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= 0028.0052.p (129 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311281|ref|YP_003775373.1| LuxR family response regulator ... 224 2e-60 gi|300311885|ref|YP_003775977.1| LuxR family two component respo... 106 6e-25 gi|300310532|ref|YP_003774624.1| virulence regulator protein [He... 91 4e-20 gi|300312431|ref|YP_003776523.1| two component LuxR family trans... 80 5e-17 gi|300312940|ref|YP_003777032.1| nitrate/nitrite response regula... 76 9e-16 >gi|300311281|ref|YP_003775373.1| LuxR family response regulator protein [Herbaspirillum seropedicae SmR1] Length = 217 Score = 224 bits (570), Expect = 2e-60, Method: Compositional matrix adjust. Identities = 121/128 (94%), Positives = 123/128 (96%) Query: 1 MLIDDHPLVRDGLRARLETVPGLEVVAEAGNAEEALAAAARHPIDLTLMDINMRGINGIE 60 MLIDDHPLVRDGLRARLETVPGLEVVAEAG+A+EALAAAA IDLTLMDINMRGINGIE Sbjct: 15 MLIDDHPLVRDGLRARLETVPGLEVVAEAGHADEALAAAAAQEIDLTLMDINMRGINGIE 74 Query: 61 LTARFHALHPEIAVLILSMHDKAEYVMQSIQAGARGYVLKDAPSQDIVHAIETVRSGGIY 120 LTA FHA HPEIAVLILSMHDKAEYVMQSIQAGARGYVLKDAPSQDIVHAIETVRSGGIY Sbjct: 75 LTALFHARHPEIAVLILSMHDKAEYVMQSIQAGARGYVLKDAPSQDIVHAIETVRSGGIY 134 Query: 121 YSAALARQ 128 YSAALARQ Sbjct: 135 YSAALARQ 142 >gi|300311885|ref|YP_003775977.1| LuxR family two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 216 Score = 106 bits (265), Expect = 6e-25, Method: Compositional matrix adjust. Identities = 53/128 (41%), Positives = 80/128 (62%) Query: 1 MLIDDHPLVRDGLRARLETVPGLEVVAEAGNAEEALAAAARHPIDLTLMDINMRGINGIE 60 ML DDH LVR G++A L +PG+EVV EA + E + + DL L+DI M+G+NG+E Sbjct: 6 MLADDHALVRSGIKALLTAMPGVEVVGEASDGAEVIEMIPQLKPDLVLLDIAMKGMNGLE 65 Query: 61 LTARFHALHPEIAVLILSMHDKAEYVMQSIQAGARGYVLKDAPSQDIVHAIETVRSGGIY 120 R +P I L+LSM+ EYVMQ++ AGA GY+ KD+ + ++ A+ V+ G Y Sbjct: 66 ALRRLRGEYPTIRFLMLSMYGSEEYVMQALNAGANGYLFKDSAATELEKALYEVKHGRQY 125 Query: 121 YSAALARQ 128 + ++R+ Sbjct: 126 LDSHISRE 133 >gi|300310532|ref|YP_003774624.1| virulence regulator protein [Herbaspirillum seropedicae SmR1] Length = 209 Score = 90.5 bits (223), Expect = 4e-20, Method: Compositional matrix adjust. Identities = 46/126 (36%), Positives = 77/126 (61%) Query: 1 MLIDDHPLVRDGLRARLETVPGLEVVAEAGNAEEALAAAARHPIDLTLMDINMRGINGIE 60 +++DDH +VR G+ + +P +E+ EA AEEA+ D+ L+DI M +G+E Sbjct: 5 LVVDDHAVVRAGVHHFISEIPSMEIGGEASTAEEAIRLVRTQDWDIVLLDIAMPDKSGVE 64 Query: 61 LTARFHALHPEIAVLILSMHDKAEYVMQSIQAGARGYVLKDAPSQDIVHAIETVRSGGIY 120 + + PE+ VL+LSMH ++ Y +Q +++GA GYV K+A + ++V+AI T+ G Y Sbjct: 65 VLKQIKREKPELPVLMLSMHPESRYAVQVLRSGASGYVQKEALATELVNAINTILRGHKY 124 Query: 121 YSAALA 126 S +A Sbjct: 125 ISYGVA 130 >gi|300312431|ref|YP_003776523.1| two component LuxR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 282 Score = 80.1 bits (196), Expect = 5e-17, Method: Compositional matrix adjust. Identities = 49/129 (37%), Positives = 71/129 (55%), Gaps = 2/129 (1%) Query: 2 LIDDHPLVRDGLRARLETVPGLEVVAEAGNAEEALAAAARHPIDLTLMDINM--RGINGI 59 L+DDH +VR GL ARL P LEVV ++E + A P DL L+D ++ I+G+ Sbjct: 51 LLDDHAVVRYGLAARLAEEPDLEVVGSFATSKELMTALRASPADLLLIDYSLGSNDIDGL 110 Query: 60 ELTARFHALHPEIAVLILSMHDKAEYVMQSIQAGARGYVLKDAPSQDIVHAIETVRSGGI 119 L P +L+ S H+ V +++AGARG+V K ++V AI TV G Sbjct: 111 NLIRALRVRFPRSKILVTSAHNNPATVALAMKAGARGFVGKSQELGELVQAIRTVSVGRE 170 Query: 120 YYSAALARQ 128 Y +AA+AR+ Sbjct: 171 YLNAAMARE 179 >gi|300312940|ref|YP_003777032.1| nitrate/nitrite response regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 219 Score = 75.9 bits (185), Expect = 9e-16, Method: Compositional matrix adjust. Identities = 42/117 (35%), Positives = 72/117 (61%) Query: 1 MLIDDHPLVRDGLRARLETVPGLEVVAEAGNAEEALAAAARHPIDLTLMDINMRGINGIE 60 +L+DDH L R G+R L+ P ++VV EA + + + A + D+ LMD+NM G++G+E Sbjct: 6 LLVDDHTLFRSGIRLLLQRHPDIDVVGEAVDGLDGVKRALQLRPDVVLMDLNMPGLSGLE 65 Query: 61 LTARFHALHPEIAVLILSMHDKAEYVMQSIQAGARGYVLKDAPSQDIVHAIETVRSG 117 PE AVL+LS+ ++A+ + ++ GARGY+LK+ + +V +I+ +G Sbjct: 66 AMQLIVQDLPETAVLMLSVSEEADDLTTALHNGARGYLLKNIEADYLVQSIKRAAAG 122 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 0.321 0.136 0.379 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: 328,852 Number of extensions: 10174 Number of successful extensions: 96 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 99 Number of HSP's successfully gapped: 7 Length of query: 129 Length of database: 1,619,870 Length adjustment: 75 Effective length of query: 54 Effective length of database: 1,264,745 Effective search space: 68296230 Effective search space used: 68296230 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: 125 (52.8 bits)