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= 0001.0943.p (298 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... 279 3e-76 gi|300313396|ref|YP_003777488.1| LysR family transcription regul... 93 3e-20 gi|300309864|ref|YP_003773956.1| LysR family transcription regul... 87 1e-18 gi|300312305|ref|YP_003776397.1| LysR family transcription regul... 87 2e-18 gi|300312111|ref|YP_003776203.1| LysR family transcription regul... 87 2e-18 >gi|300312102|ref|YP_003776194.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 305 Score = 279 bits (713), Expect = 3e-76, Method: Compositional matrix adjust. Identities = 158/302 (52%), Positives = 203/302 (67%), Gaps = 10/302 (3%) Query: 1 MRELSLDQLRTLVSIVDLGTFSAAANALHLAQPTISLHVSELEARIGAPLLMRGSRRAQP 60 MRELSLD+LRTLV+I DLG+F+AAA LHLA PT+SLH+SELE RIGAPLL+R + +P Sbjct: 1 MRELSLDRLRTLVAIADLGSFAAAARELHLAPPTVSLHISELEERIGAPLLLRQRAQVRP 60 Query: 61 TALGTILIERARRLLRDVDDLLDVAQKHVEGKVGRVRLGTSTGVVVHLLPRVLKKLESAF 120 + +G LI RAR+LL D L+ + V+G GRVRLG STG + +LLP+ L++L + Sbjct: 61 SGIGETLIARARQLLAAADQALEEVGRQVQGLAGRVRLGASTGAIAYLLPQALEQLGRSH 120 Query: 121 PGIDVEVNILGSVETMDRLQQGTLDIGLVSTPIQKTKEIRISHWRSDKMMAYLPASWDCP 180 PGIDV+V +L S ET+ RL G LDIGLV+ P + + WR D +MA+LPASW P Sbjct: 121 PGIDVQVMVLTSQETLARLAAGALDIGLVALPQAPVAGLTVQPWRRDPVMAFLPASWRAP 180 Query: 181 ATIRPAWLADKPMIFNDATTQMYRLTMEWFAAAGENPRARIELNYTEAMKSLVSAGYGAA 240 + PAWLA +P+I N T++ RLT EWFA GE+P ARI+LN+ +A+KSLV AGYGA Sbjct: 181 RVVTPAWLAAQPLILNAPETRLSRLTTEWFARGGEHPVARIQLNFNDAIKSLVGAGYGAT 240 Query: 241 VLPLE---QPLAAELGRHKDIRIV--PLSPVLRRHVGVAHRALATLDQATANVLETIRQF 295 +LP E Q A L D RIV PL P L R +G+AHR + AT +VLE + Sbjct: 241 LLPHEASAQGAAVAL----DPRIVMRPLRPALWRPLGIAHRT-GQPEPATRHVLEALWAL 295 Query: 296 DQ 297 Q Sbjct: 296 KQ 297 >gi|300313396|ref|YP_003777488.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 305 Score = 93.2 bits (230), Expect = 3e-20, Method: Compositional matrix adjust. Identities = 78/295 (26%), Positives = 140/295 (47%), Gaps = 8/295 (2%) Query: 4 LSLDQLRTLVSIVDLGTFSAAANALHLAQPTISLHVSELEARIGAPLLMRGSRRAQPTAL 63 ++L Q+R V+ ++G S AA LH++Q +++ + ELEA +GAPL +R + T Sbjct: 3 ITLRQIRYFVATAEVGQISQAAIHLHISQSSVTSAIQELEALLGAPLFIRSPQGMILTDS 62 Query: 64 GTILIERARRLLRDVDDLLDVAQKHVEGKVGRVRLGTSTGVVVHLLPRVLKKLESAFPGI 123 G + A +LR VDD + G +R+ S V+ + LP L++L ++PGI Sbjct: 63 GRHFLNHAYSILRSVDDAMKSPLPDNTAS-GSLRVAASYTVLGYFLPHHLQRLSQSYPGI 121 Query: 124 DVEVNILGSVETMDRLQQGTLDIGLVSTPIQKTKEIRISHWRSDKMMAYLPASWDCP--A 181 + V+ E L +G +D+ +V T + +EI +LPA Sbjct: 122 KIHVHEKERAEIEQSLVEGEIDMAVVLTSNLRHREIAYETLFGSVRRLWLPARHPLGERT 181 Query: 182 TIRPAWLADKPMIFNDATTQMYRLTMEWFAAAGENPRARIELNYTEAMKSLVSAGYGAAV 241 + A +A++P I + + + ++ +G P + + EA++S+V+ G G A+ Sbjct: 182 AVNLAEVANEPFIL-LTVDEADKTALRYWNQSGRKPNIIMRTSSIEAVRSMVANGSGVAI 240 Query: 242 LP--LEQPLAAELGRHKDIRIVPLSPVLRRHVGVAHRALATLDQATANVLETIRQ 294 L + +P + E R + + ++ P + +VG+A R A V E RQ Sbjct: 241 LSDLVYRPWSLEGLRIETVLLMDHVPAM--NVGLAWRKGVEFTPAMEAVREYFRQ 293 >gi|300309864|ref|YP_003773956.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 306 Score = 87.4 bits (215), Expect = 1e-18, Method: Compositional matrix adjust. Identities = 69/247 (27%), Positives = 113/247 (45%), Gaps = 11/247 (4%) Query: 4 LSLDQLRTLVSIVDLGTFSAAANALHLAQPTISLHVSELEARIGAPLLMRGSRRAQPTAL 63 L L Q+R V F AA L++ QP +S + LE R+G L R R + T Sbjct: 2 LDLAQVRCFVVAATELNFRRAAALLNMTQPPLSRQIHLLEHRLGVQLFERVGRTVRLTTE 61 Query: 64 GTILIERARRLLRDVDDLLDVAQKHVEGKVGRVRLGTSTGVVVHLLPRVLKKLESAFPGI 123 G + + A RLL+ + ++ +GK GRVR+G + L+P +L + ++ P I Sbjct: 62 GRVFLADASRLLQLSEQAESTVRRASQGKTGRVRVGFTGAAGYELIPELLMQARTSLPEI 121 Query: 124 DVEVNILGSVETMDRLQQGTLDIGLVSTPIQKTKEIRISHWRSDKMMAYLP-----ASWD 178 DV + L SV ++ T+DIG + P+ + + + + ++ +P A++D Sbjct: 122 DVVLFELISVAQLEAFTANTIDIGFLR-PVASRQPLELQLVDEEALVLAMPQGHALAAYD 180 Query: 179 CPATIRPAWLADKPMIFNDAT--TQMYRLTMEWFAAAGENPRARIELNYTEAMKSLVSAG 236 AT + L +P I + T Y M AA P ++ + + SLV AG Sbjct: 181 RIATTQ---LDGQPFIMHSPTHGKYFYERIMAMLGAADVKPDFTQYIDQSHTILSLVRAG 237 Query: 237 YGAAVLP 243 G +LP Sbjct: 238 LGVGILP 244 >gi|300312305|ref|YP_003776397.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 297 Score = 86.7 bits (213), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 80/300 (26%), Positives = 131/300 (43%), Gaps = 20/300 (6%) Query: 4 LSLDQLRTLVSIVDLGTFSAAANALHLAQPTISLHVSELEARIGAPLLMRGSRRAQPTAL 63 L LR + IV+ G+ + A H+A + S + +E +G PLL RG R Q T Sbjct: 5 FELSDLRLFLHIVESGSITGGAQRAHMALASASARIRNMEDALGTPLLERGRRGVQTTDA 64 Query: 64 GTILIERARRLLRDVDDLLDVAQKHVEGKVGRVRLGTSTGVVVHLLPRVLKKLESAFPGI 123 G L AR + + ++ L D ++ G G +RL +T + LP VL + + P Sbjct: 65 GRALAHHARMMAQQMEQLRDELGQYARGLKGHIRLLCNTSAMTEFLPEVLARFLARHPHT 124 Query: 124 DVEVNILGSVETMDRLQQGTLDIGLV-----STPIQKTKEIRISHWRSDKMMAYLPASWD 178 D+E+ S E + + G D+G++ S P+Q +R D ++A L S Sbjct: 125 DIELEEKLSYEVVQAVIDGVADVGIIADSTDSGPLQTYP------FRQDHLVAVL--SKR 176 Query: 179 CPATIRP----AWLADKPMIFNDATTQMYRLTMEWFAAAGENPRARIELNYTEAMKSLVS 234 P R A L + + + + + AG+ + R+ L + + +V Sbjct: 177 HPLARRKSLAFAELLGEDFVGLSGDSALQQHLSGHATRAGKRLQYRVRLRSFDGICRMVE 236 Query: 235 AGYGAAVLPLEQPLAAELGRHKDIRIVPLSPVL-RRHVGVAHRALATLDQATANVLETIR 293 G AVLP LA+ H DIR +PLS RR + + R L L T +++ ++ Sbjct: 237 HQVGVAVLPETAALAST--PHMDIRAIPLSDGWSRRQLLICVRGLEGLPGPTRELIQALQ 294 >gi|300312111|ref|YP_003776203.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 321 Score = 86.7 bits (213), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 75/300 (25%), Positives = 147/300 (49%), Gaps = 18/300 (6%) Query: 4 LSLDQLRTLVSIVDLGTFSAAANALHLAQPTISLHVSELEARIGAPLLMRGSRRAQPTAL 63 L LR + I + + + +A ++L+ S + ELE R G LL R S+ Q T Sbjct: 3 FDLTDLRLFILIAEHNSLTRSAERMNLSLGATSNRIKELETRFGTRLLYRESKGVQLTPA 62 Query: 64 GTILIERARRLLRDVDDLLDVAQKHVEGKVGRVRLGTSTGVVVHLLPRVLKKLESAFPGI 123 G L+ A++ ++ V+ L Q++ G G +R+ +T V +P +L K + P + Sbjct: 63 GHTLLHHAQQFMQQVEHLKSDMQQYNNGIKGYIRIFANTTAVTEFMPEILGKFLARHPQV 122 Query: 124 DVEVNILGSVETMDRLQQGTLDIGLVSTPIQKTKEIRISHWRSDKMMAYLPASWDCPATI 183 +V + + + + +Q+GT DIG+V+ P+Q + ++I ++ +D+++ L + + P Sbjct: 123 NVALEERLNHDILRGIQEGTADIGIVAGPVQG-EGLQILNFSTDRLV--LATALEHPLAD 179 Query: 184 RPAW-----LADKPMIFNDATTQMYRLTMEWFAAAGENPRARIELNYTEAMKSLVSAGYG 238 P+ L + + ++ +T ++ + A G+ + RI++ EAM ++ G Sbjct: 180 APSLPFIQTLEYEHIGLHEGST-LHHFLSKIVAENGQRLKLRIQVRSFEAMCRMIETNVG 238 Query: 239 AAVLPLEQPLAAELGRHK---DIRIVPLS-PVLRRHVGVAHRALATLDQATANVLETIRQ 294 +LP AA+ RH+ + +V LS P R + + + TL N++E IR+ Sbjct: 239 IGILPRS---AAQ--RHQQTMQLSVVELSDPWSVRERSMVVQDIDTLSPHARNLVEFIRE 293 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 0.387 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: 891,954 Number of extensions: 36289 Number of successful extensions: 261 Number of sequences better than 1.0e-08: 60 Number of HSP's gapped: 235 Number of HSP's successfully gapped: 60 Length of query: 298 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 213 Effective length of database: 1,217,395 Effective search space: 259305135 Effective search space used: 259305135 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)