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= 0001.0099.p (139 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310423|ref|YP_003774515.1| GntR family transcription regul... 269 6e-74 gi|300311238|ref|YP_003775330.1| LacI family transcription regul... 101 2e-23 gi|300310488|ref|YP_003774580.1| LacI family transcription regul... 85 2e-18 gi|300311611|ref|YP_003775703.1| transcription regulator DNA-bin... 68 2e-13 gi|300309618|ref|YP_003773710.1| LacI family transcription regul... 67 5e-13 >gi|300310423|ref|YP_003774515.1| GntR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 269 bits (688), Expect = 6e-74, Method: Compositional matrix adjust. Identities = 125/139 (89%), Positives = 134/139 (96%) Query: 1 MMKRREGFRKGLLEAGIKPEIEVLLPEPTTVDMGAQLLRRVLEQHPECDSVFCCNDDLAL 60 MMKRREGFRKGL EAG+ +IEVLLP+PTTVDMGAQLLRRVL+ HP+CDSVFCCNDDLAL Sbjct: 214 MMKRREGFRKGLQEAGLAADIEVLLPQPTTVDMGAQLLRRVLQDHPDCDSVFCCNDDLAL 273 Query: 61 GALFECQRQGISVPREMAIAGFNDLSWAACATPSITTVVTPRYDIGYKSAEMLVRQLKGE 120 GALFECQRQGISVPR+MAIAGFNDLSWAACATPSITTVVTPRYDIGY+SAEMLVRQLKGE Sbjct: 274 GALFECQRQGISVPRQMAIAGFNDLSWAACATPSITTVVTPRYDIGYQSAEMLVRQLKGE 333 Query: 121 DIPKGRLDLGFELALREST 139 +I KGRLDLGFELA+REST Sbjct: 334 EIAKGRLDLGFELAVREST 352 >gi|300311238|ref|YP_003775330.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 340 Score = 101 bits (252), Expect = 2e-23, Method: Compositional matrix adjust. Identities = 51/138 (36%), Positives = 79/138 (57%) Query: 2 MKRREGFRKGLLEAGIKPEIEVLLPEPTTVDMGAQLLRRVLEQHPECDSVFCCNDDLALG 61 M R G R+ L G + +++P + G + + R+L QHPE D+ F ND +A G Sbjct: 203 MARVAGLRESLRHHGAAEPVHLVMPMGAFLQAGREAIGRLLTQHPEVDAAFFSNDVIAAG 262 Query: 62 ALFECQRQGISVPREMAIAGFNDLSWAACATPSITTVVTPRYDIGYKSAEMLVRQLKGED 121 A EC R+GI+VP +A+AGF +L A P++TTV + IG +AEML+ + G+ Sbjct: 263 AALECARRGIAVPGRIALAGFANLEIATEVLPALTTVQISAHQIGLTAAEMLLTRFDGDP 322 Query: 122 IPKGRLDLGFELALREST 139 + + DLG+ + R+ST Sbjct: 323 LDQAVHDLGYSILERDST 340 >gi|300310488|ref|YP_003774580.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 85.1 bits (209), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 39/111 (35%), Positives = 68/111 (61%) Query: 28 PTTVDMGAQLLRRVLEQHPECDSVFCCNDDLALGALFECQRQGISVPREMAIAGFNDLSW 87 PTT+ G Q L +L+ P+ D++FC +D LALG + E Q +GI++P ++A+ GF DL + Sbjct: 254 PTTLGQGRQGLAELLQAQPDLDAIFCSSDLLALGVMIEAQSRGIAIPEQLAVVGFGDLEF 313 Query: 88 AACATPSITTVVTPRYDIGYKSAEMLVRQLKGEDIPKGRLDLGFELALRES 138 + P +TTV IG ++A ++ + G ++ + +D+GF + R+S Sbjct: 314 SRDLQPRLTTVRIDGTGIGQRAARFIIDRAAGIEVAERVVDVGFSIIARDS 364 >gi|300311611|ref|YP_003775703.1| transcription regulator DNA-binding repressor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 68.2 bits (165), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 44/140 (31%), Positives = 70/140 (50%), Gaps = 3/140 (2%) Query: 3 KRREGFRKGLLEAGIKPEIEVLLPEPTTVDMGAQLLRRVLEQHP---ECDSVFCCNDDLA 59 +R GFR+ L + G+ LL + G Q R+L+ P D++FCCND +A Sbjct: 191 ERVRGFRQTLEQGGLALADSDLLHADFSGIGGYQAAMRLLQGRPADQRPDAIFCCNDMMA 250 Query: 60 LGALFECQRQGISVPREMAIAGFNDLSWAACATPSITTVVTPRYDIGYKSAEMLVRQLKG 119 +G L I VP E+++ GF+D+ A P +TTV +G +A+ L+ ++ Sbjct: 251 IGVLRAAGELQIEVPGELSVVGFDDIELAQFVHPPLTTVAQNTRKLGNLTAQFLLERIAD 310 Query: 120 EDIPKGRLDLGFELALREST 139 +P R + +L LR ST Sbjct: 311 PSLPARRETVAPQLQLRGST 330 >gi|300309618|ref|YP_003773710.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 338 Score = 67.0 bits (162), Expect = 5e-13, Method: Compositional matrix adjust. Identities = 38/120 (31%), Positives = 59/120 (49%), Gaps = 16/120 (13%) Query: 3 KRREGFRKGLLEAGIKPEIEVLLPEPT--------TVDMGAQLLRRVLEQHPECDSVFCC 54 +R GF EAG P PT TV+ G + +L +HP+ ++F Sbjct: 195 ERYRGFASACKEAG--------HPHPTQRTRYINDTVESGYRATMELLREHPQVTAIFAS 246 Query: 55 NDDLALGALFECQRQGISVPREMAIAGFNDLSWAACATPSITTVVTPRYDIGYKSAEMLV 114 ND ALGA+ G++VPR++++ G D+ WA + P++TTV P S E+L+ Sbjct: 247 NDLPALGAMNAIADMGMNVPRDVSVTGITDIQWARVSRPALTTVAVPTEAAARMSIELLL 306 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 0.139 0.415 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: 446,896 Number of extensions: 17240 Number of successful extensions: 48 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 48 Number of HSP's successfully gapped: 7 Length of query: 139 Length of database: 1,619,870 Length adjustment: 76 Effective length of query: 63 Effective length of database: 1,260,010 Effective search space: 79380630 Effective search space used: 79380630 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: 126 (53.1 bits)