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= 0116.0001.p (147 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310849|ref|YP_003774941.1| two component transcription reg... 266 7e-73 gi|300313665|ref|YP_003777757.1| two component transcription reg... 157 2e-40 gi|300313830|ref|YP_003777922.1| response regulator protein [Her... 134 2e-33 gi|300311469|ref|YP_003775561.1| oxidative stress resistance two... 108 2e-25 gi|300310592|ref|YP_003774684.1| phosphate regulon two-component... 92 2e-20 >gi|300310849|ref|YP_003774941.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 248 Score = 266 bits (679), Expect = 7e-73, Method: Compositional matrix adjust. Identities = 127/147 (86%), Positives = 138/147 (93%) Query: 1 MGADDYLAKPFEPRELFARIRSVLRRTLALPPSMMRPEAKTMHFSGWTLDLTARHLLNPE 60 MGADDYLAKPFEPRELFARIRSVLRRT ALPP+M +P+ M F+GWTLDLTARHL+N + Sbjct: 99 MGADDYLAKPFEPRELFARIRSVLRRTQALPPNMAQPDVAAMRFAGWTLDLTARHLVNRD 158 Query: 61 GVVVALSGAEFRMLKVFLDHPNRILNRDQLLELTQGREADPFDRSVDIQISRLRQKLGDD 120 GVVVALSGAEFR+LKVFLDHPNR+LNRDQLLELTQGRE+DPFDRSVDIQISRLRQKLGDD Sbjct: 159 GVVVALSGAEFRLLKVFLDHPNRVLNRDQLLELTQGRESDPFDRSVDIQISRLRQKLGDD 218 Query: 121 ARTPTIIKTIRNEGYVLATAVTSEDAG 147 ARTPTIIKT+RNEGYVLAT VT+E AG Sbjct: 219 ARTPTIIKTVRNEGYVLATTVTTEGAG 245 >gi|300313665|ref|YP_003777757.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 240 Score = 157 bits (398), Expect = 2e-40, Method: Compositional matrix adjust. Identities = 71/141 (50%), Positives = 99/141 (70%) Query: 1 MGADDYLAKPFEPRELFARIRSVLRRTLALPPSMMRPEAKTMHFSGWTLDLTARHLLNPE 60 +GADDYL KPF+PREL ARI+ +LRR + P + +HF+GW LD AR ++P Sbjct: 96 VGADDYLPKPFDPRELLARIKVILRRARSFPEKLEADRVSHIHFAGWKLDTQARQAISPS 155 Query: 61 GVVVALSGAEFRMLKVFLDHPNRILNRDQLLELTQGREADPFDRSVDIQISRLRQKLGDD 120 GV + L G+++++L+ L+HP R L+RD LL G+EA PFDRS+D+ ISRLRQ+LGD+ Sbjct: 156 GVTITLGGSDYQVLRALLEHPRRALSRDFLLNTVYGKEAMPFDRSIDVCISRLRQQLGDN 215 Query: 121 ARTPTIIKTIRNEGYVLATAV 141 R P +I+T+RN GY+L V Sbjct: 216 PREPALIRTVRNTGYMLMADV 236 >gi|300313830|ref|YP_003777922.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 237 Score = 134 bits (338), Expect = 2e-33, Method: Compositional matrix adjust. Identities = 64/146 (43%), Positives = 101/146 (69%), Gaps = 4/146 (2%) Query: 1 MGADDYLAKPFEPRELFARIRSVLRRTLALPPSMMRPEAKTMHFSGWTLDLTARHLLNPE 60 +GADDY+AKP+ PREL ARI+++ RR + + S + F+G++LD R L++ + Sbjct: 96 LGADDYIAKPYSPRELLARIKAIHRR-IGIDSS---AAPRYYRFAGFSLDTVERTLVDSQ 151 Query: 61 GVVVALSGAEFRMLKVFLDHPNRILNRDQLLELTQGREADPFDRSVDIQISRLRQKLGDD 120 G +V L+G ++++LK F++HP +L+R+ L E T+GR+A P DRS+D+QIS+LR +L D Sbjct: 152 GDIVPLTGMDYQLLKYFVEHPGDVLDRNVLCEETRGRDAGPLDRSLDVQISKLRLRLNDG 211 Query: 121 ARTPTIIKTIRNEGYVLATAVTSEDA 146 R P +IKT+R GYV + V++ A Sbjct: 212 GRQPHLIKTVRGAGYVFSADVSAAAA 237 >gi|300311469|ref|YP_003775561.1| oxidative stress resistance two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 253 Score = 108 bits (270), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 66/141 (46%), Positives = 87/141 (61%), Gaps = 8/141 (5%) Query: 1 MGADDYLAKPFEPRELFARIRSVLRRT----LALPPSMMRPEAKTMHFSGWTLDLTARHL 56 MGADDYL KPF PREL ARI +VLRR L PS PE T F + LDL R L Sbjct: 110 MGADDYLPKPFNPRELVARINAVLRRKGPDELPGAPSET-PE--TFEFGDFILDLGTRTL 166 Query: 57 LNPEGVVVALSGAEFRMLKVFLDHPNRILNRDQLLELTQGREADPFDRSVDIQISRLRQK 116 G ++L+ EF +LKVF + + L+R++L+E+ +GRE + FDRS+D+QISRLR+ Sbjct: 167 -KKNGDTISLTTGEFSVLKVFARNARQPLSREKLMEMARGREYEVFDRSLDVQISRLRKL 225 Query: 117 LGDDARTPTIIKTIRNEGYVL 137 + D P I+T+ GYV Sbjct: 226 IEPDPANPLYIQTVWGLGYVF 246 >gi|300310592|ref|YP_003774684.1| phosphate regulon two-component response regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 245 Score = 92.0 bits (227), Expect = 2e-20, Method: Compositional matrix adjust. Identities = 57/145 (39%), Positives = 81/145 (55%), Gaps = 24/145 (16%) Query: 2 GADDYLAKPFEPRELFARIRSVLRRTLALPPSMMRPEAKTMHFSGWTLDLTARHLLNPEG 61 GADDY+ KPF PREL ARI+++LRR PE S + L +P Sbjct: 117 GADDYITKPFSPRELTARIKALLRRK--------SPEHAQEVMSAGPITL------DPAS 162 Query: 62 VVVALSGA-------EFRMLKVFLDHPNRILNRDQLLELTQGREADPFDRSVDIQISRLR 114 V+LSGA E+++LK FL HP+R+ +R QLL+ G +R+VD+ + RLR Sbjct: 163 CSVSLSGARIDIGHAEYKLLKFFLAHPDRVFSRSQLLDRVWGDHVVIEERTVDVHVLRLR 222 Query: 115 QKLGDDARTPTIIKTIRNEGYVLAT 139 + L D +IKT+R+ GY+L+T Sbjct: 223 KALRD---AEYLIKTVRSVGYMLST 244 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 0.137 0.396 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: 445,066 Number of extensions: 16965 Number of successful extensions: 122 Number of sequences better than 1.0e-08: 22 Number of HSP's gapped: 106 Number of HSP's successfully gapped: 22 Length of query: 147 Length of database: 1,619,870 Length adjustment: 77 Effective length of query: 70 Effective length of database: 1,255,275 Effective search space: 87869250 Effective search space used: 87869250 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)