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= 0012.0129.p (222 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310869|ref|YP_003774961.1| response regulator for colanic ... 352 1e-98 gi|300312431|ref|YP_003776523.1| two component LuxR family trans... 97 1e-21 gi|300310532|ref|YP_003774624.1| virulence regulator protein [He... 77 1e-15 gi|300311885|ref|YP_003775977.1| LuxR family two component respo... 70 1e-13 gi|300312077|ref|YP_003776169.1| response regulator containing a... 60 1e-10 >gi|300310869|ref|YP_003774961.1| response regulator for colanic capsule biosynthesis protein [Herbaspirillum seropedicae SmR1] Length = 221 Score = 352 bits (904), Expect = 1e-98, Method: Compositional matrix adjust. Identities = 162/218 (74%), Positives = 193/218 (88%) Query: 5 LNKVLQIAIADDHPVVLNALKHELGRLPEFRIVLMAHTGDELLESLQRTPCEVVITDFAM 64 L KVL +AIADDHP+VL AL++EL RLPE RI L TG++L+ +L+RTPCE+VITDFAM Sbjct: 3 LKKVLHVAIADDHPIVLGALRNELARLPEIRIDLEVDTGEDLINALKRTPCEIVITDFAM 62 Query: 65 PTDRGDEADGFVLIKRIRAEFPSTKLIVYTAMSNSAVVKRLYRMGVFSVISKKEKADELV 124 P + DE+DGF L+KRI+AE PSTKLIVYTAM+N AV++RLYRMGVF+VI+K+EK DEL+ Sbjct: 63 PNEESDESDGFALVKRIKAEHPSTKLIVYTAMNNGAVIRRLYRMGVFAVINKREKPDELI 122 Query: 125 NACLATQSTKQVYFPVSLRGELEMSWAQGDAFTQNKELTMSELEVMRLFVGGCSLGDICD 184 NACLATQS+KQ+YFPVSLRGELEMSWAQGD F +ELT SELEV+RLFV G SLG+IC Sbjct: 123 NACLATQSSKQLYFPVSLRGELEMSWAQGDGFAATRELTQSELEVVRLFVEGQSLGEICV 182 Query: 185 RLSRTPSTVSTHKNNAMRKLGLSTDADLIKYAYATGMI 222 RLSRTPST+STHKNNAMRKLGLS+DA+LIKYA++TGMI Sbjct: 183 RLSRTPSTISTHKNNAMRKLGLSSDAELIKYAFSTGMI 220 >gi|300312431|ref|YP_003776523.1| two component LuxR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 282 Score = 97.1 bits (240), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 65/235 (27%), Positives = 114/235 (48%), Gaps = 30/235 (12%) Query: 9 LQIAIADDHPVVLNALKHELGRLPEFRIVLMAHTGDELLESLQRTPCEVVITDFAMPTDR 68 ++IA+ DDH VV L L P+ +V T EL+ +L+ +P ++++ D+++ ++ Sbjct: 47 MRIALLDDHAVVRYGLAARLAEEPDLEVVGSFATSKELMTALRASPADLLLIDYSLGSN- 105 Query: 69 GDEADGFVLIKRIRAEFPSTKLIVYTAMSNSAVVKRLYRMGVFSVISKKEKADELVNACL 128 + DG LI+ +R FP +K++V +A +N A V + G + K ++ ELV A + Sbjct: 106 --DIDGLNLIRALRVRFPRSKILVTSAHNNPATVALAMKAGARGFVGKSQELGELVQA-I 162 Query: 129 ATQSTKQVYFPVSLRGEL--------------------------EMSWAQGDAFTQNKEL 162 T S + Y ++ EL S D+ ++ L Sbjct: 163 RTVSVGREYLNAAMARELTAMLASDSPTPAPEGGPPQVRPPRRKRNSPPSSDSLSEMPSL 222 Query: 163 TMSELEVMRLFVGGCSLGDICDRLSRTPSTVSTHKNNAMRKLGLSTDADLIKYAY 217 + E EV+R + G S+ I D+ +R+ T+S K +A RKLG+ +D +L K Y Sbjct: 223 SPREREVLRCCLDGLSVTAIADKFARSVKTISGQKQSAFRKLGVRSDNELFKIEY 277 >gi|300310532|ref|YP_003774624.1| virulence regulator protein [Herbaspirillum seropedicae SmR1] Length = 209 Score = 76.6 bits (187), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 56/222 (25%), Positives = 100/222 (45%), Gaps = 25/222 (11%) Query: 10 QIAIADDHPVVLNALKHELGRLPEFRIVLMAHTGDELLESLQRTPCEVVITDFAMPTDRG 69 +I + DDH VV + H + +P I A T +E + ++ ++V+ D AMP G Sbjct: 3 KILVVDDHAVVRAGVHHFISEIPSMEIGGEASTAEEAIRLVRTQDWDIVLLDIAMPDKSG 62 Query: 70 DEADGFVLIKRIRAEFPSTKLIVYTAMSNSAVVKRLYRMGVFSVISKKEKADELVNACLA 129 E ++K+I+ E P +++ + S ++ R G + K+ A ELVNA Sbjct: 63 VE-----VLKQIKREKPELPVLMLSMHPESRYAVQVLRSGASGYVQKEALATELVNA--- 114 Query: 130 TQSTKQVYFPVSLRGELEMSWAQGDAFTQ---------NKELTMSELEVMRLFVGGCSLG 180 LRG +S+ + T ++ L+ E E+ G + Sbjct: 115 --------INTILRGHKYISYGVAELLTSEPVDSEKPLHETLSQREYEIFYKLGQGQGVT 166 Query: 181 DICDRLSRTPSTVSTHKNNAMRKLGLSTDADLIKYAYATGMI 222 I D L + TVST+++ ++K+ ++ +AD+I YA +I Sbjct: 167 QIADELCLSVKTVSTYRSRVLQKMSMTNNADIIYYAIKNNLI 208 >gi|300311885|ref|YP_003775977.1| LuxR family two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 216 Score = 70.1 bits (170), Expect = 1e-13, Method: Compositional matrix adjust. Identities = 53/214 (24%), Positives = 102/214 (47%), Gaps = 8/214 (3%) Query: 10 QIAIADDHPVVLNALKHELGRLPEFRIVLMAHTGDELLESLQRTPCEVVITDFAMPTDRG 69 +I +ADDH +V + +K L +P +V A G E++E + + ++V+ D AM G Sbjct: 4 RIMLADDHALVRSGIKALLTAMPGVEVVGEASDGAEVIEMIPQLKPDLVLLDIAMKGMNG 63 Query: 70 DEADGFVLIKRIRAEFPSTKLIVYTAMSNSAVVKRLYRMGVFSVISKKEKADELVNACLA 129 EA ++R+R E+P+ + ++ + + V + G + K A EL A Sbjct: 64 LEA-----LRRLRGEYPTIRFLMLSMYGSEEYVMQALNAGANGYLFKDSAATELEKALYE 118 Query: 130 TQSTKQVYFPVSLRGELEMSWAQ--GDAFTQNKELTMSELEVMRLFVGGCSLGDICDRLS 187 + +Q Y + E ++ + T + LT + E+++L G + +I +L+ Sbjct: 119 VKHGRQ-YLDSHISREALDNYMKRVAQNGTPVEVLTPRQREILQLIAEGNNTKEIAYQLN 177 Query: 188 RTPSTVSTHKNNAMRKLGLSTDADLIKYAYATGM 221 + T+ TH+ M +L + L++YA TG+ Sbjct: 178 VSAKTIETHRAQLMERLDIRDVPGLVRYAIRTGI 211 >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 = 60.1 bits (144), Expect = 1e-10, Method: Compositional matrix adjust. Identities = 49/222 (22%), Positives = 99/222 (44%), Gaps = 6/222 (2%) Query: 1 MSLILNKVLQIAIADDHPVVLNALKHELGRLPEFRIVLMAHTGDELLESLQRTPCEVVIT 60 MS + +++ IADDH +V L+ + + A G E ++ + +V++ Sbjct: 1 MSKKVTAAIKVLIADDHAIVREGLRQICAGSKDIMVAGNAANGLEAIKLAREGNGDVLLL 60 Query: 61 DFAMPTDRGDEADGFVLIKRIRAEFPSTKLIVYTAMSNSAVVKRLYRMGVFSVISKKEKA 120 D +P DR +G ++K+IR E P +++ + R + G ++K+ Sbjct: 61 DIVLP-DR----NGIDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQAAP 115 Query: 121 DELVNACLATQSTKQVYFPVSLRGELEMSWAQGDAFTQNKELTMSELEVMRLFVGGCSLG 180 EL+ A S ++ P SL EL ++ L+ E + M + G ++ Sbjct: 116 AELLAAIRQAASGRKYVSP-SLAQELANQIGFDHETPLHETLSDREYQTMVMIASGKTVS 174 Query: 181 DICDRLSRTPSTVSTHKNNAMRKLGLSTDADLIKYAYATGMI 222 DI L+ + T+S +++ + K+ + +A+L YA ++ Sbjct: 175 DIAAELTLSVKTISMYRSRVLSKMKMRHNAELTHYALKNALV 216 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 0.134 0.379 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: 609,641 Number of extensions: 21871 Number of successful extensions: 80 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 76 Number of HSP's successfully gapped: 7 Length of query: 222 Length of database: 1,619,870 Length adjustment: 82 Effective length of query: 140 Effective length of database: 1,231,600 Effective search space: 172424000 Effective search space used: 172424000 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: 129 (54.3 bits)