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= 0002.0080.p (236 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... 474 e-135 gi|300312077|ref|YP_003776169.1| response regulator containing a... 97 1e-21 gi|300311281|ref|YP_003775373.1| LuxR family response regulator ... 97 2e-21 gi|300311885|ref|YP_003775977.1| LuxR family two component respo... 95 5e-21 gi|300310532|ref|YP_003774624.1| virulence regulator protein [He... 92 5e-20 >gi|300312431|ref|YP_003776523.1| two component LuxR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 282 Score = 474 bits (1221), Expect = e-135, Method: Compositional matrix adjust. Identities = 236/236 (100%), Positives = 236/236 (100%) Query: 1 MRIALLDDHAVVRYGLAARLAEEPDLEVVGSFATSKELMTALRASPADLLLIDYSLGSND 60 MRIALLDDHAVVRYGLAARLAEEPDLEVVGSFATSKELMTALRASPADLLLIDYSLGSND Sbjct: 47 MRIALLDDHAVVRYGLAARLAEEPDLEVVGSFATSKELMTALRASPADLLLIDYSLGSND 106 Query: 61 IDGLNLIRALRVRFPRSKILVTSAHNNPATVALAMKAGARGFVGKSQELGELVQAIRTVS 120 IDGLNLIRALRVRFPRSKILVTSAHNNPATVALAMKAGARGFVGKSQELGELVQAIRTVS Sbjct: 107 IDGLNLIRALRVRFPRSKILVTSAHNNPATVALAMKAGARGFVGKSQELGELVQAIRTVS 166 Query: 121 VGREYLNAAMARELTAMLASDSPTPAPEGGPPQVRPPRRKRNSPPSSDSLSEMPSLSPRE 180 VGREYLNAAMARELTAMLASDSPTPAPEGGPPQVRPPRRKRNSPPSSDSLSEMPSLSPRE Sbjct: 167 VGREYLNAAMARELTAMLASDSPTPAPEGGPPQVRPPRRKRNSPPSSDSLSEMPSLSPRE 226 Query: 181 REVLRCCLDGLSVTAIADKFARSVKTISGQKQSAFRKLGVRSDNELFKIEYQIKDL 236 REVLRCCLDGLSVTAIADKFARSVKTISGQKQSAFRKLGVRSDNELFKIEYQIKDL Sbjct: 227 REVLRCCLDGLSVTAIADKFARSVKTISGQKQSAFRKLGVRSDNELFKIEYQIKDL 282 >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 = 97.1 bits (240), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 70/235 (29%), Positives = 112/235 (47%), Gaps = 30/235 (12%) Query: 1 MRIALLDDHAVVRYGLAARLAEEPDLEVVGSFATSKELMTALRASPADLLLIDYSLGSND 60 +++ + DDHA+VR GL A D+ V G+ A E + R D+LL+D L D Sbjct: 9 IKVLIADDHAIVREGLRQICAGSKDIMVAGNAANGLEAIKLAREGNGDVLLLDIVLP--D 66 Query: 61 IDGLNLIRALRVRFPRSKILVTSAHNNPATVALAMKAGARGFVGKSQELGELVQAIRTVS 120 +G+++++ +R P +L+ S H A+KAGA GF+ K EL+ AIR + Sbjct: 67 RNGIDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQAAPAELLAAIRQAA 126 Query: 121 VGREYLNAAMARELTAMLASDSPTPAPEGGPPQVRPPRRKRNSPPSSDSLSEMPSLSPRE 180 GR+Y++ ++A+EL + D TP E +LS RE Sbjct: 127 SGRKYVSPSLAQELANQIGFDHETPLHE--------------------------TLSDRE 160 Query: 181 REVLRCCLDGLSVTAIADKFARSVKTISGQKQSAFRKLGVRSDNELFKIEYQIKD 235 + + G +V+ IA + SVKTIS + K+ +R + EL Y +K+ Sbjct: 161 YQTMVMIASGKTVSDIAAELTLSVKTISMYRSRVLSKMKMRHNAEL--THYALKN 213 >gi|300311281|ref|YP_003775373.1| LuxR family response regulator protein [Herbaspirillum seropedicae SmR1] Length = 217 Score = 96.7 bits (239), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 77/226 (34%), Positives = 106/226 (46%), Gaps = 34/226 (15%) Query: 3 IALLDDHAVVRYGLAARLAEEPDLEVVGSFATSKELMTALRASPADLLLIDYSLGSNDID 62 I L+DDH +VR GL ARL P LEVV + E + A A DL L+D ++ I+ Sbjct: 14 IMLIDDHPLVRDGLRARLETVPGLEVVAEAGHADEALAAAAAQEIDLTLMDINM--RGIN 71 Query: 63 GLNLIRALRVRFPRSKILVTSAHNNPATVALAMKAGARGFVGKSQELGELVQAIRTVSVG 122 G+ L R P +L+ S H+ V +++AGARG+V K ++V AI TV G Sbjct: 72 GIELTALFHARHPEIAVLILSMHDKAEYVMQSIQAGARGYVLKDAPSQDIVHAIETVRSG 131 Query: 123 REYLNAAMARELTAMLASDSPTPAPEGGPPQVRPPRRKRNSPPSSDSLSEMPSLSPRERE 182 Y +AA+AR+LT Q PPR L+ RERE Sbjct: 132 GIYYSAALARQLT-----------------QPLPPRE---------------LLTQRERE 159 Query: 183 VLRCCLDGLSVTAIADKFARSVKTISGQKQSAFRKLGVRSDNELFK 228 VL +G S IA + SV+T+ + + RKL + EL K Sbjct: 160 VLMHIANGESNKQIARELDLSVRTVETHRLNIKRKLNIDGQAELIK 205 >gi|300311885|ref|YP_003775977.1| LuxR family two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 216 Score = 95.1 bits (235), Expect = 5e-21, Method: Compositional matrix adjust. Identities = 67/220 (30%), Positives = 108/220 (49%), Gaps = 26/220 (11%) Query: 2 RIALLDDHAVVRYGLAARLAEEPDLEVVGSFATSKELMTALRASPADLLLIDYSLGSNDI 61 RI L DDHA+VR G+ A L P +EVVG + E++ + DL+L+D ++ + Sbjct: 4 RIMLADDHALVRSGIKALLTAMPGVEVVGEASDGAEVIEMIPQLKPDLVLLDIAM--KGM 61 Query: 62 DGLNLIRALRVRFPRSKILVTSAHNNPATVALAMKAGARGFVGKSQELGELVQAIRTVSV 121 +GL +R LR +P + L+ S + + V A+ AGA G++ K EL +A+ V Sbjct: 62 NGLEALRRLRGEYPTIRFLMLSMYGSEEYVMQALNAGANGYLFKDSAATELEKALYEVKH 121 Query: 122 GREYLNAAMARELTAMLASDSPTPAPEGGPPQVRPPRRKRNSPPSSDSLSEMPSLSPRER 181 GR+YL++ ++RE L + A G P +V L+PR+R Sbjct: 122 GRQYLDSHISRE---ALDNYMKRVAQNGTPVEV---------------------LTPRQR 157 Query: 182 EVLRCCLDGLSVTAIADKFARSVKTISGQKQSAFRKLGVR 221 E+L+ +G + IA + S KTI + +L +R Sbjct: 158 EILQLIAEGNNTKEIAYQLNVSAKTIETHRAQLMERLDIR 197 >gi|300310532|ref|YP_003774624.1| virulence regulator protein [Herbaspirillum seropedicae SmR1] Length = 209 Score = 91.7 bits (226), Expect = 5e-20, Method: Compositional matrix adjust. Identities = 66/234 (28%), Positives = 115/234 (49%), Gaps = 31/234 (13%) Query: 2 RIALLDDHAVVRYGLAARLAEEPDLEVVGSFATSKELMTALRASPADLLLIDYSLGSNDI 61 +I ++DDHAVVR G+ ++E P +E+ G +T++E + +R D++L+D ++ D Sbjct: 3 KILVVDDHAVVRAGVHHFISEIPSMEIGGEASTAEEAIRLVRTQDWDIVLLDIAMP--DK 60 Query: 62 DGLNLIRALRVRFPRSKILVTSAHNNPATVALAMKAGARGFVGKSQELGELVQAIRTVSV 121 G+ +++ ++ P +L+ S H +++GA G+V K ELV AI T+ Sbjct: 61 SGVEVLKQIKREKPELPVLMLSMHPESRYAVQVLRSGASGYVQKEALATELVNAINTILR 120 Query: 122 GREYLNAAMARELTAMLASDSPTPAPEGGPPQVRPPRRKRNSPPSSDSLSEMPSLSPRER 181 G +Y++ +A LT+ DS P E +LS RE Sbjct: 121 GHKYISYGVAELLTSE-PVDSEKPLHE--------------------------TLSQREY 153 Query: 182 EVLRCCLDGLSVTAIADKFARSVKTISGQKQSAFRKLGVRSDNELFKIEYQIKD 235 E+ G VT IAD+ SVKT+S + +K+ + ++ ++ I Y IK+ Sbjct: 154 EIFYKLGQGQGVTQIADELCLSVKTVSTYRSRVLQKMSMTNNADI--IYYAIKN 205 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 0.132 0.364 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: 605,695 Number of extensions: 21127 Number of successful extensions: 149 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 141 Number of HSP's successfully gapped: 7 Length of query: 236 Length of database: 1,619,870 Length adjustment: 82 Effective length of query: 154 Effective length of database: 1,231,600 Effective search space: 189666400 Effective search space used: 189666400 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)