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= 0005.0170.p (216 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312077|ref|YP_003776169.1| response regulator containing a... 384 e-108 gi|300310532|ref|YP_003774624.1| virulence regulator protein [He... 209 1e-55 gi|300311885|ref|YP_003775977.1| LuxR family two component respo... 123 1e-29 gi|300312940|ref|YP_003777032.1| nitrate/nitrite response regula... 107 1e-24 gi|300312431|ref|YP_003776523.1| two component LuxR family trans... 100 7e-23 >gi|300312077|ref|YP_003776169.1| response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 217 Score = 384 bits (986), Expect = e-108, Method: Compositional matrix adjust. Identities = 186/215 (86%), Positives = 201/215 (93%) Query: 2 KKNSSAIKVAIADDHAIVREGLRQICSGTKDIIVVGNAENGLETIKLTRLGNCDVLLLDI 61 KK ++AIKV IADDHAIVREGLRQIC+G+KDI+V GNA NGLE IKL R GN DVLLLDI Sbjct: 3 KKVTAAIKVLIADDHAIVREGLRQICAGSKDIMVAGNAANGLEAIKLAREGNGDVLLLDI 62 Query: 62 ILPDRTGIDVLKQIKKEIPKLPVLMLSIHREDQYAIRALKAGAAGFLNKQAAPAELINAI 121 +LPDR GID+LKQI+KE P+LPVL+LSIHREDQYAIRALKAGAAGFLNKQAAPAEL+ AI Sbjct: 63 VLPDRNGIDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQAAPAELLAAI 122 Query: 122 RQVAAGRKYISPSLAQELANQIGFDHETPLHETLSDREYQTMVMIASGKTVSDIAAELLL 181 RQ A+GRKY+SPSLAQELANQIGFDHETPLHETLSDREYQTMVMIASGKTVSDIAAEL L Sbjct: 123 RQAASGRKYVSPSLAQELANQIGFDHETPLHETLSDREYQTMVMIASGKTVSDIAAELTL 182 Query: 182 SVKTISMYRSRVLAKMKLRHNAELTHYALKNNLVE 216 SVKTISMYRSRVL+KMK+RHNAELTHYALKN LVE Sbjct: 183 SVKTISMYRSRVLSKMKMRHNAELTHYALKNALVE 217 >gi|300310532|ref|YP_003774624.1| virulence regulator protein [Herbaspirillum seropedicae SmR1] Length = 209 Score = 209 bits (533), Expect = 1e-55, Method: Compositional matrix adjust. Identities = 100/208 (48%), Positives = 146/208 (70%), Gaps = 1/208 (0%) Query: 9 KVAIADDHAIVREGLRQICSGTKDIIVVGNAENGLETIKLTRLGNCDVLLLDIILPDRTG 68 K+ + DDHA+VR G+ S + + G A E I+L R + D++LLDI +PD++G Sbjct: 3 KILVVDDHAVVRAGVHHFISEIPSMEIGGEASTAEEAIRLVRTQDWDIVLLDIAMPDKSG 62 Query: 69 IDVLKQIKKEIPKLPVLMLSIHREDQYAIRALKAGAAGFLNKQAAPAELINAIRQVAAGR 128 ++VLKQIK+E P+LPVLMLS+H E +YA++ L++GA+G++ K+A EL+NAI + G Sbjct: 63 VEVLKQIKREKPELPVLMLSMHPESRYAVQVLRSGASGYVQKEALATELVNAINTILRGH 122 Query: 129 KYISPSLAQELANQIGFDHETPLHETLSDREYQTMVMIASGKTVSDIAAELLLSVKTISM 188 KYIS +A+ L ++ D E PLHETLS REY+ + G+ V+ IA EL LSVKT+S Sbjct: 123 KYISYGVAELLTSE-PVDSEKPLHETLSQREYEIFYKLGQGQGVTQIADELCLSVKTVST 181 Query: 189 YRSRVLAKMKLRHNAELTHYALKNNLVE 216 YRSRVL KM + +NA++ +YA+KNNL++ Sbjct: 182 YRSRVLQKMSMTNNADIIYYAIKNNLID 209 >gi|300311885|ref|YP_003775977.1| LuxR family two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 216 Score = 123 bits (309), Expect = 1e-29, Method: Compositional matrix adjust. Identities = 68/209 (32%), Positives = 127/209 (60%), Gaps = 4/209 (1%) Query: 9 KVAIADDHAIVREGLRQICSGTKDIIVVGNAENGLETIKLTRLGNCDVLLLDIILPDRTG 68 ++ +ADDHA+VR G++ + + + VVG A +G E I++ D++LLDI + G Sbjct: 4 RIMLADDHALVRSGIKALLTAMPGVEVVGEASDGAEVIEMIPQLKPDLVLLDIAMKGMNG 63 Query: 69 IDVLKQIKKEIPKLPVLMLSIHREDQYAIRALKAGAAGFLNKQAAPAELINAIRQVAAGR 128 ++ L++++ E P + LMLS++ ++Y ++AL AGA G+L K +A EL A+ +V GR Sbjct: 64 LEALRRLRGEYPTIRFLMLSMYGSEEYVMQALNAGANGYLFKDSAATELEKALYEVKHGR 123 Query: 129 KYISPSLAQE-LANQIG--FDHETPLHETLSDREYQTMVMIASGKTVSDIAAELLLSVKT 185 +Y+ +++E L N + + TP+ E L+ R+ + + +IA G +IA +L +S KT Sbjct: 124 QYLDSHISREALDNYMKRVAQNGTPV-EVLTPRQREILQLIAEGNNTKEIAYQLNVSAKT 182 Query: 186 ISMYRSRVLAKMKLRHNAELTHYALKNNL 214 I +R++++ ++ +R L YA++ + Sbjct: 183 IETHRAQLMERLDIRDVPGLVRYAIRTGI 211 >gi|300312940|ref|YP_003777032.1| nitrate/nitrite response regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 219 Score = 107 bits (266), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 68/214 (31%), Positives = 117/214 (54%), Gaps = 6/214 (2%) Query: 7 AIKVAIADDHAIVREGLRQICSGTKDIIVVGNAENGLETIKLTRLGNCDVLLLDIILPDR 66 AI++ + DDH + R G+R + DI VVG A +GL+ +K DV+L+D+ +P Sbjct: 2 AIRILLVDDHTLFRSGIRLLLQRHPDIDVVGEAVDGLDGVKRALQLRPDVVLMDLNMPGL 61 Query: 67 TGIDVLKQIKKEIPKLPVLMLSIHREDQYAIRALKAGAAGFLNKQAAPAELINAIRQVAA 126 +G++ ++ I +++P+ VLMLS+ E AL GA G+L K L+ +I++ AA Sbjct: 62 SGLEAMQLIVQDLPETAVLMLSVSEEADDLTTALHNGARGYLLKNIEADYLVQSIKRAAA 121 Query: 127 GRKYISPSLAQELANQIGFDHETPL------HETLSDREYQTMVMIASGKTVSDIAAELL 180 G IS S+ +L Q+ P + L+ RE TMV IA G++ +IA L Sbjct: 122 GEPVISESMTAKLVMQLRAGAGNPAASAAEPTDKLTARERATMVCIARGQSNKEIARSLE 181 Query: 181 LSVKTISMYRSRVLAKMKLRHNAELTHYALKNNL 214 ++ T+ ++ +L K++L ++ YA+++ L Sbjct: 182 VAESTVKIHVQNLLRKLQLSSRVQIAVYAVEHGL 215 >gi|300312431|ref|YP_003776523.1| two component LuxR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 282 Score = 100 bits (250), Expect = 7e-23, Method: Compositional matrix adjust. Identities = 71/238 (29%), Positives = 116/238 (48%), Gaps = 30/238 (12%) Query: 5 SSAIKVAIADDHAIVREGLRQICSGTKDIIVVGNAENGLETIKLTRLGNCDVLLLDIILP 64 +S +++A+ DDHA+VR GL + D+ VVG+ E + R D+LL+D L Sbjct: 44 ASRMRIALLDDHAVVRYGLAARLAEEPDLEVVGSFATSKELMTALRASPADLLLIDYSLG 103 Query: 65 --DRTGIDVLKQIKKEIPKLPVLMLSIHREDQYAIRALKAGAAGFLNKQAAPAELINAIR 122 D G+++++ ++ P+ +L+ S H A+KAGA GF+ K EL+ AIR Sbjct: 104 SNDIDGLNLIRALRVRFPRSKILVTSAHNNPATVALAMKAGARGFVGKSQELGELVQAIR 163 Query: 123 QVAAGRKYISPSLAQELANQIGFDHETPLHE--------------------------TLS 156 V+ GR+Y++ ++A+EL + D TP E +LS Sbjct: 164 TVSVGREYLNAAMARELTAMLASDSPTPAPEGGPPQVRPPRRKRNSPPSSDSLSEMPSLS 223 Query: 157 DREYQTMVMIASGKTVSDIAAELLLSVKTISMYRSRVLAKMKLRHNAEL--THYALKN 212 RE + + G +V+ IA + SVKTIS + K+ +R + EL Y +K+ Sbjct: 224 PREREVLRCCLDGLSVTAIADKFARSVKTISGQKQSAFRKLGVRSDNELFKIEYQIKD 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 0.318 0.134 0.362 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: 577,858 Number of extensions: 21948 Number of successful extensions: 166 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 184 Number of HSP's successfully gapped: 14 Length of query: 216 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 135 Effective length of database: 1,236,335 Effective search space: 166905225 Effective search space used: 166905225 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 (21.7 bits) S2: 128 (53.9 bits)