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= 0001.4413.p (300 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313807|ref|YP_003777899.1| AraC family transcription regul... 502 e-143 gi|300313797|ref|YP_003777889.1| AraC family transcription regul... 127 1e-30 gi|300311694|ref|YP_003775786.1| AraC family transcription regul... 63 3e-11 gi|300309514|ref|YP_003773606.1| AraC family transcription regul... 59 6e-10 gi|300311726|ref|YP_003775818.1| AraC family transcription regul... 56 4e-09 >gi|300313807|ref|YP_003777899.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 299 Score = 502 bits (1292), Expect = e-143, Method: Compositional matrix adjust. Identities = 244/300 (81%), Positives = 272/300 (90%), Gaps = 1/300 (0%) Query: 1 MSALATVSPHAMRSDSLGCSATHLKQSQELQGSEFSFYRKRVEGQEVSQVYTPASDRGFL 60 M+ALA +S A RSDSLGCSA LK SQELQGS+FSFYRKRVEG+E++QV TPASDRGFL Sbjct: 1 MAALAPLSTIAERSDSLGCSARSLKHSQELQGSDFSFYRKRVEGEEIAQVVTPASDRGFL 60 Query: 61 VGISLAPRHQRSILRGRQRTQFDFAPGAVYTRDFSEDYRADLQTPFDFLLVELPLSWFAA 120 +GISLAP H+RSI RGRQ +F+FAPGA+YTRDFSEDYRADLQ PFDFLLVE+PLSWFAA Sbjct: 61 LGISLAP-HRRSIFRGRQGAKFEFAPGAIYTRDFSEDYRADLQAPFDFLLVEMPLSWFAA 119 Query: 121 ASDELRGRRVSGLSTVTGQADPVLAHLAWALAPALAWPDPDNQLFIDQLGLAMGTHLLQR 180 ASDELR RRV+GL+TVTGQ DPVL HLA+AL PALA PDPD++LFIDQLG+A+GTHLLQR Sbjct: 120 ASDELRRRRVAGLATVTGQHDPVLQHLAYALTPALANPDPDSRLFIDQLGVALGTHLLQR 179 Query: 181 YGGVTLPTTRPVRLSRLHEERAKEMLLQKVKGNVCIPDIARECNMSASYFLRAFKASTGY 240 YGG PT R LSRLHEERAK MLL+KVKGNV IP+IARECNMSASYFLRAFKASTG+ Sbjct: 180 YGGAPAPTLRTAPLSRLHEERAKMMLLEKVKGNVSIPEIARECNMSASYFLRAFKASTGH 239 Query: 241 TPHQWLLVQRVEMAREYLRHTQLSLAEIAVACDFYDQSHFSRVFSQVVGSTPGAWRRKLR 300 TPHQWL+VQRVEMA++YLR TQL+LAEIA+ACDFYDQSHFSRVFSQVVGSTPGAWRR+LR Sbjct: 240 TPHQWLMVQRVEMAQQYLRSTQLTLAEIALACDFYDQSHFSRVFSQVVGSTPGAWRRRLR 299 >gi|300313797|ref|YP_003777889.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 294 Score = 127 bits (318), Expect = 1e-30, Method: Compositional matrix adjust. Identities = 80/220 (36%), Positives = 114/220 (51%), Gaps = 9/220 (4%) Query: 87 GAVYTRDFSEDYRADLQTPFDFLLVELPLSWFAAASDELRGRRVSGLSTVTGQADPVLAH 146 G V D E +R + ++ + + +P + +E+ R V L V G ADPVL H Sbjct: 74 GEVAVTDLREQWRCQHLSGYENVRLLVPRTAMEELGEEI-ARPVGELRPVQGAADPVLFH 132 Query: 147 LAWALAPALAWPDPD-------NQLFIDQLGLAMGTHLLQRYGG-VTLPTTRPVRLSRLH 198 LA A+ PA LF+D + LA+ THL QRYG + P + RL+ Sbjct: 133 LAQAMLPAARTAGAAGAASVASETLFLDSMMLALTTHLWQRYGQQSSRPASAAGRLAGWQ 192 Query: 199 EERAKEMLLQKVKGNVCIPDIARECNMSASYFLRAFKASTGYTPHQWLLVQRVEMAREYL 258 E R ++ +L + + + +IA + +S ++F RAFK S G +PH WL QR+ +A L Sbjct: 193 EARVRDFMLSHLAQRLSLAEIAAQSGLSRAHFSRAFKQSFGLSPHAWLQQQRIALACRLL 252 Query: 259 RHTQLSLAEIAVACDFYDQSHFSRVFSQVVGSTPGAWRRK 298 S+ IA+ C F DQSHFSRVF QV G P AW R+ Sbjct: 253 HEGGKSMTTIALECGFSDQSHFSRVFKQVQGMGPAAWLRR 292 >gi|300311694|ref|YP_003775786.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 375 Score = 63.2 bits (152), Expect = 3e-11, Method: Compositional matrix adjust. Identities = 35/106 (33%), Positives = 56/106 (52%), Gaps = 3/106 (2%) Query: 196 RLHEERAKEMLL---QKVKGNVCIPDIARECNMSASYFLRAFKASTGYTPHQWLLVQRVE 252 R ER ++ L+ + + ++ + + A +MS F R FK TG TPH +L R+E Sbjct: 249 RHRSERIQKALIWLDEHMSSSINMSEAADHVSMSERNFQREFKRETGETPHCFLTKIRIE 308 Query: 253 MAREYLRHTQLSLAEIAVACDFYDQSHFSRVFSQVVGSTPGAWRRK 298 A YL+ T L + +IA C H +R+F + G +PG +R+K Sbjct: 309 AACLYLKETDLPIEKIARRCGLVSGEHLARLFRKHHGVSPGEYRKK 354 >gi|300309514|ref|YP_003773606.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 323 Score = 58.5 bits (140), Expect = 6e-10, Method: Compositional matrix adjust. Identities = 31/100 (31%), Positives = 55/100 (55%) Query: 201 RAKEMLLQKVKGNVCIPDIARECNMSASYFLRAFKASTGYTPHQWLLVQRVEMAREYLRH 260 +A + +L+ + +P +A C+MS + F+R F TP Q L+ R+ A L + Sbjct: 217 KAMQAMLKAPAEDWSLPRLAALCHMSRATFIRRFAEVGASTPAQVLMQLRMAQAARLLSY 276 Query: 261 TQLSLAEIAVACDFYDQSHFSRVFSQVVGSTPGAWRRKLR 300 ++ + A+I A + ++ F+RVF + G PGA+RR+ R Sbjct: 277 SKQATAQIGEAVGYQSEAAFNRVFRKYSGMGPGAYRRQAR 316 >gi|300311726|ref|YP_003775818.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 304 Score = 55.8 bits (133), Expect = 4e-09, Method: Compositional matrix adjust. Identities = 30/80 (37%), Positives = 44/80 (55%) Query: 216 IPDIARECNMSASYFLRAFKASTGYTPHQWLLVQRVEMAREYLRHTQLSLAEIAVACDFY 275 + +AR +S S F F + G P +LL R+E+ARE LR +LS++EIA + Sbjct: 214 VAQLARIAALSRSSFFERFTRTLGVAPMAYLLAWRMEIARELLRRGELSVSEIAERTGYG 273 Query: 276 DQSHFSRVFSQVVGSTPGAW 295 S FS F++ VG PG + Sbjct: 274 STSAFSVAFTRQVGQPPGLY 293 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 0.134 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: 893,024 Number of extensions: 33505 Number of successful extensions: 126 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 124 Number of HSP's successfully gapped: 5 Length of query: 300 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 215 Effective length of database: 1,217,395 Effective search space: 261739925 Effective search space used: 261739925 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 (22.0 bits) S2: 130 (54.7 bits)