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= 0001.4399.p (206 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313791|ref|YP_003777883.1| response regulator protein [Her... 366 e-103 gi|300310669|ref|YP_003774761.1| two component response regulato... 139 2e-34 gi|300310176|ref|YP_003774268.1| C4-dicarboxylate transport tran... 122 3e-29 gi|300313031|ref|YP_003777123.1| two component response regulato... 97 1e-21 gi|300311885|ref|YP_003775977.1| LuxR family two component respo... 82 2e-17 >gi|300313791|ref|YP_003777883.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 206 Score = 366 bits (939), Expect = e-103, Method: Compositional matrix adjust. Identities = 181/206 (87%), Positives = 189/206 (91%) Query: 1 MESTVYVVDDDGMVRTALLRLLAAAGYTARGFASADEFLQVPLPSTPCCLLLDMKMPGAD 60 ME TV+VVDDD MVRTALLRLLA+AGY A GFASADEFLQ LP+ PCCLLLDMKMPG+D Sbjct: 1 MERTVFVVDDDNMVRTALLRLLASAGYAAHGFASADEFLQARLPAVPCCLLLDMKMPGSD 60 Query: 61 GFDVVHRLEQRGDAIPVIFISGYGTIPTTVQAMKAGAHEFLTKPIEDERLLGAVEEALTV 120 GF+VV RLE+RGDAIPVIFISGYGTIPTTVQAMKAGAHEFLTKPI+DERLLGAVEEAL + Sbjct: 61 GFEVVRRLERRGDAIPVIFISGYGTIPTTVQAMKAGAHEFLTKPIQDERLLGAVEEALQI 120 Query: 121 AGRQLHKRVEHAANASRLEKLTPREREVLELAIGGLLNKQIATELGISEITVKVHKRRVM 180 A RQL R EHAA SRLE LTPREREVLELAIGGLLNKQIATELGISEITVKVHKRRVM Sbjct: 121 AERQLQSRTEHAACTSRLETLTPREREVLELAIGGLLNKQIATELGISEITVKVHKRRVM 180 Query: 181 DKMQTKTLADLVRAAERLQIHSARQR 206 DKMQTKTLADLVRAAERLQI SARQR Sbjct: 181 DKMQTKTLADLVRAAERLQISSARQR 206 >gi|300310669|ref|YP_003774761.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 214 Score = 139 bits (349), Expect = 2e-34, Method: Compositional matrix adjust. Identities = 77/189 (40%), Positives = 111/189 (58%) Query: 5 VYVVDDDGMVRTALLRLLAAAGYTARGFASADEFLQVPLPSTPCCLLLDMKMPGADGFDV 64 VY+VDDD VRT+L LL++ F + FL+ ++ CL+LD++MP GF + Sbjct: 9 VYIVDDDEAVRTSLAWLLSSVNIRTECFEGPEAFLKAYDANSLSCLILDVRMPEISGFQL 68 Query: 65 VHRLEQRGDAIPVIFISGYGTIPTTVQAMKAGAHEFLTKPIEDERLLGAVEEALTVAGRQ 124 RL++ G IPVIF+SG+G IP +V+A+ GA +FL KP +++L ++ L Sbjct: 69 QDRLKEIGADIPVIFVSGHGDIPMSVRALHNGAVDFLEKPYNSQQMLERIQMTLKHVAGN 128 Query: 125 LHKRVEHAANASRLEKLTPREREVLELAIGGLLNKQIATELGISEITVKVHKRRVMDKMQ 184 + R +RL+ LT RERE+LE I G +K IA EL IS TV VH+ V DK+ Sbjct: 129 MQARTRRQQLKARLKTLTAREREILEKVIMGQSSKLIARELNISVKTVDVHRASVKDKLG 188 Query: 185 TKTLADLVR 193 ++ A LVR Sbjct: 189 CQSTATLVR 197 >gi|300310176|ref|YP_003774268.1| C4-dicarboxylate transport transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 196 Score = 122 bits (305), Expect = 3e-29, Method: Compositional matrix adjust. Identities = 77/199 (38%), Positives = 111/199 (55%), Gaps = 17/199 (8%) Query: 5 VYVVDDDGMVRTALLRLLAAAGYTARGFASADEFLQVPLPSTPC------CLLLDMKMPG 58 +++VDD+ ++R +L L + A + S L L ++P CLLLD++MPG Sbjct: 2 LHIVDDEEIIRDSLAWLARSRNIAATAYDSGPTLLAA-LAASPGIDAEGECLLLDVRMPG 60 Query: 59 ADGFDVVHRLEQRG--DAIPVIFISGYGTIPTTVQAMKAGAHEFLTKPIEDERLLGAVEE 116 G + + L+ +G PVIF++G+G +P V +K GA +F KP D +L+ V E Sbjct: 61 TSGVALFNDLKTKGLLHRRPVIFLTGHGDVPMAVDMLKNGAFDFFEKPFNDNQLMDRVLE 120 Query: 117 ALTVAGRQLHKRVEHAANA--SRLEKLTPREREVLELAIGGLLNKQIATELGISEITVKV 174 AL R A +A SRL L+ REREVL+L + G +NK IA ELGIS TV+V Sbjct: 121 ALA------SSRAGGAEDAVQSRLAALSVREREVLDLILAGKMNKVIADELGISMRTVEV 174 Query: 175 HKRRVMDKMQTKTLADLVR 193 H+ + DKM KT +L R Sbjct: 175 HRAHIFDKMNVKTAVELAR 193 >gi|300313031|ref|YP_003777123.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 195 Score = 96.7 bits (239), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 73/196 (37%), Positives = 104/196 (53%), Gaps = 13/196 (6%) Query: 6 YVVDDDGMVRTALLRLLAAAGYTARGFASADEFLQVPLPSTPCCLLLDMKMPGADGFDVV 65 ++V D + L RLL AG+ SAD+FL+ + P L+L + M D + Sbjct: 8 HIVGGDDSLGGPLGRLLEEAGFHVAHHRSADQFLEHATATGPGGLVLAVNMRNMDAPQLR 67 Query: 66 HRLEQRGDAIPVIFISGYGTIPTTVQAMKAGAHEFLTKPIEDERLLGAVEEALT----VA 121 L+++ + IP+I I+G P ++ A + +P ++L+ A EAL A Sbjct: 68 SLLDEKKEGIPLIVITG--NQPGAAPLGQSSAQQ---EPEVAQQLVAAFREALMPYDESA 122 Query: 122 GRQLHKRVEHAANASRLEKLTPREREVLELAIGGLLNKQIATELGISEITVKVHKRRVMD 181 Q +R+ A RL LT REREVL L + G LNKQIA ELG SE TVK H+++VM Sbjct: 123 PHQQQRRIHQA----RLATLTRREREVLMLLVKGRLNKQIAAELGTSERTVKAHRQQVMR 178 Query: 182 KMQTKTLADLVRAAER 197 KM +LA+LV A R Sbjct: 179 KMYAGSLAELVAAMTR 194 >gi|300311885|ref|YP_003775977.1| LuxR family two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 216 Score = 82.4 bits (202), Expect = 2e-17, Method: Compositional matrix adjust. Identities = 68/215 (31%), Positives = 108/215 (50%), Gaps = 19/215 (8%) Query: 1 MESTVYVVDDDGMVRTALLRLLAA-AGYTARGFAS-ADEFLQVPLPSTPCCLLLDMKMPG 58 M + + + DD +VR+ + LL A G G AS E +++ P +LLD+ M G Sbjct: 1 MLTRIMLADDHALVRSGIKALLTAMPGVEVVGEASDGAEVIEMIPQLKPDLVLLDIAMKG 60 Query: 59 ADGFDVVHRLEQRGDAIPVIFISGYGTIPTTVQAMKAGAHEFLTKPIEDERLLGAVEEAL 118 +G + + RL I + +S YG+ +QA+ AGA+ +L K L A+ E Sbjct: 61 MNGLEALRRLRGEYPTIRFLMLSMYGSEEYVMQALNAGANGYLFKDSAATELEKALYE-- 118 Query: 119 TVAGRQL-------------HKRVEHAANASRLEKLTPREREVLELAIGGLLNKQIATEL 165 GRQ KRV A N + +E LTPR+RE+L+L G K+IA +L Sbjct: 119 VKHGRQYLDSHISREALDNYMKRV--AQNGTPVEVLTPRQREILQLIAEGNNTKEIAYQL 176 Query: 166 GISEITVKVHKRRVMDKMQTKTLADLVRAAERLQI 200 +S T++ H+ ++M+++ + + LVR A R I Sbjct: 177 NVSAKTIETHRAQLMERLDIRDVPGLVRYAIRTGI 211 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 0.135 0.376 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: 592,478 Number of extensions: 23817 Number of successful extensions: 224 Number of sequences better than 1.0e-08: 26 Number of HSP's gapped: 242 Number of HSP's successfully gapped: 26 Length of query: 206 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 125 Effective length of database: 1,236,335 Effective search space: 154541875 Effective search space used: 154541875 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)