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= 0001.1140.p (210 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310669|ref|YP_003774761.1| two component response regulato... 411 e-116 gi|300310176|ref|YP_003774268.1| C4-dicarboxylate transport tran... 153 1e-38 gi|300313791|ref|YP_003777883.1| response regulator protein [Her... 140 7e-35 gi|300313031|ref|YP_003777123.1| two component response regulato... 75 6e-15 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 71 7e-14 >gi|300310669|ref|YP_003774761.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 214 Score = 411 bits (1056), Expect = e-116, Method: Compositional matrix adjust. Identities = 198/208 (95%), Positives = 204/208 (98%) Query: 1 METNPPVVYIVDDDEAVRTSLAWLLSSVNIRTECFDGPGAFLKAYDANSLSCLILDVRMP 60 METNPPVVYIVDDDEAVRTSLAWLLSSVNIRTECF+GP AFLKAYDANSLSCLILDVRMP Sbjct: 2 METNPPVVYIVDDDEAVRTSLAWLLSSVNIRTECFEGPEAFLKAYDANSLSCLILDVRMP 61 Query: 61 EISGFQLQDRLKEIGADIPVIFVSGHGDIPMSVRALHNGAVDFLEKPYNSQQMLERIQLT 120 EISGFQLQDRLKEIGADIPVIFVSGHGDIPMSVRALHNGAVDFLEKPYNSQQMLERIQ+T Sbjct: 62 EISGFQLQDRLKEIGADIPVIFVSGHGDIPMSVRALHNGAVDFLEKPYNSQQMLERIQMT 121 Query: 121 LKNVAGNMQARERRQQLKARLKTLTVREREILEKVIMGQSSKLIARDLNISVKTVDVHRA 180 LK+VAGNMQAR RRQQLKARLKTLT REREILEKVIMGQSSKLIAR+LNISVKTVDVHRA Sbjct: 122 LKHVAGNMQARTRRQQLKARLKTLTAREREILEKVIMGQSSKLIARELNISVKTVDVHRA 181 Query: 181 SVKDKLGCQSTATLVRDVLMDFGPEFLK 208 SVKDKLGCQSTATLVRDVLMDFG +FL+ Sbjct: 182 SVKDKLGCQSTATLVRDVLMDFGSDFLR 209 >gi|300310176|ref|YP_003774268.1| C4-dicarboxylate transport transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 196 Score = 153 bits (387), Expect = 1e-38, Method: Compositional matrix adjust. Identities = 83/197 (42%), Positives = 122/197 (61%), Gaps = 11/197 (5%) Query: 7 VVYIVDDDEAVRTSLAWLLSSVNIRTECFDGPGAFLKAYDAN-----SLSCLILDVRMPE 61 +++IVDD+E +R SLAWL S NI +D L A A+ CL+LDVRMP Sbjct: 1 MLHIVDDEEIIRDSLAWLARSRNIAATAYDSGPTLLAALAASPGIDAEGECLLLDVRMPG 60 Query: 62 ISGFQLQDRLKEIG--ADIPVIFVSGHGDIPMSVRALHNGAVDFLEKPYNSQQMLERIQL 119 SG L + LK G PVIF++GHGD+PM+V L NGA DF EKP+N Q+++R+ Sbjct: 61 TSGVALFNDLKTKGLLHRRPVIFLTGHGDVPMAVDMLKNGAFDFFEKPFNDNQLMDRVLE 120 Query: 120 TLKNVAGNMQARERRQQLKARLKTLTVREREILEKVIMGQSSKLIARDLNISVKTVDVHR 179 L + +A +++RL L+VRERE+L+ ++ G+ +K+IA +L IS++TV+VHR Sbjct: 121 AL----ASSRAGGAEDAVQSRLAALSVREREVLDLILAGKMNKVIADELGISMRTVEVHR 176 Query: 180 ASVKDKLGCQSTATLVR 196 A + DK+ ++ L R Sbjct: 177 AHIFDKMNVKTAVELAR 193 >gi|300313791|ref|YP_003777883.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 206 Score = 140 bits (354), Expect = 7e-35, Method: Compositional matrix adjust. Identities = 79/189 (41%), Positives = 113/189 (59%) Query: 8 VYIVDDDEAVRTSLAWLLSSVNIRTECFDGPGAFLKAYDANSLSCLILDVRMPEISGFQL 67 V++VDDD VRT+L LL+S F FL+A CL+LD++MP GF++ Sbjct: 5 VFVVDDDNMVRTALLRLLASAGYAAHGFASADEFLQARLPAVPCCLLLDMKMPGSDGFEV 64 Query: 68 QDRLKEIGADIPVIFVSGHGDIPMSVRALHNGAVDFLEKPYNSQQMLERIQLTLKNVAGN 127 RL+ G IPVIF+SG+G IP +V+A+ GA +FL KP +++L ++ L+ Sbjct: 65 VRRLERRGDAIPVIFISGYGTIPTTVQAMKAGAHEFLTKPIQDERLLGAVEEALQIAERQ 124 Query: 128 MQARERRQQLKARLKTLTVREREILEKVIMGQSSKLIARDLNISVKTVDVHRASVKDKLG 187 +Q+R +RL+TLT RERE+LE I G +K IA +L IS TV VH+ V DK+ Sbjct: 125 LQSRTEHAACTSRLETLTPREREVLELAIGGLLNKQIATELGISEITVKVHKRRVMDKMQ 184 Query: 188 CQSTATLVR 196 ++ A LVR Sbjct: 185 TKTLADLVR 193 >gi|300313031|ref|YP_003777123.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 195 Score = 74.7 bits (182), Expect = 6e-15, Method: Compositional matrix adjust. Identities = 58/195 (29%), Positives = 92/195 (47%), Gaps = 9/195 (4%) Query: 3 TNPPVVYIVDDDEAVRTSLAWLLSSVNIRTECFDGPGAFLKAYDANSLSCLILDVRMPEI 62 TN + +IV D+++ L LL FL+ A L+L V M + Sbjct: 2 TNAHLAHIVGGDDSLGGPLGRLLEEAGFHVAHHRSADQFLEHATATGPGGLVLAVNMRNM 61 Query: 63 SGFQLQDRLKEIGADIPVIFVSGH--GDIPMSVRALHNGAVDFLEKPYNSQQMLERIQLT 120 QL+ L E IP+I ++G+ G P+ G ++P +QQ++ + Sbjct: 62 DAPQLRSLLDEKKEGIPLIVITGNQPGAAPL-------GQSSAQQEPEVAQQLVAAFREA 114 Query: 121 LKNVAGNMQARERRQQLKARLKTLTVREREILEKVIMGQSSKLIARDLNISVKTVDVHRA 180 L + +++R+ +ARL TLT RERE+L ++ G+ +K IA +L S +TV HR Sbjct: 115 LMPYDESAPHQQQRRIHQARLATLTRREREVLMLLVKGRLNKQIAAELGTSERTVKAHRQ 174 Query: 181 SVKDKLGCQSTATLV 195 V K+ S A LV Sbjct: 175 QVMRKMYAGSLAELV 189 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 70.9 bits (172), Expect = 7e-14, Method: Compositional matrix adjust. Identities = 37/114 (32%), Positives = 61/114 (53%) Query: 8 VYIVDDDEAVRTSLAWLLSSVNIRTECFDGPGAFLKAYDANSLSCLILDVRMPEISGFQL 67 ++IVDDDE++R L L+ N+ T+ F + A + L+ D+RMP SG +L Sbjct: 4 IWIVDDDESIRWVLEKALARENLATQSFSSARDAIAALQNGTPQVLVSDIRMPGASGLEL 63 Query: 68 QDRLKEIGADIPVIFVSGHGDIPMSVRALHNGAVDFLEKPYNSQQMLERIQLTL 121 +K IPVI ++ D+ +V A GA ++L KP++ + +E I+ L Sbjct: 64 LQTVKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRAL 117 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 0.382 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: 588,795 Number of extensions: 21570 Number of successful extensions: 177 Number of sequences better than 1.0e-08: 20 Number of HSP's gapped: 188 Number of HSP's successfully gapped: 20 Length of query: 210 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 129 Effective length of database: 1,236,335 Effective search space: 159487215 Effective search space used: 159487215 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)