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= 0001.2797.p (307 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... 490 e-140 gi|300312305|ref|YP_003776397.1| LysR family transcription regul... 99 4e-22 gi|300313396|ref|YP_003777488.1| LysR family transcription regul... 84 1e-17 gi|300312835|ref|YP_003776927.1| LysR family transcription regul... 83 3e-17 gi|300312111|ref|YP_003776203.1| LysR family transcription regul... 80 2e-16 >gi|300312102|ref|YP_003776194.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 305 Score = 490 bits (1262), Expect = e-140, Method: Compositional matrix adjust. Identities = 260/300 (86%), Positives = 279/300 (93%) Query: 1 MRELSLDRLRTLVAIADLGSFAAAARALHLAPPTVSLHISELEERIGAPLLLRQRSQVRP 60 MRELSLDRLRTLVAIADLGSFAAAAR LHLAPPTVSLHISELEERIGAPLLLRQR+QVRP Sbjct: 1 MRELSLDRLRTLVAIADLGSFAAAARELHLAPPTVSLHISELEERIGAPLLLRQRAQVRP 60 Query: 61 SGIGATLVARARQLLAAAEQALEEVGRQVQGLAGRVRLGASTGAIAYLLPQVLERLGQSH 120 SGIG TL+ARARQLLAAA+QALEEVGRQVQGLAGRVRLGASTGAIAYLLPQ LE+LG+SH Sbjct: 61 SGIGETLIARARQLLAAADQALEEVGRQVQGLAGRVRLGASTGAIAYLLPQALEQLGRSH 120 Query: 121 PGIDVQIHILTSQETLSQLVEGSLDIGLVALPQSPVGGLTVKPWRRDPVMAFVPAAWHAP 180 PGIDVQ+ +LTSQETL++L G+LDIGLVALPQ+PV GLTV+PWRRDPVMAF+PA+W AP Sbjct: 121 PGIDVQVMVLTSQETLARLAAGALDIGLVALPQAPVAGLTVQPWRRDPVMAFLPASWRAP 180 Query: 181 RVVTPAWLAAQPLILNAPETRLSRLSAEWFAAAGEHPLPRIQLNFNDAIKSLVAAGYGAT 240 RVVTPAWLAAQPLILNAPETRLSRL+ EWFA GEHP+ RIQLNFNDAIKSLV AGYGAT Sbjct: 181 RVVTPAWLAAQPLILNAPETRLSRLTTEWFARGGEHPVARIQLNFNDAIKSLVGAGYGAT 240 Query: 241 LLPHEASAQGRTVPLDPRIVMRPLRPALWRPLGIAHRAAQLEPATLHVLQALWELKQLKK 300 LLPHEASAQG V LDPRIVMRPLRPALWRPLGIAHR Q EPAT HVL+ALW LKQL++ Sbjct: 241 LLPHEASAQGAAVALDPRIVMRPLRPALWRPLGIAHRTGQPEPATRHVLEALWALKQLRQ 300 >gi|300312305|ref|YP_003776397.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 297 Score = 99.0 bits (245), Expect = 4e-22, Method: Compositional matrix adjust. Identities = 73/259 (28%), Positives = 125/259 (48%), Gaps = 4/259 (1%) Query: 4 LSLDRLRTLVAIADLGSFAAAARALHLAPPTVSLHISELEERIGAPLLLRQRSQVRPSGI 63 L LR + I + GS A+ H+A + S I +E+ +G PLL R R V+ + Sbjct: 5 FELSDLRLFLHIVESGSITGGAQRAHMALASASARIRNMEDALGTPLLERGRRGVQTTDA 64 Query: 64 GATLVARARQLLAAAEQALEEVGRQVQGLAGRVRLGASTGAIAYLLPQVLERLGQSHPGI 123 G L AR + EQ +E+G+ +GL G +RL +T A+ LP+VL R HP Sbjct: 65 GRALAHHARMMAQQMEQLRDELGQYARGLKGHIRLLCNTSAMTEFLPEVLARFLARHPHT 124 Query: 124 DVQIHILTSQETLSQLVEGSLDIGLVALPQSPVGGLTVKPWRRDPVMAFVPAAWHAPRVV 183 D+++ S E + +++G D+G++A + G L P+R+D ++A + R Sbjct: 125 DIELEEKLSYEVVQAVIDGVADVGIIA-DSTDSGPLQTYPFRQDHLVAVLSKRHPLARRK 183 Query: 184 TPAW--LAAQPLILNAPETRLSRLSAEWFAAAGEHPLPRIQLNFNDAIKSLVAAGYGATL 241 + A+ L + + + ++ L + + AG+ R++L D I +V G + Sbjct: 184 SLAFAELLGEDFVGLSGDSALQQHLSGHATRAGKRLQYRVRLRSFDGICRMVEHQVGVAV 243 Query: 242 LPHEASAQGRTVPLDPRIV 260 LP E +A T +D R + Sbjct: 244 LP-ETAALASTPHMDIRAI 261 >gi|300313396|ref|YP_003777488.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 305 Score = 84.0 bits (206), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 70/252 (27%), Positives = 116/252 (46%), Gaps = 26/252 (10%) Query: 4 LSLDRLRTLVAIADLGSFAAAARALHLAPPTVSLHISELEERIGAPLLLRQRSQVRPSGI 63 ++L ++R VA A++G + AA LH++ +V+ I ELE +GAPL +R P G+ Sbjct: 3 ITLRQIRYFVATAEVGQISQAAIHLHISQSSVTSAIQELEALLGAPLFIRS-----PQGM 57 Query: 64 GATLVARARQLLAAAEQALEEVGRQVQG------LAGRVRLGASTGAIAYLLPQVLERLG 117 L R L A L V ++ +G +R+ AS + Y LP L+RL Sbjct: 58 --ILTDSGRHFLNHAYSILRSVDDAMKSPLPDNTASGSLRVAASYTVLGYFLPHHLQRLS 115 Query: 118 QSHPGIDVQIHILTSQETLSQLVEGSLDIGLVALPQSPVGGLTVKPWRRDPVMAFVPAAW 177 QS+PGI + +H E LVEG +D+ +V L + + + V W Sbjct: 116 QSYPGIKIHVHEKERAEIEQSLVEGEIDMAVVL-----TSNLRHREIAYETLFGSVRRLW 170 Query: 178 HAPR-------VVTPAWLAAQPLILNAPETRLSRLSAEWFAAAGEHPLPRIQLNFNDAIK 230 R V A +A +P IL + + + ++ +G P ++ + +A++ Sbjct: 171 LPARHPLGERTAVNLAEVANEPFILLTVD-EADKTALRYWNQSGRKPNIIMRTSSIEAVR 229 Query: 231 SLVAAGYGATLL 242 S+VA G G +L Sbjct: 230 SMVANGSGVAIL 241 >gi|300312835|ref|YP_003776927.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 283 Score = 82.8 bits (203), Expect = 3e-17, Method: Compositional matrix adjust. Identities = 56/177 (31%), Positives = 97/177 (54%), Gaps = 7/177 (3%) Query: 1 MRELSLDRLRTLVAIADLGSFAAAARALHLAPPTVSLHISELEERIGAPLLLRQRSQVRP 60 M+ L LD L +VA+AD G+F+ AA +H VS+ I LE +G PL LR+ V P Sbjct: 1 MKTLDLDVLAMIVAVADTGNFSRAAELVHRTQSAVSMQIKTLELALGKPLFLRKPRSVVP 60 Query: 61 SGIGATLVARARQLLAAAEQALEEVGRQVQGLAGRVRLGASTGAIAYLLPQVLERLGQSH 120 + G L+ AR++L ++A V R + GRV +G + LLP +L++ ++ Sbjct: 61 TQDGEVLLTYARRMLTLRDEAWAAVVR--PDVTGRVVIGVPDDYASSLLPSILKKFSATY 118 Query: 121 PGIDVQIHILTSQETLSQLVEGSLDIGLVALPQSPVGGLTVKPWRRDPVM-AFVPAA 176 P +++Q+ L S + +G++D+ + + V G++ + R +P++ A VP+A Sbjct: 119 PKVEIQVVGLPSSALAPMVKDGTVDL----VCATRVKGISGEFIRFEPMVWATVPSA 171 >gi|300312111|ref|YP_003776203.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 321 Score = 80.5 bits (197), Expect = 2e-16, Method: Compositional matrix adjust. Identities = 66/248 (26%), Positives = 115/248 (46%), Gaps = 7/248 (2%) Query: 4 LSLDRLRTLVAIADLGSFAAAARALHLAPPTVSLHISELEERIGAPLLLRQRSQVRPSGI 63 L LR + IA+ S +A ++L+ S I ELE R G LL R+ V+ + Sbjct: 3 FDLTDLRLFILIAEHNSLTRSAERMNLSLGATSNRIKELETRFGTRLLYRESKGVQLTPA 62 Query: 64 GATLVARARQLLAAAEQALEEVGRQVQGLAGRVRLGASTGAIAYLLPQVLERLGQSHPGI 123 G TL+ A+Q + E ++ + G+ G +R+ A+T A+ +P++L + HP + Sbjct: 63 GHTLLHHAQQFMQQVEHLKSDMQQYNNGIKGYIRIFANTTAVTEFMPEILGKFLARHPQV 122 Query: 124 DVQIHILTSQETLSQLVEGSLDIGLVALPQSPVGGLTVKPWRRDPVMAFVPAAWH----A 179 +V + + + L + EG+ DIG+VA P GL + + D + A H A Sbjct: 123 NVALEERLNHDILRGIQEGTADIGIVAGPVQG-EGLQILNFSTDR-LVLATALEHPLADA 180 Query: 180 PRVVTPAWLAAQPLILNAPETRLSRLSAEWFAAAGEHPLPRIQLNFNDAIKSLVAAGYGA 239 P + L + + L+ T L ++ A G+ RIQ+ +A+ ++ G Sbjct: 181 PSLPFIQTLEYEHIGLHEGST-LHHFLSKIVAENGQRLKLRIQVRSFEAMCRMIETNVGI 239 Query: 240 TLLPHEAS 247 +LP A+ Sbjct: 240 GILPRSAA 247 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 0.321 0.134 0.398 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: 933,727 Number of extensions: 38928 Number of successful extensions: 277 Number of sequences better than 1.0e-08: 56 Number of HSP's gapped: 253 Number of HSP's successfully gapped: 56 Length of query: 307 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 222 Effective length of database: 1,217,395 Effective search space: 270261690 Effective search space used: 270261690 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 (21.9 bits) S2: 130 (54.7 bits)