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= 0028.0012.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|300311885|ref|YP_003775977.1| LuxR family two component respo... 365 e-102 gi|300311281|ref|YP_003775373.1| LuxR family response regulator ... 135 2e-33 gi|300312940|ref|YP_003777032.1| nitrate/nitrite response regula... 128 4e-31 gi|300310532|ref|YP_003774624.1| virulence regulator protein [He... 127 6e-31 gi|300312077|ref|YP_003776169.1| response regulator containing a... 115 3e-27 >gi|300311885|ref|YP_003775977.1| LuxR family two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 216 Score = 365 bits (937), Expect = e-102, Method: Compositional matrix adjust. Identities = 178/216 (82%), Positives = 197/216 (91%) Query: 1 MLTRIVLADDHALVRSGIKSLLMAMPGIEVVGEADDGNAAIELTEKLRPDVVVMDIAMKG 60 MLTRI+LADDHALVRSGIK+LL AMPG+EVVGEA DG IE+ +L+PD+V++DIAMKG Sbjct: 1 MLTRIMLADDHALVRSGIKALLTAMPGVEVVGEASDGAEVIEMIPQLKPDLVLLDIAMKG 60 Query: 61 MNGLEAVRRLRADHPATKFLMLSMYGSEEYVMQALNAGANGYLFKDSAAYELEKALIEVI 120 MNGLEA+RRLR ++P +FLMLSMYGSEEYVMQALNAGANGYLFKDSAA ELEKAL EV Sbjct: 61 MNGLEALRRLRGEYPTIRFLMLSMYGSEEYVMQALNAGANGYLFKDSAATELEKALYEVK 120 Query: 121 QGRQYLDSHISKDALDLYMKKVAQGGMPVEVLTPRQREILQLIAEGNNTKEIAYRLNVSA 180 GRQYLDSHIS++ALD YMK+VAQ G PVEVLTPRQREILQLIAEGNNTKEIAY+LNVSA Sbjct: 121 HGRQYLDSHISREALDNYMKRVAQNGTPVEVLTPRQREILQLIAEGNNTKEIAYQLNVSA 180 Query: 181 KTIETHRAQLMERLEIRDVPGLVRYAIRTGLTTSDK 216 KTIETHRAQLMERL+IRDVPGLVRYAIRTG+ T DK Sbjct: 181 KTIETHRAQLMERLDIRDVPGLVRYAIRTGIATPDK 216 >gi|300311281|ref|YP_003775373.1| LuxR family response regulator protein [Herbaspirillum seropedicae SmR1] Length = 217 Score = 135 bits (341), Expect = 2e-33, Method: Compositional matrix adjust. Identities = 76/205 (37%), Positives = 121/205 (59%), Gaps = 8/205 (3%) Query: 5 IVLADDHALVRSGIKSLLMAMPGIEVVGEADDGNAAIELTEKLRPDVVVMDIAMKGMNGL 64 I+L DDH LVR G+++ L +PG+EVV EA + A+ D+ +MDI M+G+NG+ Sbjct: 14 IMLIDDHPLVRDGLRARLETVPGLEVVAEAGHADEALAAAAAQEIDLTLMDINMRGINGI 73 Query: 65 EAVRRLRADHPATKFLMLSMYGSEEYVMQALNAGANGYLFKDSAAYELEKALIEVIQGRQ 124 E A HP L+LSM+ EYVMQ++ AGA GY+ KD+ + ++ A+ V G Sbjct: 74 ELTALFHARHPEIAVLILSMHDKAEYVMQSIQAGARGYVLKDAPSQDIVHAIETVRSGGI 133 Query: 125 YLDSHISKDALDLYMKKVAQGGMPVEVLTPRQREILQLIAEGNNTKEIAYRLNVSAKTIE 184 Y + ++ +++ Q P E+LT R+RE+L IA G + K+IA L++S +T+E Sbjct: 134 YYSAALA--------RQLTQPLPPRELLTQREREVLMHIANGESNKQIARELDLSVRTVE 185 Query: 185 THRAQLMERLEIRDVPGLVRYAIRT 209 THR + +L I L+++A+ + Sbjct: 186 THRLNIKRKLNIDGQAELIKFAVES 210 >gi|300312940|ref|YP_003777032.1| nitrate/nitrite response regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 219 Score = 128 bits (322), Expect = 4e-31, Method: Compositional matrix adjust. Identities = 82/218 (37%), Positives = 120/218 (55%), Gaps = 4/218 (1%) Query: 1 MLTRIVLADDHALVRSGIKSLLMAMPGIEVVGEADDGNAAIELTEKLRPDVVVMDIAMKG 60 M RI+L DDH L RSGI+ LL P I+VVGEA DG ++ +LRPDVV+MD+ M G Sbjct: 1 MAIRILLVDDHTLFRSGIRLLLQRHPDIDVVGEAVDGLDGVKRALQLRPDVVLMDLNMPG 60 Query: 61 MNGLEAVRRLRADHPATKFLMLSMYGSEEYVMQALNAGANGYLFKDSAAYELEKALIEVI 120 ++GLEA++ + D P T LMLS+ + + AL+ GA GYL K+ A L +++ Sbjct: 61 LSGLEAMQLIVQDLPETAVLMLSVSEEADDLTTALHNGARGYLLKNIEADYLVQSIKRAA 120 Query: 121 QGRQYL-DSHISKDALDLYM---KKVAQGGMPVEVLTPRQREILQLIAEGNNTKEIAYRL 176 G + +S +K + L A P + LT R+R + IA G + KEIA L Sbjct: 121 AGEPVISESMTAKLVMQLRAGAGNPAASAAEPTDKLTARERATMVCIARGQSNKEIARSL 180 Query: 177 NVSAKTIETHRAQLMERLEIRDVPGLVRYAIRTGLTTS 214 V+ T++ H L+ +L++ + YA+ GL S Sbjct: 181 EVAESTVKIHVQNLLRKLQLSSRVQIAVYAVEHGLDKS 218 >gi|300310532|ref|YP_003774624.1| virulence regulator protein [Herbaspirillum seropedicae SmR1] Length = 209 Score = 127 bits (319), Expect = 6e-31, Method: Compositional matrix adjust. Identities = 67/211 (31%), Positives = 124/211 (58%), Gaps = 5/211 (2%) Query: 2 LTRIVLADDHALVRSGIKSLLMAMPGIEVVGEADDGNAAIELTEKLRPDVVVMDIAMKGM 61 +T+I++ DDHA+VR+G+ + +P +E+ GEA AI L D+V++DIAM Sbjct: 1 MTKILVVDDHAVVRAGVHHFISEIPSMEIGGEASTAEEAIRLVRTQDWDIVLLDIAMPDK 60 Query: 62 NGLEAVRRLRADHPATKFLMLSMYGSEEYVMQALNAGANGYLFKDSAAYELEKALIEVIQ 121 +G+E +++++ + P LMLSM+ Y +Q L +GA+GY+ K++ A EL A+ +++ Sbjct: 61 SGVEVLKQIKREKPELPVLMLSMHPESRYAVQVLRSGASGYVQKEALATELVNAINTILR 120 Query: 122 GRQYLDSHISKDALDLYMKKVAQGGMPV-EVLTPRQREILQLIAEGNNTKEIAYRLNVSA 180 G +Y IS +L + P+ E L+ R+ EI + +G +IA L +S Sbjct: 121 GHKY----ISYGVAELLTSEPVDSEKPLHETLSQREYEIFYKLGQGQGVTQIADELCLSV 176 Query: 181 KTIETHRAQLMERLEIRDVPGLVRYAIRTGL 211 KT+ T+R+++++++ + + ++ YAI+ L Sbjct: 177 KTVSTYRSRVLQKMSMTNNADIIYYAIKNNL 207 >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 = 115 bits (288), Expect = 3e-27, Method: Compositional matrix adjust. Identities = 65/213 (30%), Positives = 124/213 (58%), Gaps = 12/213 (5%) Query: 4 RIVLADDHALVRSGIKSLLMAMPGIEVVGEADDGNAAIELTEKLRPDVVVMDIAMKGMNG 63 ++++ADDHA+VR G++ + I V G A +G AI+L + DV+++DI + NG Sbjct: 10 KVLIADDHAIVREGLRQICAGSKDIMVAGNAANGLEAIKLAREGNGDVLLLDIVLPDRNG 69 Query: 64 LEAVRRLRADHPATKFLMLSMYGSEEYVMQALNAGANGYLFKDSAAYELEKALIEVIQGR 123 ++ ++++R + P L+LS++ ++Y ++AL AGA G+L K +A EL A+ + GR Sbjct: 70 IDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQAAPAELLAAIRQAASGR 129 Query: 124 QYLDSHISKDALDLYMKKVAQGGM----PV-EVLTPRQREILQLIAEGNNTKEIAYRLNV 178 +Y+ ++++ + Q G P+ E L+ R+ + + +IA G +IA L + Sbjct: 130 KYVSPSLAQELAN-------QIGFDHETPLHETLSDREYQTMVMIASGKTVSDIAAELTL 182 Query: 179 SAKTIETHRAQLMERLEIRDVPGLVRYAIRTGL 211 S KTI +R++++ ++++R L YA++ L Sbjct: 183 SVKTISMYRSRVLSKMKMRHNAELTHYALKNAL 215 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 0.135 0.364 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: 624,106 Number of extensions: 24060 Number of successful extensions: 193 Number of sequences better than 1.0e-08: 17 Number of HSP's gapped: 192 Number of HSP's successfully gapped: 17 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)