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= 0003.0013.p (305 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313065|ref|YP_003777157.1| LysR family transcription regul... 551 e-158 gi|300312334|ref|YP_003776426.1| transcription regulator protein... 186 1e-48 gi|300310802|ref|YP_003774894.1| LysR family transcription regul... 158 4e-40 gi|300312196|ref|YP_003776288.1| LysR family transcription regul... 142 4e-35 gi|300311458|ref|YP_003775550.1| LysR family transcription regul... 142 5e-35 >gi|300313065|ref|YP_003777157.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 301 Score = 551 bits (1419), Expect = e-158, Method: Compositional matrix adjust. Identities = 270/301 (89%), Positives = 285/301 (94%) Query: 5 MIRLEDLAIFVCAADNGSLSAAARQHDVTPAVASAAMKRLEGELGARLLARSTRSLRLTP 64 MIRLEDLAIFVCAADNGSLSAAARQHDVTPAVASAAMKRLEGELGARLLARSTRSLRLTP Sbjct: 1 MIRLEDLAIFVCAADNGSLSAAARQHDVTPAVASAAMKRLEGELGARLLARSTRSLRLTP 60 Query: 65 DGERYLQYARNVLAEVNAGRDAVAHGRRVVGGNLSLSVPSDLGRNLMCQWLDEFLAQHPA 124 DGERYLQ+ARNVLAEVNAGRDAVAHGRRV+GGNLSLS PSD GRNL+ QWLDEF AQHPA Sbjct: 61 DGERYLQHARNVLAEVNAGRDAVAHGRRVIGGNLSLSAPSDFGRNLIGQWLDEFQAQHPA 120 Query: 125 VSLQVRISDRVADMFRQPVEVAIRYSPPEDSSLVALPLAPDNRRVLCASPDYLARHGRPR 184 VSLQV +SDRVADM+RQPV+VAIRYS P+DSSLVALPLAPDNRRVLCASPDYLARHGRPR Sbjct: 121 VSLQVHVSDRVADMYRQPVDVAIRYSAPDDSSLVALPLAPDNRRVLCASPDYLARHGRPR 180 Query: 185 TPADLRQHNCLRYLLSDMLHSQWTFFKDGTPVQVQVSGDRVCDDGELVHRWAVEGRGIAY 244 +PADLRQHNCLRY+LSD LHSQW FFKD PVQVQVSGDR CDDGELV RWAV GRGIAY Sbjct: 181 SPADLRQHNCLRYVLSDTLHSQWNFFKDDEPVQVQVSGDRTCDDGELVRRWAVNGRGIAY 240 Query: 245 KSRLDVLADLRNGKLEALMEDYQGEASPLNLVCTHRMSLSPTVRALRELLGERVARYLTD 304 KSRLDVLADLRNG+LEAL+EDY+GE SPL+LVCTHRM +SPTVRALRELLGER+ARYL D Sbjct: 241 KSRLDVLADLRNGRLEALLEDYEGEPSPLHLVCTHRMCVSPTVRALRELLGERIARYLKD 300 Query: 305 R 305 R Sbjct: 301 R 301 >gi|300312334|ref|YP_003776426.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 302 Score = 186 bits (473), Expect = 1e-48, Method: Compositional matrix adjust. Identities = 104/290 (35%), Positives = 168/290 (57%), Gaps = 2/290 (0%) Query: 5 MIRLEDLAIFVCAADNGSLSAAARQHDVTPAVASAAMKRLEGELGARLLARSTRSLRLTP 64 M + + ++ F A GSLSAAAR + PA+ + LE LG +LL R+TR + LT Sbjct: 1 MDQFKQISTFAEVAARGSLSAAARAEGIAPAMIGRRLDALEERLGVKLLQRTTRKIVLTN 60 Query: 65 DGERYLQYARNVLAEVNAGRDAVAHGRRVVGGNLSLSVPSDLGRNLMCQWLDEFLAQHPA 124 +G +L+ + +LA++ AV+ G L +S P+ GR + L FLA+H Sbjct: 61 EGAAFLEDCQRILADLEDAESAVSERSARASGQLLISAPAGFGRQHVAPLLPSFLAEHRD 120 Query: 125 VSLQVRISDRVADMFRQPVEVAIRYSPPEDSSLVALPLAPDNRRVLCASPDYLARHGRPR 184 V+L + ++DR+AD+ + ++VAIR + DS+LV++ LA +N RV+ A+P YL RHG P+ Sbjct: 121 VTLTLNLNDRIADVIGEGIDVAIRIATLTDSNLVSVKLA-ENHRVIVAAPAYLRRHGTPQ 179 Query: 185 TPADLRQHNCLRYLLSDMLHSQWTFFKDGTPVQVQVSGDRVCDDGELVHRWAVEGRGIAY 244 +P +L +HNCL + S+ WT + G +V G+ VC+DGE++H WA+ GRG+A+ Sbjct: 180 SPDELMRHNCL-AMSSEGSQRGWTLRQSGKVSVYKVGGNMVCNDGEVLHNWALAGRGLAW 238 Query: 245 KSRLDVLADLRNGKLEALMEDYQGEASPLNLVCTHRMSLSPTVRALRELL 294 +S +V A + G+L +++ + A + V R L +RA + L Sbjct: 239 RSMWEVGAAIEAGELVTVLDKFAAPAPSIYAVFAQRRHLPLRIRAFVDFL 288 >gi|300310802|ref|YP_003774894.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 304 Score = 158 bits (400), Expect = 4e-40, Method: Compositional matrix adjust. Identities = 91/263 (34%), Positives = 141/263 (53%), Gaps = 1/263 (0%) Query: 8 LEDLAIFVCAADNGSLSAAARQHDVTPAVASAAMKRLEGELGARLLARSTRSLRLTPDGE 67 LEDL +F A + S + +AR+ +PA S + LE LG RL R+TRS+ +T +G Sbjct: 7 LEDLRLFCVVARHSSFAGSAREVGASPAYISKRIALLEQALGVRLFHRTTRSVVMTEEGG 66 Query: 68 RYLQYARNVLAEVNAGRDAVAHGRRVVGGNLSLSVPSDLGRNLMCQWLDEFLAQHPAVSL 127 ++AR +L +V + V+ +RV G L +S LGR ++ L F ++HP + + Sbjct: 67 NVHEWARRILDDVEQMMETVSSAKRVPRGLLKISTSFGLGRKVVSPLLSRFASEHPELKI 126 Query: 128 QVRISDRVADMFRQPVEVAIRYSPPEDSSLVALPLAPDNRRVLCASPDYLARHGRPRTPA 187 Q+ + DR D+ + +++ IR + L + + P ++RVLCASP YL +HG P A Sbjct: 127 QLELVDRQIDLVNEGIDLDIRVGAGHEPHLFSKRILP-SQRVLCASPAYLKKHGLPADLA 185 Query: 188 DLRQHNCLRYLLSDMLHSQWTFFKDGTPVQVQVSGDRVCDDGELVHRWAVEGRGIAYKSR 247 LRQH CL + W V+VSG + GE++H+WAV+G GI +S Sbjct: 186 ALRQHQCLVIRERNQSFGIWRMMGPKGVETVKVSGMLASNHGEIIHQWAVDGHGIILRSA 245 Query: 248 LDVLADLRNGKLEALMEDYQGEA 270 DV L+ G+L ++ Y EA Sbjct: 246 WDVADSLKRGRLVRVLPQYYQEA 268 >gi|300312196|ref|YP_003776288.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 308 Score = 142 bits (357), Expect = 4e-35, Method: Compositional matrix adjust. Identities = 95/295 (32%), Positives = 144/295 (48%), Gaps = 4/295 (1%) Query: 5 MIRLEDLAIFVCAADNGSLSAAARQHDVTPAVASAAMKRLEGELGARLLARSTRSLRLTP 64 M +L+ + FV ++GS AA + S + LE LG RLL R+TR L LT Sbjct: 1 MDKLQAMQTFVAVVESGSFVAAVDVTGQSKPAVSRQVSELEQFLGIRLLHRTTRRLSLTD 60 Query: 65 DGERYLQYARNVLAEVNAGRDAVAHGRRVVGGNLSLSVPSDLGRNLMCQWLDEFLAQHPA 124 +G Y + +L + V G L + P D G + +F QHP Sbjct: 61 EGRVYFARCKELLETIQDVESEVGLNSDQACGRLRIGAPQDFGVEQLAPLWGKFTEQHPL 120 Query: 125 VSLQVRISDRVADMFRQPVEVAIRYSPPEDSSLVALPLAPDNRRVLCASPDYLARHGRPR 184 ++L + +SDR D+ + ++AIR S DS +VA PLAP R + CA+P++LARHG P Sbjct: 121 ITLNITLSDRTIDLLEEGFDMAIRISALGDSRMVARPLAP-VRMIACAAPEFLARHGTPG 179 Query: 185 TPADLRQHNCLRYLLSDMLHSQWTF-FKDGTPVQVQVSGDRVCDDGELVHRWAVEGRGIA 243 TPA+LR + + Y W+F G QV+V ++G A+ G+GIA Sbjct: 180 TPAELRDYPFISYSYRAG-GDDWSFRHVHGDTCQVRVRSTVYVNNGATCRAMAIAGQGIA 238 Query: 244 YKSRLDVLADLRNGKLEALMEDYQ-GEASPLNLVCTHRMSLSPTVRALRELLGER 297 + V A ++ G+L L E + GE ++ + R L P V+ +R+ L E+ Sbjct: 239 IQPDFIVNAAIQAGQLVELFEGWSTGEQLVVHTLYPTRTHLPPKVQRMRDFLIEQ 293 >gi|300311458|ref|YP_003775550.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 303 Score = 142 bits (357), Expect = 5e-35, Method: Compositional matrix adjust. Identities = 90/294 (30%), Positives = 149/294 (50%), Gaps = 3/294 (1%) Query: 5 MIRLEDLAIFVCAADNGSLSAAARQHDVTPAVASAAMKRLEGELGARLLARSTRSLRLTP 64 M RL+ + +F + GS AA D++ AVA+ + LE LG RLL RSTR L LT Sbjct: 1 MDRLQSMRVFAKVVEQGSFVRAAELLDISNAVATRFIADLEAHLGTRLLNRSTRRLSLTE 60 Query: 65 DGERYLQYARNVLAEVNAGRDAVAHGRRVVGGNLSLSVPSDLGRNLMCQWLDEFLAQHPA 124 G+ YL+ R +LAEV+ V+ + G L++ + G++ + + L + +P Sbjct: 61 AGQAYLERVRMILAEVDDAEALVSLETKRPAGTLAIYCNAGFGQSQLGEMLSAYSQAYPE 120 Query: 125 VSLQVRISDRVADMFRQPVEVAIRYSPPE-DSSLVALPLAPDNRRVLCASPDYLARHGRP 183 V+L + +S+R D+ + +++ S + D+S++ L R +LC SP Y+AR G P Sbjct: 121 VALDISLSERSIDLVEEGIDIGFFSSMQKFDASMIVRQLGV-ARVILCTSPAYIARQGAP 179 Query: 184 RTPADLRQHNCLRYLLSDMLHSQWTFFKDGTPVQVQVSGDRVCDDGELVHRWAVEGRGIA 243 P DL +HNCL + + L W +G + V + V + G L+ A+ G GI Sbjct: 180 EQPEDLSRHNCLNF-SHEYLRHHWHVNTNGGVLDVPIVSKVVSNSGVLLRDLALAGMGIV 238 Query: 244 YKSRLDVLADLRNGKLEALMEDYQGEASPLNLVCTHRMSLSPTVRALRELLGER 297 + + DLR+G+L ++ + +++V R LS VR+ E + R Sbjct: 239 LRPSYSLGDDLRSGRLVQVLPGFDMGQVIMSMVYPSRRLLSAKVRSFAEFISAR 292 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 0.136 0.406 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: 985,287 Number of extensions: 41562 Number of successful extensions: 264 Number of sequences better than 1.0e-08: 47 Number of HSP's gapped: 215 Number of HSP's successfully gapped: 47 Length of query: 305 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 220 Effective length of database: 1,217,395 Effective search space: 267826900 Effective search space used: 267826900 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)