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= 0001.0129.p (158 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310436|ref|YP_003774528.1| LysR family transcription regul... 291 2e-80 gi|300312961|ref|YP_003777053.1| transcription regulator protein... 77 5e-16 gi|300313102|ref|YP_003777194.1| LysR family transcription regul... 71 4e-14 gi|300312750|ref|YP_003776842.1| LysR family transcription regul... 65 2e-12 gi|300309864|ref|YP_003773956.1| LysR family transcription regul... 65 3e-12 >gi|300310436|ref|YP_003774528.1| LysR family transcription regulator [Herbaspirillum seropedicae SmR1] Length = 300 Score = 291 bits (744), Expect = 2e-80, Method: Compositional matrix adjust. Identities = 145/158 (91%), Positives = 153/158 (96%) Query: 1 MQGKIDAGLLLPPLPEKAAAVLDVRPVLSEPLIAALPEGAVKRRGPVSLKSLRELPLIIF 60 +QGKIDAGLLLPPLPEKAAA+L+VRPVLSEPLIAALPEGAV++RGPVSLKSLRELPLIIF Sbjct: 143 LQGKIDAGLLLPPLPEKAAALLEVRPVLSEPLIAALPEGAVRKRGPVSLKSLRELPLIIF 202 Query: 61 PRRIAPAFHDTILSCFRDAGVTPHIGQEAIQMQTIVGLVSAGMGMALVPQSVSNLKRPGV 120 PRRIAPAFHDTILSCFRDAGVTPHIGQEAIQMQTIVGLVSAGMGMALVPQSVSNLKRPGV Sbjct: 203 PRRIAPAFHDTILSCFRDAGVTPHIGQEAIQMQTIVGLVSAGMGMALVPQSVSNLKRPGV 262 Query: 121 DYRRLSDAAPEIQTGLAWRRDNPSGVLRALLDLLEMPA 158 DYRRLSD AP IQT LAWRRD+PS VLRALL+LL+ PA Sbjct: 263 DYRRLSDPAPAIQTSLAWRRDSPSSVLRALLELLDEPA 300 >gi|300312961|ref|YP_003777053.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 77.4 bits (189), Expect = 5e-16, Method: Compositional matrix adjust. Identities = 51/149 (34%), Positives = 79/149 (53%), Gaps = 4/149 (2%) Query: 3 GKIDAGLLLPPLPEKAAAVLDVRPVLSEPLIAALPEGA-VKRRGPVSLKSLRELPLIIFP 61 G+ID G P+ + + ++ EPL+A P G + R V+L L I++P Sbjct: 139 GRIDVGFGRLPISDPD---IVCETIVEEPLVAVFPLGHPLLARNKVTLAQLAAQRFILYP 195 Query: 62 RRIAPAFHDTILSCFRDAGVTPHIGQEAIQMQTIVGLVSAGMGMALVPQSVSNLKRPGVD 121 R P++ D +L F + P I +EA +MQT +GLV+AG+G+ LVP+SV L R V Sbjct: 196 ARPRPSYADQVLDIFSSRALRPSIVKEANEMQTAIGLVAAGVGVTLVPRSVQGLHRSDVV 255 Query: 122 YRRLSDAAPEIQTGLAWRRDNPSGVLRAL 150 YR LS+ + +R ++ S +L L Sbjct: 256 YRPLSNKGVHSPVIMNFRANDRSLLLERL 284 >gi|300313102|ref|YP_003777194.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 71.2 bits (173), Expect = 4e-14, Method: Compositional matrix adjust. Identities = 49/150 (32%), Positives = 73/150 (48%), Gaps = 5/150 (3%) Query: 4 KIDAGLLLPPLPEKAAAVLDVRPVLSEPLIAALP-EGAVKRRGPVSLKSLRELPLIIFPR 62 KID G++ P + LD + +EPL+A LP + + R +S L E I PR Sbjct: 141 KIDVGIMYRP---EDCRRLDSHTIYAEPLLAVLPRDHRLAGRQSISAAELAEDAFISIPR 197 Query: 63 RIAPAFHDTILSCFRDAGVTPHIGQEAIQMQTIVGLVSAGMGMALVPQSVSNLKRPGVDY 122 IAP +D I + G P I E QTIV LV G+G+ALVP S+ + + Sbjct: 198 MIAPVVYDLIQQHCQLHGFRPRIVLETNLQQTIVNLVGEGLGVALVPTSMQAMHLDTTVF 257 Query: 123 RRLSDAAPEIQTGLAWRRDNPSGVLRALLD 152 + L AP ++ + W +DN + +R + Sbjct: 258 KPLI-GAPMVEVAVIWNKDNTNPCIRTFAE 286 >gi|300312750|ref|YP_003776842.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 322 Score = 65.5 bits (158), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 45/153 (29%), Positives = 83/153 (54%), Gaps = 13/153 (8%) Query: 4 KIDAGLLLPPLPEKAAAVLDVRPVLSEPLIAALP------EGAVKRRGPVSLKSLRELPL 57 ++D + P+ + L + +L E ++AALP +G +R ++L +L E Sbjct: 159 RLDLAFVRSPVGDSGG--LTIETMLEEDMVAALPIDHPLVDGG--KRKSIALHALAEESF 214 Query: 58 IIFPRRIAPAFHDTILSCFRDAGVTPHIGQEAIQMQTIVGLVSAGMGMALVPQSVSNLKR 117 I+ R P +DTI++ AG +P + QEA + + + LV+AG+G+ ++P S++ + Sbjct: 215 IMTRRPNGPGLYDTIIAACHAAGFSPQVIQEARKNLSTLSLVAAGVGVTVIPASMTRVNA 274 Query: 118 PGVDYRRLSDAAPEIQT--GLAWRRDNPSGVLR 148 GV Y +L+ AP+++ LA+R + SG R Sbjct: 275 EGVVYLKLT-GAPDLKAPLHLAYRTGSISGAAR 306 >gi|300309864|ref|YP_003773956.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 306 Score = 65.1 bits (157), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 44/145 (30%), Positives = 71/145 (48%), Gaps = 6/145 (4%) Query: 3 GKIDAGLLLPPLPEKAAAVLDVRPVLSEPLIAALPEG-AVKRRGPVSLKSLRELPLIIFP 61 ID G L P + L+++ V E L+ A+P+G A+ ++ L P I+ Sbjct: 140 NTIDIGFLRPVASRQP---LELQLVDEEALVLAMPQGHALAAYDRIATTQLDGQPFIMHS 196 Query: 62 RRIAPAFHDTILSCFRDAGVTPHIGQEAIQMQTIVGLVSAGMGMALVPQSVSNLKRPGVD 121 F++ I++ A V P Q Q TI+ LV AG+G+ ++P S V+ Sbjct: 197 PTHGKYFYERIMAMLGAADVKPDFTQYIDQSHTILSLVRAGLGVGILPASAQRFHYDRVE 256 Query: 122 YRRLSDAAPEIQTGLAWR--RDNPS 144 +R L+D AP + +AWR +DNP+ Sbjct: 257 FRPLADEAPRAEMSMAWRPDQDNPA 281 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 0.139 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: 513,036 Number of extensions: 21724 Number of successful extensions: 96 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 96 Number of HSP's successfully gapped: 7 Length of query: 158 Length of database: 1,619,870 Length adjustment: 78 Effective length of query: 80 Effective length of database: 1,250,540 Effective search space: 100043200 Effective search space used: 100043200 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 (21.8 bits) S2: 127 (53.5 bits)