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= 0008.0142.p (219 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312431|ref|YP_003776523.1| two component LuxR family trans... 114 5e-27 gi|300310869|ref|YP_003774961.1| response regulator for colanic ... 109 2e-25 gi|300312077|ref|YP_003776169.1| response regulator containing a... 92 3e-20 gi|300311885|ref|YP_003775977.1| LuxR family two component respo... 87 1e-18 gi|300310532|ref|YP_003774624.1| virulence regulator protein [He... 76 2e-15 >gi|300312431|ref|YP_003776523.1| two component LuxR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 282 Score = 114 bits (286), Expect = 5e-27, Method: Compositional matrix adjust. Identities = 81/236 (34%), Positives = 126/236 (53%), Gaps = 27/236 (11%) Query: 3 TKGTLIRVGIADDYPVVLRGIEAILATCADLALAFSAESIAQLMSCLERDPVDVLLCDYA 62 T + +R+ + DD+ VV G+ A LA DL + S + +LM+ L P D+LL DY+ Sbjct: 42 TLASRMRIALLDDHAVVRYGLAARLAEEPDLEVVGSFATSKELMTALRASPADLLLIDYS 101 Query: 63 FDDDPQADGLDLLKRLRRQHPAMKVIFLSAHAQPQIISSALELGAAGFIGKNRSDFVNLP 122 + DGL+L++ LR + P K++ SAH P ++ A++ GA GF+GK++ + L Sbjct: 102 LGSN-DIDGLNLIRALRVRFPRSKILVTSAHNNPATVALAMKAGARGFVGKSQ-ELGELV 159 Query: 123 QAVCSVHHGQVYLPQSLS---SALLGSLFNVNARQTGLAQ-------------------- 159 QA+ +V G+ YL +++ +A+L S A + G Q Sbjct: 160 QAIRTVSVGREYLNAAMARELTAMLASDSPTPAPEGGPPQVRPPRRKRNSPPSSDSLSEM 219 Query: 160 --LSERELVVARMICQGMSISDIAERLNRSPKTISNQKVAAMKKLGVSNDVELSRI 213 LS RE V R G+S++ IA++ RS KTIS QK +A +KLGV +D EL +I Sbjct: 220 PSLSPREREVLRCCLDGLSVTAIADKFARSVKTISGQKQSAFRKLGVRSDNELFKI 275 >gi|300310869|ref|YP_003774961.1| response regulator for colanic capsule biosynthesis protein [Herbaspirillum seropedicae SmR1] Length = 221 Score = 109 bits (272), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 65/209 (31%), Positives = 113/209 (54%), Gaps = 9/209 (4%) Query: 7 LIRVGIADDYPVVLRGIEAILATCADLALAFSAESIAQLMSCLERDPVDVLLCDYAF--D 64 ++ V IADD+P+VL + LA ++ + ++ L++ L+R P ++++ D+A + Sbjct: 6 VLHVAIADDHPIVLGALRNELARLPEIRIDLEVDTGEDLINALKRTPCEIVITDFAMPNE 65 Query: 65 DDPQADGLDLLKRLRRQHPAMKVIFLSAHAQPQIISSALELGAAGFIGKNRSDFVNLPQA 124 + ++DG L+KR++ +HP+ K+I +A +I +G I K + Sbjct: 66 ESDESDGFALVKRIKAEHPSTKLIVYTAMNNGAVIRRLYRMGVFAVINKREKPDELINAC 125 Query: 125 VCSVHHGQVYLPQSLSSALLGSLFNVNARQTGLA---QLSERELVVARMICQGMSISDIA 181 + + Q+Y P SL L S A+ G A +L++ EL V R+ +G S+ +I Sbjct: 126 LATQSSKQLYFPVSLRGELEMSW----AQGDGFAATRELTQSELEVVRLFVEGQSLGEIC 181 Query: 182 ERLNRSPKTISNQKVAAMKKLGVSNDVEL 210 RL+R+P TIS K AM+KLG+S+D EL Sbjct: 182 VRLSRTPSTISTHKNNAMRKLGLSSDAEL 210 >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 = 92.0 bits (227), Expect = 3e-20, Method: Compositional matrix adjust. Identities = 68/206 (33%), Positives = 109/206 (52%), Gaps = 9/206 (4%) Query: 8 IRVGIADDYPVVLRGIEAILATCADLALAFSAESIAQLMSCLERDPVDVLLCDYAFDDDP 67 I+V IADD+ +V G+ I A D+ +A +A + + + DVLL D P Sbjct: 9 IKVLIADDHAIVREGLRQICAGSKDIMVAGNAANGLEAIKLAREGNGDVLLLDIVL---P 65 Query: 68 QADGLDLLKRLRRQHPAMKVIFLSAHAQPQIISSALELGAAGFIGKNRSDFVNLPQAVCS 127 +G+D+LK++R++ P + V+ LS H + Q AL+ GAAGF+ K + L A+ Sbjct: 66 DRNGIDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQAAP-AELLAAIRQ 124 Query: 128 VHHGQVYLPQSLSSALLGSL-FNVNARQTGLAQ-LSERELVVARMICQGMSISDIAERLN 185 G+ Y+ SL+ L + F+ +T L + LS+RE MI G ++SDIA L Sbjct: 125 AASGRKYVSPSLAQELANQIGFD---HETPLHETLSDREYQTMVMIASGKTVSDIAAELT 181 Query: 186 RSPKTISNQKVAAMKKLGVSNDVELS 211 S KTIS + + K+ + ++ EL+ Sbjct: 182 LSVKTISMYRSRVLSKMKMRHNAELT 207 >gi|300311885|ref|YP_003775977.1| LuxR family two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 216 Score = 87.0 bits (214), Expect = 1e-18, Method: Compositional matrix adjust. Identities = 58/201 (28%), Positives = 107/201 (53%), Gaps = 5/201 (2%) Query: 7 LIRVGIADDYPVVLRGIEAILATCADLALAFSAESIAQLMSCLERDPVDVLLCDYAFDDD 66 L R+ +ADD+ +V GI+A+L + + A A+++ + + D++L D A Sbjct: 2 LTRIMLADDHALVRSGIKALLTAMPGVEVVGEASDGAEVIEMIPQLKPDLVLLDIAMKG- 60 Query: 67 PQADGLDLLKRLRRQHPAMKVIFLSAHAQPQIISSALELGAAGFIGKNRSDFVNLPQAVC 126 +GL+ L+RLR ++P ++ + LS + + + AL GA G++ K+ S L +A+ Sbjct: 61 --MNGLEALRRLRGEYPTIRFLMLSMYGSEEYVMQALNAGANGYLFKD-SAATELEKALY 117 Query: 127 SVHHGQVYLPQSLS-SALLGSLFNVNARQTGLAQLSERELVVARMICQGMSISDIAERLN 185 V HG+ YL +S AL + V T + L+ R+ + ++I +G + +IA +LN Sbjct: 118 EVKHGRQYLDSHISREALDNYMKRVAQNGTPVEVLTPRQREILQLIAEGNNTKEIAYQLN 177 Query: 186 RSPKTISNQKVAAMKKLGVSN 206 S KTI + M++L + + Sbjct: 178 VSAKTIETHRAQLMERLDIRD 198 >gi|300310532|ref|YP_003774624.1| virulence regulator protein [Herbaspirillum seropedicae SmR1] Length = 209 Score = 75.9 bits (185), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 47/206 (22%), Positives = 104/206 (50%), Gaps = 10/206 (4%) Query: 7 LIRVGIADDYPVVLRGIEAILATCADLALAFSAESIAQLMSCLERDPVDVLLCDYAFDDD 66 + ++ + DD+ VV G+ ++ + + A + + + + D++L D A Sbjct: 1 MTKILVVDDHAVVRAGVHHFISEIPSMEIGGEASTAEEAIRLVRTQDWDIVLLDIAM--- 57 Query: 67 PQADGLDLLKRLRRQHPAMKVIFLSAHAQPQIISSALELGAAGFIGKN--RSDFVNLPQA 124 P G+++LK+++R+ P + V+ LS H + + L GA+G++ K ++ VN A Sbjct: 58 PDKSGVEVLKQIKREKPELPVLMLSMHPESRYAVQVLRSGASGYVQKEALATELVN---A 114 Query: 125 VCSVHHGQVYLPQSLSSALLGSLFNVNARQTGLAQLSERELVVARMICQGMSISDIAERL 184 + ++ G Y+ ++ L V++ + LS+RE + + QG ++ IA+ L Sbjct: 115 INTILRGHKYISYGVAELLTSE--PVDSEKPLHETLSQREYEIFYKLGQGQGVTQIADEL 172 Query: 185 NRSPKTISNQKVAAMKKLGVSNDVEL 210 S KT+S + ++K+ ++N+ ++ Sbjct: 173 CLSVKTVSTYRSRVLQKMSMTNNADI 198 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 0.322 0.135 0.380 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: 622,476 Number of extensions: 23637 Number of successful extensions: 117 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 110 Number of HSP's successfully gapped: 6 Length of query: 219 Length of database: 1,619,870 Length adjustment: 82 Effective length of query: 137 Effective length of database: 1,231,600 Effective search space: 168729200 Effective search space used: 168729200 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: 128 (53.9 bits)