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= 0001.3100.p (242 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... 387 e-109 gi|300312077|ref|YP_003776169.1| response regulator containing a... 103 2e-23 gi|300311885|ref|YP_003775977.1| LuxR family two component respo... 94 1e-20 gi|300311281|ref|YP_003775373.1| LuxR family response regulator ... 91 7e-20 gi|300310532|ref|YP_003774624.1| virulence regulator protein [He... 89 5e-19 >gi|300312431|ref|YP_003776523.1| two component LuxR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 282 Score = 387 bits (995), Expect = e-109, Method: Compositional matrix adjust. Identities = 194/243 (79%), Positives = 213/243 (87%), Gaps = 4/243 (1%) Query: 3 WKVGSKMRIALLDDHAVVRYGLAKRLAEEPDFSVIGAFATSKELMTALRAEPADLLLIDY 62 W + S+MRIALLDDHAVVRYGLA RLAEEPD V+G+FATSKELMTALRA PADLLLIDY Sbjct: 41 WTLASRMRIALLDDHAVVRYGLAARLAEEPDLEVVGSFATSKELMTALRASPADLLLIDY 100 Query: 63 SLGSNDIDGLNLIRALRVRFPRSKILVTSAHSSPATVVMAMKAGARGFVGKSQELSELIL 122 SLGSNDIDGLNLIRALRVRFPRSKILVTSAH++PATV +AMKAGARGFVGKSQEL EL+ Sbjct: 101 SLGSNDIDGLNLIRALRVRFPRSKILVTSAHNNPATVALAMKAGARGFVGKSQELGELVQ 160 Query: 123 AIRAIHTGREYLSIAMSRELAALQAADPGARSEPEPAPPR---RRRARNTPPSSDTLSDM 179 AIR + GREYL+ AM+REL A+ A+D PE PP+ RR RN+PPSSD+LS+M Sbjct: 161 AIRTVSVGREYLNAAMARELTAMLASD-SPTPAPEGGPPQVRPPRRKRNSPPSSDSLSEM 219 Query: 180 PNLSPREREVLRCCLDGLSVTDIAEKFARSVKTISCQKQSAFRKLGVRSDNELFKIEYQI 239 P+LSPREREVLRCCLDGLSVT IA+KFARSVKTIS QKQSAFRKLGVRSDNELFKIEYQI Sbjct: 220 PSLSPREREVLRCCLDGLSVTAIADKFARSVKTISGQKQSAFRKLGVRSDNELFKIEYQI 279 Query: 240 KDL 242 KDL Sbjct: 280 KDL 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 = 103 bits (256), Expect = 2e-23, Method: Compositional matrix adjust. Identities = 75/241 (31%), Positives = 120/241 (49%), Gaps = 28/241 (11%) Query: 1 MTWKVGSKMRIALLDDHAVVRYGLAKRLAEEPDFSVIGAFATSKELMTALRAEPADLLLI 60 M+ KV + +++ + DDHA+VR GL + A D V G A E + R D+LL+ Sbjct: 1 MSKKVTAAIKVLIADDHAIVREGLRQICAGSKDIMVAGNAANGLEAIKLAREGNGDVLLL 60 Query: 61 DYSLGSNDIDGLNLIRALRVRFPRSKILVTSAHSSPATVVMAMKAGARGFVGKSQELSEL 120 D L D +G+++++ +R P +L+ S H + A+KAGA GF+ K +EL Sbjct: 61 DIVL--PDRNGIDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQAAPAEL 118 Query: 121 ILAIRAIHTGREYLSIAMSRELAALQAADPGARSEPEPAPPRRRRARNTPPSSDTLSDMP 180 + AIR +GR+Y+S ++++ELA D + P +TLSD Sbjct: 119 LAAIRQAASGRKYVSPSLAQELANQIGFD------------------HETPLHETLSD-- 158 Query: 181 NLSPREREVLRCCLDGLSVTDIAEKFARSVKTISCQKQSAFRKLGVRSDNELFKIEYQIK 240 RE + + G +V+DIA + SVKTIS + K+ +R + EL Y +K Sbjct: 159 ----REYQTMVMIASGKTVSDIAAELTLSVKTISMYRSRVLSKMKMRHNAEL--THYALK 212 Query: 241 D 241 + Sbjct: 213 N 213 >gi|300311885|ref|YP_003775977.1| LuxR family two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 216 Score = 93.6 bits (231), Expect = 1e-20, Method: Compositional matrix adjust. Identities = 66/218 (30%), Positives = 107/218 (49%), Gaps = 24/218 (11%) Query: 10 RIALLDDHAVVRYGLAKRLAEEPDFSVIGAFATSKELMTALRAEPADLLLIDYSLGSNDI 69 RI L DDHA+VR G+ L P V+G + E++ + DL+L+D ++ + Sbjct: 4 RIMLADDHALVRSGIKALLTAMPGVEVVGEASDGAEVIEMIPQLKPDLVLLDIAM--KGM 61 Query: 70 DGLNLIRALRVRFPRSKILVTSAHSSPATVVMAMKAGARGFVGKSQELSELILAIRAIHT 129 +GL +R LR +P + L+ S + S V+ A+ AGA G++ K +EL A+ + Sbjct: 62 NGLEALRRLRGEYPTIRFLMLSMYGSEEYVMQALNAGANGYLFKDSAATELEKALYEVKH 121 Query: 130 GREYLSIAMSRELAALQAADPGARSEPEPAPPRRRRARNTPPSSDTLSDMPNLSPREREV 189 GR+YL +SRE A D +R A+N P + L+PR+RE+ Sbjct: 122 GRQYLDSHISRE-----ALD----------NYMKRVAQNGTP-------VEVLTPRQREI 159 Query: 190 LRCCLDGLSVTDIAEKFARSVKTISCQKQSAFRKLGVR 227 L+ +G + +IA + S KTI + +L +R Sbjct: 160 LQLIAEGNNTKEIAYQLNVSAKTIETHRAQLMERLDIR 197 >gi|300311281|ref|YP_003775373.1| LuxR family response regulator protein [Herbaspirillum seropedicae SmR1] Length = 217 Score = 91.3 bits (225), Expect = 7e-20, Method: Compositional matrix adjust. Identities = 68/224 (30%), Positives = 103/224 (45%), Gaps = 32/224 (14%) Query: 11 IALLDDHAVVRYGLAKRLAEEPDFSVIGAFATSKELMTALRAEPADLLLIDYSLGSNDID 70 I L+DDH +VR GL RL P V+ + E + A A+ DL L+D ++ I+ Sbjct: 14 IMLIDDHPLVRDGLRARLETVPGLEVVAEAGHADEALAAAAAQEIDLTLMDINM--RGIN 71 Query: 71 GLNLIRALRVRFPRSKILVTSAHSSPATVVMAMKAGARGFVGKSQELSELILAIRAIHTG 130 G+ L R P +L+ S H V+ +++AGARG+V K +++ AI + +G Sbjct: 72 GIELTALFHARHPEIAVLILSMHDKAEYVMQSIQAGARGYVLKDAPSQDIVHAIETVRSG 131 Query: 131 REYLSIAMSRELAALQAADPGARSEPEPAPPRRRRARNTPPSSDTLSDMPNLSPREREVL 190 Y S A++R+L +P PPR L+ REREVL Sbjct: 132 GIYYSAALARQLT-------------QPLPPREL-----------------LTQREREVL 161 Query: 191 RCCLDGLSVTDIAEKFARSVKTISCQKQSAFRKLGVRSDNELFK 234 +G S IA + SV+T+ + + RKL + EL K Sbjct: 162 MHIANGESNKQIARELDLSVRTVETHRLNIKRKLNIDGQAELIK 205 >gi|300310532|ref|YP_003774624.1| virulence regulator protein [Herbaspirillum seropedicae SmR1] Length = 209 Score = 88.6 bits (218), Expect = 5e-19, Method: Compositional matrix adjust. Identities = 63/232 (27%), Positives = 115/232 (49%), Gaps = 29/232 (12%) Query: 10 RIALLDDHAVVRYGLAKRLAEEPDFSVIGAFATSKELMTALRAEPADLLLIDYSLGSNDI 69 +I ++DDHAVVR G+ ++E P + G +T++E + +R + D++L+D ++ D Sbjct: 3 KILVVDDHAVVRAGVHHFISEIPSMEIGGEASTAEEAIRLVRTQDWDIVLLDIAMP--DK 60 Query: 70 DGLNLIRALRVRFPRSKILVTSAHSSPATVVMAMKAGARGFVGKSQELSELILAIRAIHT 129 G+ +++ ++ P +L+ S H V +++GA G+V K +EL+ AI I Sbjct: 61 SGVEVLKQIKREKPELPVLMLSMHPESRYAVQVLRSGASGYVQKEALATELVNAINTILR 120 Query: 130 GREYLSIAMSRELAALQAADPGARSEPEPAPPRRRRARNTPPSSDTLSDMPNLSPREREV 189 G +Y+S ++ L + EP + P +TLS RE E+ Sbjct: 121 GHKYISYGVAELLTS------------EPVDSEK-------PLHETLSQ------REYEI 155 Query: 190 LRCCLDGLSVTDIAEKFARSVKTISCQKQSAFRKLGVRSDNELFKIEYQIKD 241 G VT IA++ SVKT+S + +K+ + ++ ++ I Y IK+ Sbjct: 156 FYKLGQGQGVTQIADELCLSVKTVSTYRSRVLQKMSMTNNADI--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 0.319 0.133 0.371 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: 596,453 Number of extensions: 19982 Number of successful extensions: 130 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 124 Number of HSP's successfully gapped: 8 Length of query: 242 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 159 Effective length of database: 1,226,865 Effective search space: 195071535 Effective search space used: 195071535 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: 129 (54.3 bits)