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= 0001.1039.p (203 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310563|ref|YP_003774655.1| response regulator protein [Her... 260 7e-71 gi|300312940|ref|YP_003777032.1| nitrate/nitrite response regula... 96 2e-21 gi|300311281|ref|YP_003775373.1| LuxR family response regulator ... 92 4e-20 gi|300311885|ref|YP_003775977.1| LuxR family two component respo... 90 2e-19 gi|300312077|ref|YP_003776169.1| response regulator containing a... 77 8e-16 >gi|300310563|ref|YP_003774655.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 204 Score = 260 bits (664), Expect = 7e-71, Method: Compositional matrix adjust. Identities = 151/205 (73%), Positives = 168/205 (81%), Gaps = 3/205 (1%) Query: 1 MPISRLLIIDDHALFRCGLRLVLQAALPQATISEAGSLEDAM--RAEDAQAPDMVLLDIQ 58 M LLIIDDHALFR GLRLVLQ +LPQA +SEA SLE+A+ + ++ AP ++L+DIQ Sbjct: 1 MSTPHLLIIDDHALFRSGLRLVLQNSLPQARLSEAASLEEALHLQGDEEDAPTLLLIDIQ 60 Query: 59 LGGLNGIDGMAVLARKWPDVPIIILSADDTDGTVRAATQRGAAAFVSKAATAEHILQVLL 118 LGGLNGIDGMAVLAR+WP VP IILSADDTD TVR A QRGA+AFVSKAATAEHI+ V+ Sbjct: 61 LGGLNGIDGMAVLARRWPGVPAIILSADDTDHTVRQALQRGASAFVSKAATAEHIMAVIA 120 Query: 119 EVAGGRHTLPTPSGQVEASAKPQFTPRQYEVLGLLSQGLTNKAIGRRLNLSENTIRGHVQ 178 +V GG G + K QFTPRQYEVLGLLSQGLTNKAIGRRLNLSENTIRGHVQ Sbjct: 121 KVGGGLTPCQNLRGD-QPDDKAQFTPRQYEVLGLLSQGLTNKAIGRRLNLSENTIRGHVQ 179 Query: 179 AILAALEVDNRAEAAFAARRRGLVS 203 AIL AL+VDNRAEAAFAARRRGLVS Sbjct: 180 AILLALDVDNRAEAAFAARRRGLVS 204 >gi|300312940|ref|YP_003777032.1| nitrate/nitrite response regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 219 Score = 95.9 bits (237), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 61/212 (28%), Positives = 112/212 (52%), Gaps = 15/212 (7%) Query: 5 RLLIIDDHALFRCGLRLVLQAALPQATISEAGSLEDAMRAEDAQAPDMVLLDIQLGGLNG 64 R+L++DDH LFR G+RL+LQ + EA D ++ PD+VL+D+ + GL+G Sbjct: 4 RILLVDDHTLFRSGIRLLLQRHPDIDVVGEAVDGLDGVKRALQLRPDVVLMDLNMPGLSG 63 Query: 65 IDGMAVLARKWPDVPIIILSADDTDGTVRAATQRGAAAFVSKAATAEHILQVLLEVAGGR 124 ++ M ++ + P+ +++LS + + A GA ++ K A++++Q + A G Sbjct: 64 LEAMQLIVQDLPETAVLMLSVSEEADDLTTALHNGARGYLLKNIEADYLVQSIKRAAAGE 123 Query: 125 HTLPTP------------SGQVEAS-AKP--QFTPRQYEVLGLLSQGLTNKAIGRRLNLS 169 + +G AS A+P + T R+ + +++G +NK I R L ++ Sbjct: 124 PVISESMTAKLVMQLRAGAGNPAASAAEPTDKLTARERATMVCIARGQSNKEIARSLEVA 183 Query: 170 ENTIRGHVQAILAALEVDNRAEAAFAARRRGL 201 E+T++ HVQ +L L++ +R + A A GL Sbjct: 184 ESTVKIHVQNLLRKLQLSSRVQIAVYAVEHGL 215 >gi|300311281|ref|YP_003775373.1| LuxR family response regulator protein [Herbaspirillum seropedicae SmR1] Length = 217 Score = 91.7 bits (226), Expect = 4e-20, Method: Compositional matrix adjust. Identities = 67/198 (33%), Positives = 106/198 (53%), Gaps = 4/198 (2%) Query: 6 LLIIDDHALFRCGLRLVLQAALPQATISEAGSLEDAMRAEDAQAPDMVLLDIQLGGLNGI 65 +++IDDH L R GLR L+ ++EAG ++A+ A AQ D+ L+DI + G+NGI Sbjct: 14 IMLIDDHPLVRDGLRARLETVPGLEVVAEAGHADEALAAAAAQEIDLTLMDINMRGINGI 73 Query: 66 DGMAVLARKWPDVPIIILSADDTDGTVRAATQRGAAAFVSKAATAEHILQVLLEV-AGGR 124 + A+ + P++ ++ILS D V + Q GA +V K A ++ I+ + V +GG Sbjct: 74 ELTALFHARHPEIAVLILSMHDKAEYVMQSIQAGARGYVLKDAPSQDIVHAIETVRSGGI 133 Query: 125 HTLPTPSGQVEASAKPQ--FTPRQYEVLGLLSQGLTNKAIGRRLNLSENTIRGHVQAILA 182 + + Q+ P+ T R+ EVL ++ G +NK I R L+LS T+ H I Sbjct: 134 YYSAALARQLTQPLPPRELLTQREREVLMHIANGESNKQIARELDLSVRTVETHRLNIKR 193 Query: 183 ALEVDNRAE-AAFAARRR 199 L +D +AE FA R Sbjct: 194 KLNIDGQAELIKFAVESR 211 >gi|300311885|ref|YP_003775977.1| LuxR family two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 216 Score = 89.7 bits (221), Expect = 2e-19, Method: Compositional matrix adjust. Identities = 57/195 (29%), Positives = 99/195 (50%), Gaps = 11/195 (5%) Query: 3 ISRLLIIDDHALFRCGLRLVLQAALPQATISEAGSLEDAMRAEDAQAPDMVLLDIQLGGL 62 ++R+++ DDHAL R G++ +L A + EA + + PD+VLLDI + G+ Sbjct: 2 LTRIMLADDHALVRSGIKALLTAMPGVEVVGEASDGAEVIEMIPQLKPDLVLLDIAMKGM 61 Query: 63 NGIDGMAVLARKWPDVPIIILSADDTDGTVRAATQRGAAAFVSKAATAEHILQVLLEVAG 122 NG++ + L ++P + ++LS ++ V A GA ++ K + A + + L EV Sbjct: 62 NGLEALRRLRGEYPTIRFLMLSMYGSEEYVMQALNAGANGYLFKDSAATELEKALYEVKH 121 Query: 123 GRHTLPTP---------SGQVEASAKP--QFTPRQYEVLGLLSQGLTNKAIGRRLNLSEN 171 GR L + +V + P TPRQ E+L L+++G K I +LN+S Sbjct: 122 GRQYLDSHISREALDNYMKRVAQNGTPVEVLTPRQREILQLIAEGNNTKEIAYQLNVSAK 181 Query: 172 TIRGHVQAILAALEV 186 TI H ++ L++ Sbjct: 182 TIETHRAQLMERLDI 196 >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 = 77.4 bits (189), Expect = 8e-16, Method: Compositional matrix adjust. Identities = 61/208 (29%), Positives = 104/208 (50%), Gaps = 11/208 (5%) Query: 5 RLLIIDDHALFRCGLRLVLQAALPQATISEAGSLEDAMRAEDAQAPDMVLLDIQLGGLNG 64 ++LI DDHA+ R GLR + + A + +A++ D++LLDI L NG Sbjct: 10 KVLIADDHAIVREGLRQICAGSKDIMVAGNAANGLEAIKLAREGNGDVLLLDIVLPDRNG 69 Query: 65 IDGMAVLARKWPDVPIIILSADDTDGTVRAATQRGAAAFVSKAATAEHILQVLLEVAGGR 124 ID + + ++ P++P++ILS D A + GAA F++K A +L + + A GR Sbjct: 70 IDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQAAPAELLAAIRQAASGR 129 Query: 125 HTLPTPSGQVEASAKPQF---TP-------RQYEVLGLLSQGLTNKAIGRRLNLSENTIR 174 + +PS E + + F TP R+Y+ + +++ G T I L LS TI Sbjct: 130 KYV-SPSLAQELANQIGFDHETPLHETLSDREYQTMVMIASGKTVSDIAAELTLSVKTIS 188 Query: 175 GHVQAILAALEVDNRAEAAFAARRRGLV 202 + +L+ +++ + AE A + LV Sbjct: 189 MYRSRVLSKMKMRHNAELTHYALKNALV 216 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 0.320 0.134 0.374 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: 591,491 Number of extensions: 23875 Number of successful extensions: 186 Number of sequences better than 1.0e-08: 9 Number of HSP's gapped: 181 Number of HSP's successfully gapped: 9 Length of query: 203 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 122 Effective length of database: 1,236,335 Effective search space: 150832870 Effective search space used: 150832870 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 (21.8 bits) S2: 128 (53.9 bits)