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= 0003.0072.p (246 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310375|ref|YP_003774467.1| LysR family transcription regul... 396 e-112 gi|300313164|ref|YP_003777256.1| LysR family transcription regul... 117 8e-28 gi|300310701|ref|YP_003774793.1| LysR family transcription regul... 108 3e-25 gi|300309487|ref|YP_003773579.1| LysR family transcription regul... 102 3e-23 gi|300313740|ref|YP_003777832.1| LysR family transcription regul... 63 2e-11 >gi|300310375|ref|YP_003774467.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 313 Score = 396 bits (1018), Expect = e-112, Method: Compositional matrix adjust. Identities = 189/246 (76%), Positives = 216/246 (87%) Query: 1 MRPTIYGEAMIRHSRMALTSLSKAHEDIVALKSGLSGQVDVGVILSPGLSLVPAAIARVK 60 MRPTIYGEAMIRH+RMALTSLSKAHEDIVALKSGLSGQVDVG ILSP ++L+P AIARVK Sbjct: 68 MRPTIYGEAMIRHARMALTSLSKAHEDIVALKSGLSGQVDVGGILSPAMALLPPAIARVK 127 Query: 61 EHSPMLRIGVEVESSNILLARLLRGDLDFLVARILDEEVSHNLHYEELSDEPICAVARVG 120 E +PMLRIGVEVESSNILL+RLL G+LDF++ RILD+E L YEEL+DEPICAVARVG Sbjct: 128 EQAPMLRIGVEVESSNILLSRLLHGELDFIIGRILDDEARGGLLYEELADEPICAVARVG 187 Query: 121 HPLHEHKNMTLKDIVDHPWIMAPKGSILRSRVDLMFRKSGLTPPANVVDTTAILTITSLL 180 HP H +++L D+ WIMAPKGSILR+R D MFR+ GL PP+NVVDTTAIL ITSLL Sbjct: 188 HPFHARTDLSLADLASEAWIMAPKGSILRARCDQMFREQGLAPPSNVVDTTAILFITSLL 247 Query: 181 QQTDFLYAMPTEVARYYSQARLMDLLPIELPCKMDGFGIITRREQLLSPGATILQQAIRD 240 QQTDF+YAMPTEVARYY+QARLMD+LPIELPC+M GFGIITR++ LLSPGA ++ QAIR+ Sbjct: 248 QQTDFIYAMPTEVARYYTQARLMDILPIELPCRMAGFGIITRQDNLLSPGANLVLQAIRE 307 Query: 241 VAKTIY 246 VAK IY Sbjct: 308 VAKMIY 313 >gi|300313164|ref|YP_003777256.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 117 bits (294), Expect = 8e-28, Method: Compositional matrix adjust. Identities = 61/237 (25%), Positives = 129/237 (54%), Gaps = 1/237 (0%) Query: 4 TIYGEAMIRHSRMALTSLSKAHEDIVALKSGLSGQVDVGVILSPGLSLVPAAIARVKEHS 63 T G +IR++R+ + ++ +++ + SG G++ +G I+ V A++R++E Sbjct: 87 TELGRCVIRYARLIQSDVANLRDELQNMISGRGGRLAIGTIMGAA-PFVTRALSRLREIQ 145 Query: 64 PMLRIGVEVESSNILLARLLRGDLDFLVARILDEEVSHNLHYEELSDEPICAVARVGHPL 123 P + I + ++S L L +G +D ++ R + HYE L EP+C V+ + HPL Sbjct: 146 PEVSIEISEDTSARQLLLLDQGRIDLMIGRSSVSSQPNLYHYEMLRGEPMCIVSGIDHPL 205 Query: 124 HEHKNMTLKDIVDHPWIMAPKGSILRSRVDLMFRKSGLTPPANVVDTTAILTITSLLQQT 183 + + L+++ + WI+ +R ++ F+ G+ P NV++T + +LL Q+ Sbjct: 206 ATAQKVRLQELAEASWILYSSNMPMRIWIEHEFKLEGVKVPGNVIETASPFVTITLLAQS 265 Query: 184 DFLYAMPTEVARYYSQARLMDLLPIELPCKMDGFGIITRREQLLSPGATILQQAIRD 240 + + MP ++A +++ +++ +LP+ L +++ +GI+TR+ LS A + Q +R Sbjct: 266 NMVAVMPLDIAHFFAAKQMLGILPVNLKTRIEHYGIVTRKNTTLSSLAKMFIQILRQ 322 >gi|300310701|ref|YP_003774793.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 321 Score = 108 bits (271), Expect = 3e-25, Method: Compositional matrix adjust. Identities = 68/236 (28%), Positives = 117/236 (49%), Gaps = 1/236 (0%) Query: 6 YGEAMIRHSRMALTSLSKAHEDIVALKSGLSGQVDVGVILSPGLSLVPAAIARVKEHSPM 65 +G +IR++R+ T L E++ ++SG G++ +G ++ +L+ A+ ++ P Sbjct: 83 FGHCVIRYARLMATDLGSLCEEMAQIRSGQGGRLAIGAVMGAVPALIVPAVDALQRRHPA 142 Query: 66 LRIGVEVESSNILLARLLRGDLDFLVARILDEEVSHNLHYEELSDEPICAVARVGHPLHE 125 L I + ++S +L L G LD LVAR HY+ LS+EP+ V HP Sbjct: 143 LSIEIVEDTSLHMLDLLDEGHLDLLVARASVSAHPGKYHYQSLSEEPLSVVVSAEHPRPR 202 Query: 126 HKNMTLKDIVDHPWIMAPKGSILRSRVDLMFRKSGLTPPANVVDTTAILTITSLLQQ-TD 184 K + L + + WI P L + ++ +GL+ PAN + T + +LLQQ D Sbjct: 203 GKELQLAALAGYRWITYPSHMPLHAVLEREMDLAGLSMPANTIATASTFVTVALLQQGAD 262 Query: 185 FLYAMPTEVARYYSQARLMDLLPIELPCKMDGFGIITRREQLLSPGATILQQAIRD 240 + +PT VA + Q ++ +LP++L GI+TR+ LS Q +R+ Sbjct: 263 MVSILPTAVAEMFVQRGMLRILPVKLRSMSQTIGIVTRKGGQLSGAGQAFVQLLRE 318 >gi|300309487|ref|YP_003773579.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 314 Score = 102 bits (254), Expect = 3e-23, Method: Compositional matrix adjust. Identities = 72/251 (28%), Positives = 134/251 (53%), Gaps = 15/251 (5%) Query: 1 MRPTIYGEAMIRHSRMALTSLSKAHEDIVALKSGLSGQVDVGVILSPGLSLVPAAIARVK 60 + PT G +IR++R+ T L+ E+++A+ G G++ VG I+ + L+ A+ R+ Sbjct: 69 LEPTELGHCVIRYARLIQTDLTHLREEMLAIMQGHGGRLAVGTIMG-AVPLLTDALTRLL 127 Query: 61 EHSPMLRIGVEVESSNILLARLLRGDLDFLVARIL-----DEEVSHNLHYEELSDEPICA 115 E P L + + ++S LL L +G LD + R D + N+H EEL+ Sbjct: 128 EAHPALSVEIVEDTSARLLRLLDQGRLDLAICRTSISQRPDLYDAFNIHEEELA-----V 182 Query: 116 VARVGHPLHEHKNMTLKDIVDHPWIMAPKGSILRSRVDLMFRKSGLTPPANVVDTTAILT 175 VA V HPL + ++ L D+ D W++ +R ++ F + L P ++++TT+ T Sbjct: 183 VASVQHPLADAPSLQLADLADSRWVVYSANMPMRLTLEREFHDADLRFPLHLMETTSAFT 242 Query: 176 ITSLLQQT-DFLYAMPTEVARYYSQARLMDLLPIELPCKMDGFGIITRREQLLSPGATIL 234 SLLQ+ F+ + +VA++ ++ + +LP+ L + + + ++TRR +LSP A + Sbjct: 243 TLSLLQKNPHFVALLSVDVAQFCTRFGMTRILPLRLHTRSEPYQLVTRRGTMLSPVARLF 302 Query: 235 QQAIRDVAKTI 245 + D A+T+ Sbjct: 303 ---LDDFARTV 310 >gi|300313740|ref|YP_003777832.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 307 Score = 62.8 bits (151), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 54/236 (22%), Positives = 113/236 (47%), Gaps = 9/236 (3%) Query: 1 MRPTIYGEAMIRHSRMALTSLSKAHEDIVALKSGLSGQVDVGVILSPGLSLVPAAIARVK 60 +R T GEA++ +R + + +I G G + +G + + ++P ++ Sbjct: 55 IRLTAVGEALLNRARQISLMMDETAREIGDYAHGREGNIRLGCVPTLAEHVLPGVCQQLL 114 Query: 61 EHSPMLRIGVEVESSNILLARLLRGDLDFLVA-RILDEEVSHNLHYEELSDEPICAVARV 119 + + I ++V ++ LLA L G+LD ++ I D+E+ H EE+ + + +A Sbjct: 115 GEAQKVTIDLKVSMNDALLAGLKAGELDIVLGPMIQDDEL---FHTEEIMQDQMVVMASP 171 Query: 120 GHPLHEHKNMTLKDIVDHPWIMAPKGSILRSRVDLMFRKSGLTPPANVVDTTAILTITSL 179 HP+ + K + L+ ++D+ W++ + + R +D +F + L P + T + I L Sbjct: 172 QHPIFD-KKIRLRHLLDYQWVLPAQSVLSRQWLDNVFDRHHLPRPKVQITPTVLNMILPL 230 Query: 180 LQQTDFL-YAMPTEVARYYSQARLMDLLPIELPCKMDGFGIITRREQLLSPGATIL 234 +++++ L +A ++ R + L + +M G+ RR+ LSP A L Sbjct: 231 IERSNLLGFASKLNLSEGRGHLREVVLKETTMLRRM---GLTYRRDMYLSPAAQRL 283 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 0.322 0.137 0.391 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: 755,988 Number of extensions: 30631 Number of successful extensions: 110 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 109 Number of HSP's successfully gapped: 7 Length of query: 246 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 163 Effective length of database: 1,226,865 Effective search space: 199978995 Effective search space used: 199978995 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: 129 (54.3 bits)