLLTPIPSLAESGE 300 Query: 301 IIRHQHERYDGRGVPESLSGDAIPLGSRILAVVRDFEGLCNGGITSNNVSVEKALAMLRT 360 IIRHQHERYDGRGVPESLSGDAIPLG+RILAVVRDFEGLCNGGITS N S EKAL+MLR Sbjct: 301 IIRHQHERYDGRGVPESLSGDAIPLGARILAVVRDFEGLCNGGITSLNASPEKALSMLRA 360 Query: 361 HANHRYDPLVVETFIAMMEEQRLALEQQTRLLSPQELRVGMKLAEDLRTRSGVLLLNKEH 420 HA HRYDPLVVE+FIAMMEEQ++ALEQQTRLL+ QELRVGMKLAEDLRT+SGVLLLNK+H Sbjct: 361 HAGHRYDPLVVESFIAMMEEQQMALEQQTRLLATQELRVGMKLAEDLRTKSGVLLLNKDH 420 Query: 421 ILDEAILTRLRRFELIDEMPLKARILLH 448 +LD+A+L RLRRFE +DEMPLKARI+LH Sbjct: 421 VLDDALLARLRRFEQLDEMPLKARIVLH 448 >gi|300310565|ref|YP_003774657.1| response regulator containing a CheY-like receiver domain and an HD-GYP domain [Herbaspirillum seropedicae SmR1] Length = 348 Score = 115 bits (289), Expect = 6e-27, Method: Compositional matrix adjust. Identities = 103/363 (28%), Positives = 171/363 (47%), Gaps = 39/363 (10%) Query: 25 VLLVDDEQSILSALKRTFR--PQGYQLLTATSAEAGLDILASAEVDLVISDMRMPGMNGA 82 +L+VDD+++ LS PQ ++ T A LD DL++ D MPGM+G Sbjct: 6 ILIVDDDKTNLSLFSHMLGQVPQ-TRIDTCADARQALDWCQEHAPDLILLDYMMPGMDGL 64 Query: 83 QFLAQVRQRWPATMRILLTGYSEIGSTI--SAINDGGINHYLAKPWDDRELLMTVTHALE 140 FL++ R M ++ +++G + +A+ N +L+KP + ELL V + L Sbjct: 65 DFLSRFRAMPGQEMTPVIMITADMGLQVRHTALQMSA-NDFLSKPVNRVELLARVKNMLA 123 Query: 141 EQQLRKQKMALERKVREQNLQLADFNRQLERQVQARTEELRQTVMFLESGQEEEQKAFLA 200 +R+ ++A+ +K+ + Q+++QV+ + L+S LA Sbjct: 124 ---MRRSQLAMSQKIDT-------LSEQVDQQVR------HSDTLALDSVD------LLA 161 Query: 201 MMQVFSDISELRAGLATGQS-ARVARWCEQLSLRMGMTSHHAKDAMMAGMLHGIGKLDLS 259 + D TG+ R+A + ++ RMG+ S + + A +H IGK+ + Sbjct: 162 RAAGYRDPE-------TGEHLTRMANYARIIAARMGLDSQQQELLLNAAPMHDIGKMGIP 214 Query: 260 DELVRKPIEKMSSEELQRFLWHPVKGQMLL--TPIPTLAEAGEIIRHQHERYDGRGVPES 317 D ++ KP ++ EEL+ H G +L +P P L A +I HE++DG G P Sbjct: 215 DHILLKP-GRLDEEELKVMRMHARIGADILVASPSPLLQTASQIALTHHEKWDGSGYPNG 273 Query: 318 LSGDAIPLGSRILAVVRDFEGLCNGGITSNNVSVEKALAMLRTHANHRYDPLVVETFIAM 377 L G+ IPL RI+AV F+ L + S+E+A LR + +DP VE F A Sbjct: 274 LKGEQIPLYGRIVAVADVFDALTSSRPYKPGWSLERASQYLREQSGAHFDPRCVEAFFAG 333 Query: 378 MEE 380 EE Sbjct: 334 WEE 336 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 74.3 bits (181), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 41/94 (43%), Positives = 54/94 (57%), Gaps = 1/94 (1%) Query: 46 GYQLLTATSAEAGLDILASAEVDLVISDMRMPGMNGAQFLAQVRQRWPATMRILLTGYSE 105 GY++L SAEA L LA + LVI+D+R+PGM+G A++R R+PA ILLT + Sbjct: 34 GYRILAVESAEAALAQLAISLPALVITDVRLPGMDGLALFAEIRSRYPALPVILLTAHGT 93 Query: 106 IGSTISAINDGGINHYLAKPWDDRELLMTVTHAL 139 I + A G YL KP+D LL V AL Sbjct: 94 IPDAVDATTQGAFA-YLTKPFDGHVLLDKVAQAL 126 >gi|300313282|ref|YP_003777374.1| HD-GYP domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 410 Score = 73.9 bits (180), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 38/107 (35%), Positives = 63/107 (58%), Gaps = 2/107 (1%) Query: 234 MGMTSHHAKDAMMAGMLHGIGKLDLSDELVRKPIEKMSSEELQRFLWHPVKGQMLLTPIP 293 +G++ ++A ++G LH +GK + DE++ KP K+++EE HP G L P Sbjct: 174 LGLSEAACREAGLSGYLHDVGKAFIDDEILNKP-GKLTAEEFALIKRHPELGYQYLIQTP 232 Query: 294 TL-AEAGEIIRHQHERYDGRGVPESLSGDAIPLGSRILAVVRDFEGL 339 + A A ++ RH HER DGRG P++L ++I L +R+ AV ++ L Sbjct: 233 DMPAYASDVCRHHHERLDGRGYPDALPAESITLYARMTAVCDVYDAL 279 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 71.6 bits (174), Expect = 1e-13, Method: Compositional matrix adjust. Identities = 58/174 (33%), Positives = 87/174 (50%), Gaps = 10/174 (5%) Query: 25 VLLVDDEQSILSALKRTFRPQGYQLLTATSAEAGLDILASAEVDLVISDMRMPGMNGAQF 84 +L+VDD+ + +L T G+ +L A S AGL +LA+ VD I D+RMP +G F Sbjct: 4 ILIVDDDAAFRGSLAETVSDLGHDVLEAGSTAAGLKLLAAHAVDAAIVDLRMPDEDGLAF 63 Query: 85 LAQVRQRWPATMR---ILLTGYSEIGSTISAINDGGINHYLAKPWDDRELLMTVTHALEE 141 L QR PA I+LT Y+ +TI AI G +H L KP L+ T+ AL + Sbjct: 64 L----QRAPAIAAIPCIMLTAYASGDNTIEAIRLGAFDH-LTKPVPRAALVETLERALRQ 118 Query: 142 QQLRKQKMALERKVREQNLQLADFNRQLERQVQARTEELRQTVMFL-ESGQEEE 194 + + R Q + ++ RQ+ +Q+ R TV+ L E+G +E Sbjct: 119 GASTPAAASPATEERNQLVGESEAMRQVFKQI-GRAATSDATVLVLGETGTGKE 171 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 0.377 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: 1,288,468 Number of extensions: 52603 Number of successful extensions: 351 Number of sequences better than 1.0e-08: 18 Number of HSP's gapped: 361 Number of HSP's successfully gapped: 18 Length of query: 448 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 360 Effective length of database: 1,203,190 Effective search space: 433148400 Effective search space used: 433148400 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: 132 (55.5 bits)