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= 0002.0272.p (306 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309386|ref|YP_003773478.1| LysR family transcription regul... 486 e-139 gi|300311571|ref|YP_003775663.1| LysR family transcription regul... 107 2e-24 gi|300310436|ref|YP_003774528.1| LysR family transcription regul... 103 2e-23 gi|300312961|ref|YP_003777053.1| transcription regulator protein... 99 6e-22 gi|300310637|ref|YP_003774729.1| LysR family transcription regul... 87 2e-18 >gi|300309386|ref|YP_003773478.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 301 Score = 486 bits (1251), Expect = e-139, Method: Compositional matrix adjust. Identities = 234/294 (79%), Positives = 259/294 (88%) Query: 1 MDIRALRYFSETVRLNSFSRAADALHVTQSTVSKMVRQLEDEIGAPLLIRAGRSLQLTDT 60 MDIRALRYF+ETVR +SFSRAADALHVTQSTVSKMVRQLE+E+ APLLIR GR LQLTDT Sbjct: 1 MDIRALRYFTETVRHSSFSRAADALHVTQSTVSKMVRQLEEEVDAPLLIRDGRRLQLTDT 60 Query: 61 GRVVYEQAQQILAGVQRLNTEVNNTRNLRQGHLEIGIPPMVNILCTPVLKAFRERHPDIA 120 GRVVYEQ QQILA +QRL+ EV +T+ LR G LEIGIPPM+NILCTPVLKAFRERHPDIA Sbjct: 61 GRVVYEQGQQILAAMQRLHAEVRDTKALRSGRLEIGIPPMINILCTPVLKAFRERHPDIA 120 Query: 121 ITLLEDTGPQIEQRVVAGTLEIGMTVLPIAPELELEMTPVAAYPIWAVAQAGRFQKNRST 180 + L EDTGPQIEQRV G LEIGMTVLP PEL LE PVA+YP+WAVAQAG FQKNR++ Sbjct: 121 VVLQEDTGPQIEQRVANGELEIGMTVLPADPELGLETLPVASYPMWAVAQAGSFQKNRAS 180 Query: 181 LPCRALKDMPLVLLNNEFGLTRTLRNMFRDTGIAPEVAAQSGQWDWLVAMALAGMGVALL 240 L C L MPLVLLNNEFGLTR+LR +FR+ GI PE+ AQS QWDWLVAMALAGMG ALL Sbjct: 181 LRCAQLDGMPLVLLNNEFGLTRSLRGVFREHGIKPEIVAQSAQWDWLVAMALAGMGTALL 240 Query: 241 PEPFIHRLASDQLQSVRLVEPEVQWQVAYVTRGGYLSHAARAWLALSSELFAGG 294 PEPFIHRLA+ QLQ+VRLVEPEVQW+VAYVTRGGYLSHAA AW+A+S++LFAGG Sbjct: 241 PEPFIHRLATQQLQAVRLVEPEVQWKVAYVTRGGYLSHAAHAWMAVSAQLFAGG 294 >gi|300311571|ref|YP_003775663.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 313 Score = 107 bits (266), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 81/272 (29%), Positives = 129/272 (47%), Gaps = 25/272 (9%) Query: 1 MDIRALRYFSETVRLNSFSRAADALHVTQSTVSKMVRQLEDEIGAPLLIRAGRSLQLTDT 60 M++R LRYF V S SRAA ALH+ Q +++ +RQLEDE+ A LL R+ + + TD Sbjct: 1 MELRQLRYFVAIVDHGSLSRAARALHIAQPALTQQIRQLEDELAAQLLHRSAQGVIATDA 60 Query: 61 GRVVYEQAQQILAGVQRLNTEVNNTRNLRQGHLEIGIPPMV-NILCTPVLKAFRERHPDI 119 G+V YE A IL VQ V + + G + +GIP V N L P+L A R +P+I Sbjct: 61 GKVFYEHALAILKQVQDAKQAVGQSADKPSGTVALGIPQSVSNALALPLLNAVRSTYPEI 120 Query: 120 AITLLEDTGPQIEQRVVAGTLEIG-------MTVLPIAPELELEMTPVAAYPIWAVAQAG 172 + L E+ + ++ +G + + ++ P +E EM Y A +Q G Sbjct: 121 TLQLTEELTGNLITQLKSGRINLAVLFDDGQLSSFAATPMIEEEMM----YITRAKSQYG 176 Query: 173 RFQKNRSTLPCRALKDMPLVLLNNEFGLTRTLRNMFRDTGIAPEVAAQSGQWDWLVAMAL 232 R ++P PL+L G+ + N+ R G++ + + L + L Sbjct: 177 --VAGRKSVPLARAIQAPLILPGLAHGVRPRIENLVRSQGMSLDNVIEINSVAILKSAIL 234 Query: 233 AGMGVALLP-----------EPFIHRLASDQL 253 A +G +LP E HR+A +++ Sbjct: 235 ADIGATILPVAPLLADIERGEMVAHRIAGERI 266 >gi|300310436|ref|YP_003774528.1| LysR family transcription regulator [Herbaspirillum seropedicae SmR1] Length = 300 Score = 103 bits (257), Expect = 2e-23, Method: Compositional matrix adjust. Identities = 86/295 (29%), Positives = 143/295 (48%), Gaps = 9/295 (3%) Query: 1 MDIRALRYFSETVRLNSFSRAADALHVTQSTVSKMVRQLEDEIGAPLLIRAGRSLQLTDT 60 +++R LRYF+ F RAA LH+TQ +S+ + LE+ +G PL R RS+ LT Sbjct: 7 LELRQLRYFAAVAEEMHFGRAAARLHMTQPPLSQTIAALEELLGTPLFQRTKRSVALTAA 66 Query: 61 GRVVYEQAQQILAGVQRLNTEVNNTRNLRQGHLEIGIPPMVNI-LCTPVLKAFRERHPDI 119 G + +AQ++L L V + G L + + + P+L+ FR +P + Sbjct: 67 GAALLPEAQRLLQQAAALPDLVRRAASGASGLLSLSFISSADYSILPPLLQRFRAHYPQV 126 Query: 120 AITLLEDTGPQIEQRVVAGTLEIGMTVLPIAPELE---LEMTPVAAYPIWAVAQAGRFQK 176 I L E T + ++ G ++ G+ +LP PE LE+ PV + P+ A G +K Sbjct: 127 QIELREATTDVQLEDLLQGKIDAGL-LLPPLPEKAAALLEVRPVLSEPLIAALPEGAVRK 185 Query: 177 NRSTLPCRALKDMPLVLLNNEF--GLTRTLRNMFRDTGIAPEVAAQSGQWDWLVAMALAG 234 R + ++L+++PL++ T+ + FRD G+ P + ++ Q +V + AG Sbjct: 186 -RGPVSLKSLRELPLIIFPRRIAPAFHDTILSCFRDAGVTPHIGQEAIQMQTIVGLVSAG 244 Query: 235 MGVALLPEPFIHRLASDQLQSVRLVEPEVQWQVAYVTRGGYLSHAARAWLALSSE 289 MG+AL+P+ + L + RL +P Q + R S RA L L E Sbjct: 245 MGMALVPQ-SVSNLKRPGVDYRRLSDPAPAIQTSLAWRRDSPSSVLRALLELLDE 298 >gi|300312961|ref|YP_003777053.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 98.6 bits (244), Expect = 6e-22, Method: Compositional matrix adjust. Identities = 69/245 (28%), Positives = 121/245 (49%), Gaps = 6/245 (2%) Query: 1 MDIRALRYFSETVRLNSFSRAADALHVTQSTVSKMVRQLEDEIGAPLLIRAGRSLQLTDT 60 M++R L+YF+ SFSRAA+ LH+ Q +S+ +RQLE+ +G L+ RA R + LT Sbjct: 1 MELRHLKYFNAVASTLSFSRAAELLHIAQPPLSRQIRQLEEMLGVELIDRASRPIALTMA 60 Query: 61 GRVVYEQAQQILAGVQRLNTEVNNTRNLRQGHLEIG-IPPMVNILCTPVLKAFRERHPDI 119 G+ YEQ Q+L+ ++++ RQ IG +P + L ++K FR P+I Sbjct: 61 GKFFYEQTLQVLSRLEQIEEGTRVIARGRQHWFNIGFVPSALYGLLPEMIKRFRTEMPEI 120 Query: 120 AITLLEDTGPQIEQRVVAGTLEIGMTVLPIA-PELELEMTPVAAYPIWAVAQAGR--FQK 176 I E + + + +G +++G LPI+ P++ E + P+ AV G + Sbjct: 121 EIGFSEIVTMEQVEALKSGRIDVGFGRLPISDPDIVCET--IVEEPLVAVFPLGHPLLAR 178 Query: 177 NRSTLPCRALKDMPLVLLNNEFGLTRTLRNMFRDTGIAPEVAAQSGQWDWLVAMALAGMG 236 N+ TL A + L + ++F + P + ++ + + + AG+G Sbjct: 179 NKVTLAQLAAQRFILYPARPRPSYADQVLDIFSSRALRPSIVKEANEMQTAIGLVAAGVG 238 Query: 237 VALLP 241 V L+P Sbjct: 239 VTLVP 243 >gi|300310637|ref|YP_003774729.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 326 Score = 86.7 bits (213), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 57/149 (38%), Positives = 85/149 (57%), Gaps = 9/149 (6%) Query: 1 MDIRALRYFSETVRLNSFSRAADALHVTQSTVSKMVRQLEDEIGAPLLIRAGRSLQLTDT 60 MDIR L+YF +F+RA++ LH+ Q +S+ ++ LE+E+G LL+R R L+LT+ Sbjct: 1 MDIRQLKYFVAVANTRNFTRASEQLHIAQPPLSRQIQLLEEELGVQLLLRNSRPLRLTEA 60 Query: 61 GRVVYEQAQQILAGVQRLNTEVNNTR----NLRQGHLEIGIPPMVNILCTPVL-KAFRER 115 GRV YEQA QIL RL+ N T+ N RQ L IG P+L + R+ Sbjct: 61 GRVFYEQALQIL---NRLDQLKNATQQIGLNQRQT-LSIGFVASTLYGGLPMLVRKLRQH 116 Query: 116 HPDIAITLLEDTGPQIEQRVVAGTLEIGM 144 +P++ I LLE T Q + +G +++G Sbjct: 117 YPEVDIQLLELTSMQQFAALKSGRIDVGF 145 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 0.135 0.397 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: 920,769 Number of extensions: 36989 Number of successful extensions: 271 Number of sequences better than 1.0e-08: 65 Number of HSP's gapped: 240 Number of HSP's successfully gapped: 65 Length of query: 306 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 221 Effective length of database: 1,217,395 Effective search space: 269044295 Effective search space used: 269044295 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)