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= 0001.0100.p (215 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... 291 3e-80 gi|300310488|ref|YP_003774580.1| LacI family transcription regul... 107 7e-25 gi|300311238|ref|YP_003775330.1| LacI family transcription regul... 97 2e-21 gi|300311611|ref|YP_003775703.1| transcription regulator DNA-bin... 72 4e-14 gi|300309932|ref|YP_003774024.1| transcription regulator protein... 67 1e-12 >gi|300310423|ref|YP_003774515.1| GntR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 291 bits (745), Expect = 3e-80, Method: Compositional matrix adjust. Identities = 145/160 (90%), Positives = 152/160 (95%) Query: 1 MTQRAAPKSKPKAPPAVRGSRATGRVTIIDVAAEAGVSPMTVSRALKNPRLVQEQSRQRI 60 MTQRAA KSKPK+PPAVRGSRATGRVTIIDVAAEAGVSPMTVSRALK P LVQEQSRQRI Sbjct: 1 MTQRAASKSKPKSPPAVRGSRATGRVTIIDVAAEAGVSPMTVSRALKTPALVQEQSRQRI 60 Query: 61 LEAIDRLGYVPNQAASTLASARSQVIAVLVPSLTNAVFIETLSGIRDYLAGAGYQFLIGE 120 LEAID+LGYVPNQAA+TLASARSQV+AVLVPSLTNAVFIETLSGIRDYLA GYQFLIGE Sbjct: 61 LEAIDKLGYVPNQAAATLASARSQVVAVLVPSLTNAVFIETLSGIRDYLASVGYQFLIGE 120 Query: 121 TGYVRAKEEQLIATYLAHAPAGFLLSSSEQHDILQARPGS 160 TGY R KEE+LIATYLAHAPAGFLLSSS+QHDILQ+RP S Sbjct: 121 TGYDRHKEEELIATYLAHAPAGFLLSSSQQHDILQSRPAS 160 >gi|300310488|ref|YP_003774580.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 107 bits (267), Expect = 7e-25, Method: Compositional matrix adjust. Identities = 58/143 (40%), Positives = 91/143 (63%), Gaps = 1/143 (0%) Query: 5 AAPKSKPKAPPAVRGSRAT-GRVTIIDVAAEAGVSPMTVSRALKNPRLVQEQSRQRILEA 63 A+ + A P RGSR + G VT+ DVA AGV+P+T SRAL P V + Q++ EA Sbjct: 14 ASHQDGDAASPRRRGSRKSAGGVTLRDVAQLAGVAPITASRALNTPSAVSPKVLQKVREA 73 Query: 64 IDRLGYVPNQAASTLASARSQVIAVLVPSLTNAVFIETLSGIRDYLAGAGYQFLIGETGY 123 +++ GYVPN A LAS +S+++AV+VP++ VF E + + + LA AGYQ ++G++GY Sbjct: 74 VEKTGYVPNLLAGGLASNKSRLVAVVVPTVIGPVFQEIVHTLTETLAAAGYQVMLGQSGY 133 Query: 124 VRAKEEQLIATYLAHAPAGFLLS 146 ++E+ L+ + P G +L+ Sbjct: 134 ENSREDALLEAIIGRRPDGVVLT 156 >gi|300311238|ref|YP_003775330.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 340 Score = 96.7 bits (239), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 60/165 (36%), Positives = 92/165 (55%), Gaps = 9/165 (5%) Query: 10 KPKAPPAVRGSRATGRVTIIDVAAEAGVSPMTVSRALKNPRLVQEQSRQRILEAIDRLGY 69 KP+ PPA+ T VT DVA AGVS +TVSR + +P V +R+R+ I +GY Sbjct: 4 KPE-PPAM----PTRAVTKEDVARAAGVSHITVSRVINSPEKVSPATRERVEAFIASMGY 58 Query: 70 VPNQAASTLASARSQVIAVLVPSLTNAVFIETLSGIRDYLAGAGYQFLIGETGYVRAKEE 129 +PN A LAS R++++A +VP++++++F ETL G+ + L GYQ L+G+T Y E Sbjct: 59 IPNLLAGGLASRRTRIVAAIVPTISHSIFAETLRGLSEQLCMQGYQLLLGQTNYSEEAET 118 Query: 130 QLIATYLAHAPAGFLLSSSEQHDILQARPGSXQGISRRCACSTWD 174 L+ ++ G +L+ QH + + GI TWD Sbjct: 119 GLVEVFIGRRVDGLVLTGV-QHSPMTRQRLKAAGIP---VVETWD 159 >gi|300311611|ref|YP_003775703.1| transcription regulator DNA-binding repressor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 72.0 bits (175), Expect = 4e-14, Method: Compositional matrix adjust. Identities = 43/127 (33%), Positives = 65/127 (51%) Query: 27 TIIDVAAEAGVSPMTVSRALKNPRLVQEQSRQRILEAIDRLGYVPNQAASTLASARSQVI 86 TI DVA AGVS TVS L R V +R+R+L A+ L YVP+ A +L S + I Sbjct: 3 TIKDVARLAGVSYTTVSHVLNQTRPVSSDARERVLAAVKELDYVPSALARSLRSKVTGSI 62 Query: 87 AVLVPSLTNAVFIETLSGIRDYLAGAGYQFLIGETGYVRAKEEQLIATYLAHAPAGFLLS 146 +++P+ TN F E GI D+ GAGY ++ + K+ + G +++ Sbjct: 63 GLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDPDKQRDYLQVLQTKHCDGLIIA 122 Query: 147 SSEQHDI 153 + Q D+ Sbjct: 123 TLNQADL 129 >gi|300309932|ref|YP_003774024.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 358 Score = 67.0 bits (162), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 41/125 (32%), Positives = 63/125 (50%) Query: 25 RVTIIDVAAEAGVSPMTVSRALKNPRLVQEQSRQRILEAIDRLGYVPNQAASTLASARSQ 84 R +I VA AGVS TVSR L P V ++ ++I +I LG+ PN L + S+ Sbjct: 2 RPSIKQVAHLAGVSIATVSRLLNKPGSVSAETAEKIHRSIAELGFRPNFTGRNLRAGNSR 61 Query: 85 VIAVLVPSLTNAVFIETLSGIRDYLAGAGYQFLIGETGYVRAKEEQLIATYLAHAPAGFL 144 + V+VP+L+N VF + L GI Y + T Y+ +E + L H G + Sbjct: 62 TVGVVVPTLSNTVFAQCLQGIELAARALDYSVMFTTTEYLPEEETAAVELLLGHRVDGMI 121 Query: 145 LSSSE 149 L+ ++ Sbjct: 122 LTVAD 126 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 0.318 0.128 0.377 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: 607,456 Number of extensions: 22094 Number of successful extensions: 114 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 113 Number of HSP's successfully gapped: 7 Length of query: 215 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 134 Effective length of database: 1,236,335 Effective search space: 165668890 Effective search space used: 165668890 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 128 (53.9 bits)