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= 0007.0029.p (294 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312102|ref|YP_003776194.1| LysR family transcription regul... 400 e-113 gi|300312111|ref|YP_003776203.1| LysR family transcription regul... 97 2e-21 gi|300312305|ref|YP_003776397.1| LysR family transcription regul... 91 9e-20 gi|300312961|ref|YP_003777053.1| transcription regulator protein... 87 1e-18 gi|300310159|ref|YP_003774251.1| LysR family transcription regul... 84 1e-17 >gi|300312102|ref|YP_003776194.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 305 Score = 400 bits (1027), Expect = e-113, Method: Compositional matrix adjust. Identities = 220/293 (75%), Positives = 244/293 (83%), Gaps = 4/293 (1%) Query: 1 MREINLDRLRTLVAIADHGSFAEAARVLHLAPPTISLHIADLEERIGAALLSRKRGQIRP 60 MRE++LDRLRTLVAIAD GSFA AAR LHLAPPT+SLHI++LEERIGA LL R+R Q+RP Sbjct: 1 MRELSLDRLRTLVAIADLGSFAAAARELHLAPPTVSLHISELEERIGAPLLLRQRAQVRP 60 Query: 61 TTIGETLIERARRLLADAEQALEDVQRQVQGLAGRVRLGASTGAIAHLLPQALEVLGQDH 120 + IGETLI RAR+LLA A+QALE+V RQVQGLAGRVRLGASTGAIA+LLPQALE LG+ H Sbjct: 61 SGIGETLIARARQLLAAADQALEEVGRQVQGLAGRVRLGASTGAIAYLLPQALEQLGRSH 120 Query: 121 PGIDVQVEVLTSQDTLTRLSEGTLDVGLVALPQTPVARLVVQPWRRDPVMAFLPSGWRSP 180 PGIDVQV VLTSQ+TL RL+ G LD+GLVALPQ PVA L VQPWRRDPVMAFLP+ WR+P Sbjct: 121 PGIDVQVMVLTSQETLARLAAGALDIGLVALPQAPVAGLTVQPWRRDPVMAFLPASWRAP 180 Query: 181 AQVTPEWLAAQPLILNDAGTRLSHLTQEWFAGGGQRPAPRIQLNYNDAIKSLVAAGYGAT 240 VTP WLAAQPLILN TRLS LT EWFA GG+ P RIQLN+NDAIKSLV AGYGAT Sbjct: 181 RVVTPAWLAAQPLILNAPETRLSRLTTEWFARGGEHPVARIQLNFNDAIKSLVGAGYGAT 240 Query: 241 LLPHE---QGAPLP-DPRVQMLPLRPALWRQLGIAHRAENIERPTQHVLDVLW 289 LLPHE QGA + DPR+ M PLRPALWR LGIAHR E T+HVL+ LW Sbjct: 241 LLPHEASAQGAAVALDPRIVMRPLRPALWRPLGIAHRTGQPEPATRHVLEALW 293 >gi|300312111|ref|YP_003776203.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 321 Score = 96.7 bits (239), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 70/244 (28%), Positives = 114/244 (46%), Gaps = 7/244 (2%) Query: 4 INLDRLRTLVAIADHGSFAEAARVLHLAPPTISLHIADLEERIGAALLSRKRGQIRPTTI 63 +L LR + IA+H S +A ++L+ S I +LE R G LL R+ ++ T Sbjct: 3 FDLTDLRLFILIAEHNSLTRSAERMNLSLGATSNRIKELETRFGTRLLYRESKGVQLTPA 62 Query: 64 GETLIERARRLLADAEQALEDVQRQVQGLAGRVRLGASTGAIAHLLPQALEVLGQDHPGI 123 G TL+ A++ + E D+Q+ G+ G +R+ A+T A+ +P+ L HP + Sbjct: 63 GHTLLHHAQQFMQQVEHLKSDMQQYNNGIKGYIRIFANTTAVTEFMPEILGKFLARHPQV 122 Query: 124 DVQVEVLTSQDTLTRLSEGTLDVGLVALPQTPVARLVVQPWRRDPVMAFLPSGWRSPAQV 183 +V +E + D L + EGT D+G+VA P L + + D ++ L + P Sbjct: 123 NVALEERLNHDILRGIQEGTADIGIVAGPVQGEG-LQILNFSTDRLV--LATALEHPLAD 179 Query: 184 TPEWLAAQPL----ILNDAGTRLSHLTQEWFAGGGQRPAPRIQLNYNDAIKSLVAAGYGA 239 P Q L I G+ L H + A GQR RIQ+ +A+ ++ G Sbjct: 180 APSLPFIQTLEYEHIGLHEGSTLHHFLSKIVAENGQRLKLRIQVRSFEAMCRMIETNVGI 239 Query: 240 TLLP 243 +LP Sbjct: 240 GILP 243 >gi|300312305|ref|YP_003776397.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 297 Score = 91.3 bits (225), Expect = 9e-20, Method: Compositional matrix adjust. Identities = 82/293 (27%), Positives = 132/293 (45%), Gaps = 12/293 (4%) Query: 4 INLDRLRTLVAIADHGSFAEAARVLHLAPPTISLHIADLEERIGAALLSRKRGQIRPTTI 63 L LR + I + GS A+ H+A + S I ++E+ +G LL R R ++ T Sbjct: 5 FELSDLRLFLHIVESGSITGGAQRAHMALASASARIRNMEDALGTPLLERGRRGVQTTDA 64 Query: 64 GETLIERARRLLADAEQALEDVQRQVQGLAGRVRLGASTGAIAHLLPQALEVLGQDHPGI 123 G L AR + EQ +++ + +GL G +RL +T A+ LP+ L HP Sbjct: 65 GRALAHHARMMAQQMEQLRDELGQYARGLKGHIRLLCNTSAMTEFLPEVLARFLARHPHT 124 Query: 124 DVQVEVLTSQDTLTRLSEGTLDVGLVALPQTPVARLVVQPWRRDPVMAFLPSGWRSPAQV 183 D+++E S + + + +G DVG++A T L P+R+D ++A L R P Sbjct: 125 DIELEEKLSYEVVQAVIDGVADVGIIA-DSTDSGPLQTYPFRQDHLVAVLSK--RHPLAR 181 Query: 184 TPEWLAAQPLILNDAGTRLSHLTQEWFAG----GGQRPAPRIQLNYNDAIKSLVAAGYGA 239 A+ L + G Q+ +G G+R R++L D I +V G Sbjct: 182 RKSLAFAELLGEDFVGLSGDSALQQHLSGHATRAGKRLQYRVRLRSFDGICRMVEHQVGV 241 Query: 240 TLLPHEQG-APLPDPRVQMLPLRPALW--RQLGIAHRA-ENIERPTQHVLDVL 288 +LP A P ++ +PL W RQL I R E + PT+ ++ L Sbjct: 242 AVLPETAALASTPHMDIRAIPLSDG-WSRRQLLICVRGLEGLPGPTRELIQAL 293 >gi|300312961|ref|YP_003777053.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 87.4 bits (215), Expect = 1e-18, Method: Compositional matrix adjust. Identities = 73/244 (29%), Positives = 116/244 (47%), Gaps = 5/244 (2%) Query: 4 INLDRLRTLVAIADHGSFAEAARVLHLAPPTISLHIADLEERIGAALLSRKRGQIRPTTI 63 + L L+ A+A SF+ AA +LH+A P +S I LEE +G L+ R I T Sbjct: 1 MELRHLKYFNAVASTLSFSRAAELLHIAQPPLSRQIRQLEEMLGVELIDRASRPIALTMA 60 Query: 64 GETLIERARRLLADAEQALEDVQRQVQGLAGRVRLGASTGAIAHLLPQALEVLGQDHPGI 123 G+ E+ ++L+ EQ E + +G +G A+ LLP+ ++ + P I Sbjct: 61 GKFFYEQTLQVLSRLEQIEEGTRVIARGRQHWFNIGFVPSALYGLLPEMIKRFRTEMPEI 120 Query: 124 DVQVEVLTSQDTLTRLSEGTLDVGLVALPQTPVARLVVQPWRRDPVMAFLPSG--WRSPA 181 ++ + + + + L G +DVG LP + +V + +P++A P G + Sbjct: 121 EIGFSEIVTMEQVEALKSGRIDVGFGRLPISD-PDIVCETIVEEPLVAVFPLGHPLLARN 179 Query: 182 QVTPEWLAAQPLILNDAGTRLSHLTQ--EWFAGGGQRPAPRIQLNYNDAIKSLVAAGYGA 239 +VT LAAQ IL A R S+ Q + F+ RP+ + N LVAAG G Sbjct: 180 KVTLAQLAAQRFILYPARPRPSYADQVLDIFSSRALRPSIVKEANEMQTAIGLVAAGVGV 239 Query: 240 TLLP 243 TL+P Sbjct: 240 TLVP 243 >gi|300310159|ref|YP_003774251.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 309 Score = 84.3 bits (207), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 57/150 (38%), Positives = 78/150 (52%), Gaps = 5/150 (3%) Query: 4 INLDRLRTLVAIADHGSFAEAARVLHLAPPTISLHIADLEERIGAALLSRKRGQIRPTTI 63 + LR + + +HGS AEAAR LH+A P +S I LEE +GAAL R T Sbjct: 1 MEFRHLRYFLGVVEHGSVAEAARRLHIAQPALSRQIKYLEEELGAALFDRSVRGATLTAA 60 Query: 64 GETLIERARRLLADAEQALEDVQRQVQGLAGRVRLGASTGAIAHLLPQALEVLGQDH--- 120 G+ L+ ARR+LAD ++ + V R +GL G +R+G + H P+ L L H Sbjct: 61 GQQLVIDARRMLADLQETRQRVARVAEGLEGNLRMGITPNFGWH--PRILGSLRHFHQAE 118 Query: 121 PGIDVQVEVLTSQDTLTRLSEGTLDVGLVA 150 P I V +E S L R+ G LD G +A Sbjct: 119 PQIAVSLEPGLSARQLERIRSGDLDAGFLA 148 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 0.408 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: 1,055,195 Number of extensions: 49903 Number of successful extensions: 346 Number of sequences better than 1.0e-08: 64 Number of HSP's gapped: 317 Number of HSP's successfully gapped: 64 Length of query: 294 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 210 Effective length of database: 1,222,130 Effective search space: 256647300 Effective search space used: 256647300 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)