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= 0003.0107.p (316 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313131|ref|YP_003777223.1| LysR family transcription regul... 417 e-118 gi|300313102|ref|YP_003777194.1| LysR family transcription regul... 107 2e-24 gi|300312961|ref|YP_003777053.1| transcription regulator protein... 98 9e-22 gi|300310637|ref|YP_003774729.1| LysR family transcription regul... 94 1e-20 gi|300312965|ref|YP_003777057.1| LysR family transcription regul... 93 2e-20 >gi|300313131|ref|YP_003777223.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 307 Score = 417 bits (1072), Expect = e-118, Method: Compositional matrix adjust. Identities = 210/229 (91%), Positives = 218/229 (95%) Query: 1 MISIRQLRYFVEIVEARGYTRASERLFIAQSALSRQIKELEADLDVVLIKREAKAFELTQ 60 MISIRQLRYFVEIVEARGYTRA+ERLF+AQSALSRQIKELEADLDVVL++REAK FELTQ Sbjct: 1 MISIRQLRYFVEIVEARGYTRAAERLFVAQSALSRQIKELEADLDVVLLRREAKTFELTQ 60 Query: 61 AGQDFYERSRRILLDLDRAVAQARTIGKGEHGALRLLHSSSVPLSAPLGPTLNAALKDFP 120 AGQDFYERSR+ILLDLDRAVAQARTIGKGEHGALRLLHSSSVPL+APLGP LN ALK FP Sbjct: 61 AGQDFYERSRKILLDLDRAVAQARTIGKGEHGALRLLHSSSVPLTAPLGPMLNEALKAFP 120 Query: 121 GISLEISQAPSEYQAREIVEGSADIGLARLPILRAHPNLESTVLYRERLVAAVPATHRLA 180 GISLEISQAPSEYQAREIVEGSADIGLARLPILRA+PNL STVLYRERLVAAVPA HRLA Sbjct: 121 GISLEISQAPSEYQAREIVEGSADIGLARLPILRANPNLASTVLYRERLVAAVPAGHRLA 180 Query: 181 ARSEVEIAELRDEFFVTVPHRDRGGLSYLVAERCIAHGFYPRVARXPGK 229 R EVEIAELRDEFFVTVPHRDRGGLSYLVAERCIAHGFYPRVAR + Sbjct: 181 QRQEVEIAELRDEFFVTVPHRDRGGLSYLVAERCIAHGFYPRVARATSR 229 >gi|300313102|ref|YP_003777194.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 107 bits (266), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 70/226 (30%), Positives = 116/226 (51%), Gaps = 7/226 (3%) Query: 1 MISIRQLRYFVEIVEARGYTRASERLFIAQSALSRQIKELEADLDVVLIKREAKAFELTQ 60 MI +R L YF + E + RA+E L I+Q L+RQI LE +L L R +A +LT Sbjct: 1 MIELRHLTYFRTVAETLHFGRAAELLHISQPPLTRQIAALEKELGAQLFDRSKRAIQLTA 60 Query: 61 AGQDFYERSRRILLDLDRAVAQARTIGKGEHGALRL--LHSSSVPLSAPLGPTLNAALKD 118 AG+ FY + I L+RA + G+ GAL++ + S++ + + +AA Sbjct: 61 AGKYFYRDTTEIFKALERAKRNVSSSSTGKSGALKVGFMMSTAYNILPSVTRHYSAA--- 117 Query: 119 FPGISLEISQAPSEYQAREIVEGSADIGLARLPILRAHPNLESTVLYRERLVAAVPATHR 178 +P + + +++ A +I + D+G+ P L+S +Y E L+A +P HR Sbjct: 118 YPEVDMRLTEYVPNLLATDIEDEKIDVGIMYRP--EDCRRLDSHTIYAEPLLAVLPRDHR 175 Query: 179 LAARSEVEIAELRDEFFVTVPHRDRGGLSYLVAERCIAHGFYPRVA 224 LA R + AEL ++ F+++P + L+ + C HGF PR+ Sbjct: 176 LAGRQSISAAELAEDAFISIPRMIAPVVYDLIQQHCQLHGFRPRIV 221 >gi|300312961|ref|YP_003777053.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 98.2 bits (243), Expect = 9e-22, Method: Compositional matrix adjust. Identities = 68/224 (30%), Positives = 110/224 (49%), Gaps = 3/224 (1%) Query: 2 ISIRQLRYFVEIVEARGYTRASERLFIAQSALSRQIKELEADLDVVLIKREAKAFELTQA 61 + +R L+YF + ++RA+E L IAQ LSRQI++LE L V LI R ++ LT A Sbjct: 1 MELRHLKYFNAVASTLSFSRAAELLHIAQPPLSRQIRQLEEMLGVELIDRASRPIALTMA 60 Query: 62 GQDFYERSRRILLDLDRAVAQARTIGKGEHGALRLLHSSSVPLSAPLGPTLNAALKDFPG 121 G+ FYE++ ++L L++ R I +G + S L L + + P Sbjct: 61 GKFFYEQTLQVLSRLEQIEEGTRVIARGRQHWFNIGFVPSA-LYGLLPEMIKRFRTEMPE 119 Query: 122 ISLEISQAPSEYQAREIVEGSADIGLARLPILRAHPNLESTVLYRERLVAAVPATHRLAA 181 I + S+ + Q + G D+G RLPI + P++ + E LVA P H L A Sbjct: 120 IEIGFSEIVTMEQVEALKSGRIDVGFGRLPI--SDPDIVCETIVEEPLVAVFPLGHPLLA 177 Query: 182 RSEVEIAELRDEFFVTVPHRDRGGLSYLVAERCIAHGFYPRVAR 225 R++V +A+L + F+ P R R + V + + P + + Sbjct: 178 RNKVTLAQLAAQRFILYPARPRPSYADQVLDIFSSRALRPSIVK 221 >gi|300310637|ref|YP_003774729.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 326 Score = 94.4 bits (233), Expect = 1e-20, Method: Compositional matrix adjust. Identities = 66/203 (32%), Positives = 106/203 (52%), Gaps = 4/203 (1%) Query: 2 ISIRQLRYFVEIVEARGYTRASERLFIAQSALSRQIKELEADLDVVLIKREAKAFELTQA 61 + IRQL+YFV + R +TRASE+L IAQ LSRQI+ LE +L V L+ R ++ LT+A Sbjct: 1 MDIRQLKYFVAVANTRNFTRASEQLHIAQPPLSRQIQLLEEELGVQLLLRNSRPLRLTEA 60 Query: 62 GQDFYERSRRILLDLDRAVAQARTIGKGEHGALRLLHSSSVPLSAPLGPTLNAALKDFPG 121 G+ FYE++ +IL LD+ + IG + L + +S L L + + +P Sbjct: 61 GRVFYEQALQILNRLDQLKNATQQIGLNQRQTLSIGFVAST-LYGGLPMLVRKLRQHYPE 119 Query: 122 ISLEISQAPSEYQAREIVEGSADIGLARLPILRAHPNLESTVLYRERLVAAVPATHRLAA 181 + +++ + S Q + G D+G R I + VL E+LV A+P + LA Sbjct: 120 VDIQLLELTSMQQFAALKSGRIDVGFGR--IRSNDATVARIVLREEKLVLAIPPSFALAG 177 Query: 182 RSE-VEIAELRDEFFVTVPHRDR 203 ++ V + E+ + + P R Sbjct: 178 SNQRVSLKEVHGQKLIVYPKEPR 200 >gi|300312965|ref|YP_003777057.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 93.2 bits (230), Expect = 2e-20, Method: Compositional matrix adjust. Identities = 74/228 (32%), Positives = 112/228 (49%), Gaps = 8/228 (3%) Query: 2 ISIRQLRYFVEIVEARGYTRASERLFIAQSALSRQIKELEADLDVVLIKREAKAFELTQA 61 + +R LRYF+ + E + RA+E L IA LS QI++LE L L R +A LT A Sbjct: 1 MELRHLRYFLTVAEELHFARAAEVLGIAPPTLSVQIQQLERQLQAQLFVRGKRAIALTSA 60 Query: 62 GQDFYERSRRILLDLDRAVAQARTIGKGEHGALRLLHSSSVPLSAPLGPTLNAALKDFPG 121 G+DF ++R +L ++A+ R G+GE G + + + S L L+A + +P Sbjct: 61 GEDFVVQARAVLARFEQAIDAGRRAGRGEMGRVEVGYVGSAVFGGILQQQLSAFRQRWPQ 120 Query: 122 ISLEISQAPSEYQAREIVEGSADIGLARLPILRAHPNLESTVLYRERLVAAVPATHRLAA 181 + + + P + EG DI RLP+ L+S VL R+R A+P H LA+ Sbjct: 121 VLVHAREWPMLQLGAALEEGKLDIAFVRLPVPLGQ-TLQSHVLLRDRFCLALPTDHALAS 179 Query: 182 R-SEVEIAELRDEFFVTVPHRDRGGLSYLVAERCIAHGFYPRVARXPG 228 + + L E F+ +P ++ G S V R GF PR PG Sbjct: 180 KPGAIRSRALAGEDFI-LPEQELG--SREVWRRG---GFAPRRVSRPG 221 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 0.138 0.407 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: 950,690 Number of extensions: 40020 Number of successful extensions: 242 Number of sequences better than 1.0e-08: 48 Number of HSP's gapped: 223 Number of HSP's successfully gapped: 48 Length of query: 316 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 231 Effective length of database: 1,217,395 Effective search space: 281218245 Effective search space used: 281218245 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)