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= 0001.0082.p (248 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309415|ref|YP_003773507.1| two component response regulato... 456 e-130 gi|300313791|ref|YP_003777883.1| response regulator protein [Her... 76 3e-15 gi|300313916|ref|YP_003778008.1| two component response regulato... 73 2e-14 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 66 2e-12 gi|300310849|ref|YP_003774941.1| two component transcription reg... 65 4e-12 >gi|300309415|ref|YP_003773507.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 249 Score = 456 bits (1174), Expect = e-130, Method: Compositional matrix adjust. Identities = 233/249 (93%), Positives = 234/249 (93%), Gaps = 1/249 (0%) Query: 1 MANILVVDDEMGIRELLSEILGDEGHVVTTAENAQQARELRQAGVPDLVLLDIWMPDTDG 60 MANILVVDDEMGIRELLSEILGDEGHVVTTAENAQQARELRQAGVPDLVLLDIWMPDTDG Sbjct: 1 MANILVVDDEMGIRELLSEILGDEGHVVTTAENAQQARELRQAGVPDLVLLDIWMPDTDG 60 Query: 61 VTLLKEWQRDGLLTMPVIMMSGHATIDTAVEATRIGALNFLEKPIALQKLLKAVQQGLSH 120 VTLLKEWQRDGLLTMPVIMMSGHATIDTAVEATRIGALNFLEKPIALQKLLKAVQQGLSH Sbjct: 61 VTLLKEWQRDGLLTMPVIMMSGHATIDTAVEATRIGALNFLEKPIALQKLLKAVQQGLSH 120 Query: 121 SREAVRPASYRPAPVAAVANGATDGLHV-EHVTPATTYAPALGGEALHQGAPAAAPFGQV 179 SREAVRPA YRPAPVAAV NGA DGLH EH P YAPALGGE LH G A+ PFGQV Sbjct: 121 SREAVRPAGYRPAPVAAVVNGAADGLHTPEHAAPVAAYAPALGGEPLHHGTTASTPFGQV 180 Query: 180 ADNAANISFDLPLREARDAFERAYFEYHLVRENGSMTRVAERTGLERTHLYRKLKQLGVE 239 ADNAANISFDLPLREARDAFERAYFEYHLVRENGSMTRVAERTGLERTHLYRKLKQLGVE Sbjct: 181 ADNAANISFDLPLREARDAFERAYFEYHLVRENGSMTRVAERTGLERTHLYRKLKQLGVE 240 Query: 240 PGKLARKNH 248 PGKLARKNH Sbjct: 241 PGKLARKNH 249 >gi|300313791|ref|YP_003777883.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 206 Score = 75.9 bits (185), Expect = 3e-15, Method: Compositional matrix adjust. Identities = 43/116 (37%), Positives = 67/116 (57%), Gaps = 1/116 (0%) Query: 3 NILVVDDEMGIRELLSEILGDEGHVVTTAENAQQARELRQAGVPDLVLLDIWMPDTDGVT 62 + VVDD+ +R L +L G+ +A + + R VP +LLD+ MP +DG Sbjct: 4 TVFVVDDDNMVRTALLRLLASAGYAAHGFASADEFLQARLPAVPCCLLLDMKMPGSDGFE 63 Query: 63 LLKEWQRDGLLTMPVIMMSGHATIDTAVEATRIGALNFLEKPIALQKLLKAVQQGL 118 +++ +R G +PVI +SG+ TI T V+A + GA FL KPI ++LL AV++ L Sbjct: 64 VVRRLERRGD-AIPVIFISGYGTIPTTVQAMKAGAHEFLTKPIQDERLLGAVEEAL 118 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 73.2 bits (178), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 67/205 (32%), Positives = 97/205 (47%), Gaps = 20/205 (9%) Query: 1 MANILVVDDEMGIRELLSEILGDEGHVVTTAENAQQARELRQAGVPDLVLLDIWMPDTDG 60 MA IL+VDD+ R L+E + D GH V A + +L A D ++D+ MPD DG Sbjct: 1 MARILIVDDDAAFRGSLAETVSDLGHDVLEAGSTAAGLKLLAAHAVDAAIVDLRMPDEDG 60 Query: 61 VTLLKEWQRDGLLTMPVIMMSGHATIDTAVEATRIGALNFLEKPI----ALQKLLKAVQQ 116 + L+ + + +P IM++ +A+ D +EA R+GA + L KP+ ++ L +A++Q Sbjct: 61 LAFLQ--RAPAIAAIPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETLERALRQ 118 Query: 117 GLSHSREAVRPASYRPAPVA----------AVANGATDGLHVEHVTPATTYAPALGGEAL 166 G S A R V + AT V V T L AL Sbjct: 119 GASTPAAASPATEERNQLVGESEAMRQVFKQIGRAATSDATV-LVLGETGTGKELVARAL 177 Query: 167 HQ-GAPAAAPFGQVADNAANISFDL 190 H+ GA AA PF VA N A I +L Sbjct: 178 HRNGARAARPF--VAVNCAAIPAEL 200 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 66.2 bits (160), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 65/205 (31%), Positives = 98/205 (47%), Gaps = 20/205 (9%) Query: 1 MANILVVDDEMGIRELLSEILGDEGHVVTTAENAQQARELRQAGVPDLVLLDIWMPDTDG 60 M I +VDD+ IR +L + L E + +A+ A Q G P +++ DI MP G Sbjct: 1 MKPIWIVDDDESIRWVLEKALARENLATQSFSSARDAIAALQNGTPQVLVSDIRMPGASG 60 Query: 61 VTLLK--EWQRDGLLTMPVIMMSGHATIDTAVEATRIGALNFLEKPIALQKLLKAVQQGL 118 + LL+ + + G+ PVI+++ + +D+AV A + GA +L KP + K ++ +++ L Sbjct: 61 LELLQTVKAKHPGI---PVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRAL 117 Query: 119 SHS-RE-------AVRPASYRPAPVAAVANGATDGLHVEHVTPATTYAPALGGE----AL 166 S RE A P AP A L +VT T G E AL Sbjct: 118 DESLRETDIEQGAAQTPEILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARAL 177 Query: 167 HQGAP-AAAPFGQVADNAANISFDL 190 H+ +P A+ PF VA N A I DL Sbjct: 178 HKHSPRASQPF--VALNTAAIPKDL 200 >gi|300310849|ref|YP_003774941.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 248 Score = 65.5 bits (158), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 48/162 (29%), Positives = 78/162 (48%), Gaps = 3/162 (1%) Query: 2 ANILVVDDEMGIRELLSEILGDEGHVVTTAENAQQARELRQAGVPDLVLLDIWMPDTDGV 61 +ILVVDD+ IR LL+E L G TA N + R + + DL++LD+ +P DG+ Sbjct: 8 THILVVDDDRDIRTLLAEYLDSNGLRTLTATNGSEMRRVLEESRVDLIVLDLTLPGEDGL 67 Query: 62 TLLKEWQRDGLLTMPVIMMSGHATIDTAVEATRIGALNFLEKPIALQKLLKAVQQGLSHS 121 TL + + ++PVIM++ + +GA ++L KP ++L ++ L + Sbjct: 68 TLCRNLRATS--SVPVIMLTARGEPLDRILGLEMGADDYLAKPFEPRELFARIRSVLRRT 125 Query: 122 REAVRPASYRPAPVAAVANGATDGLHVEHVTPATTYAPALGG 163 +A+ P +P A G T L H+ AL G Sbjct: 126 -QALPPNMAQPDVAAMRFAGWTLDLTARHLVNRDGVVVALSG 166 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 0.317 0.133 0.382 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: 838,716 Number of extensions: 38497 Number of successful extensions: 312 Number of sequences better than 1.0e-08: 32 Number of HSP's gapped: 318 Number of HSP's successfully gapped: 32 Length of query: 248 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 165 Effective length of database: 1,226,865 Effective search space: 202432725 Effective search space used: 202432725 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 (21.7 bits) S2: 129 (54.3 bits)