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= 0542.0013.p (250 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B1DAU1.1 B1DAU1_9BACL Two component transcriptional regulator, A... 354 4e-96 A9KTC8.1 A9KTC8_CLOPH Two component transcriptional regulator, A... 162 3e-38 B1D6K7.1 B1D6K7_9BACL Two component transcriptional regulator, A... 159 2e-37 B1D7W6.1 B1D7W6_9BACL Two component transcriptional regulator, A... 158 4e-37 Q5WBZ0.1 Q5WBZ0_BACSK Two-component response regulator 155 4e-36 >B1DAU1.1 B1DAU1_9BACL Two component transcriptional regulator, AraC family Length = 248 Score = 354 bits (908), Expect = 4e-96, Method: Compositional matrix adjust. Identities = 169/236 (71%), Positives = 200/236 (84%) Query: 1 MRVLIVDDEPLILNGLVKIIGEAAPLGTEVFKANNAFEALDLMKDYMPDVTVTDLHMPEK 60 M++LIVDDEPLIL GLVKI+ E AP G+++ A NA+EAL+ MK +MPDVT+TD++MPEK Sbjct: 1 MKILIVDDEPLILKGLVKIVEEVAPAGSDICSAFNAWEALETMKRFMPDVTITDINMPEK 60 Query: 61 NGFELIEAARDSGLCDRFIILTGYDEFEYVRKALRTGVVDYLLKPIDKNEIALLLARIDQ 120 NGFELI AR GLCDRFIILTGYDEFEYVR+ALR+GVVDYLLKP+DK EIA LL+R+ + Sbjct: 61 NGFELIHDARLEGLCDRFIILTGYDEFEYVRQALRSGVVDYLLKPLDKKEIAGLLSRVKE 120 Query: 121 ELPSEADPECSGHAKRILAYTKTHYMNDLSLDHLAELMKLHPNYISSLFKKVTGDTFVSY 180 ELP+ D E S HA+RILAY + +YMNDLSLDHLAE M LHPNYISSLFKK TGDTFV+Y Sbjct: 121 ELPAATDSEYSRHAERILAYLQLNYMNDLSLDHLAEHMSLHPNYISSLFKKETGDTFVNY 180 Query: 181 LNAFRIKEAQKLLRSQRQLSVNAIGKKVGFENKHYFTKVFKKYTGITPGAYREEGE 236 LN+ RI+EAQKLL++Q QL+V AI ++VGF+ KHYF KVFKKY G TPGAYRE E Sbjct: 181 LNSLRIREAQKLLKTQPQLTVCAISQQVGFDTKHYFAKVFKKYAGTTPGAYRENKE 236 >A9KTC8.1 A9KTC8_CLOPH Two component transcriptional regulator, AraC family Length = 253 Score = 162 bits (410), Expect = 3e-38, Method: Compositional matrix adjust. Identities = 94/241 (39%), Positives = 137/241 (56%), Gaps = 8/241 (3%) Query: 1 MRVLIVDDEPLILNGLVKIIGEAAPLGTEVFKANNAFEALDLMKDYMPDVTVTDLHMPEK 60 M++LI DDE I NG+ K I ++++ A N +ALD++ Y PD+ + D+ MP K Sbjct: 3 MKLLIADDEDTIRNGIAKYIKLHTDRFSQIYLAENGQQALDIILQYQPDMMLLDVQMPLK 62 Query: 61 NGFELIEAARDSGLCDRFIILTGYDEFEYVRKALRTGVVDYLLKPIDKNEIALLLARIDQ 120 G E+++ A+ L + IIL+GYD+FEY RKALR G DYLLKP +EI + ++ Q Sbjct: 63 TGLEVLQEAQKLSLVPKTIILSGYDDFEYARKALRYGAKDYLLKPCRSSEILEAINKLVQ 122 Query: 121 E-LPSEADPECSGHA------KRILAYTKTHYMNDLSLDHLAELMKLHPNYISSLFKKVT 173 E L ++ D EC + Y + +Y +L+L ++ + + Y+S+LF + Sbjct: 123 EQLGTKEDVECEEGTGIHYIVSSAIEYMEEYYHKNLTLIEVSNKVGITAGYLSTLFTQNM 182 Query: 174 GDTFVSYLNAFRIKEAQKLLRSQRQLSVNAIGKKVGFENKHYFTKVFKKYTGITPGAYRE 233 FV YLN RIK A L Q I KVGF+++ YF+KVFKK TGITP YR Sbjct: 183 NCGFVEYLNKIRIKHACSYLE-QNYFKTYEIAYKVGFKDEKYFSKVFKKETGITPYEYRR 241 Query: 234 E 234 + Sbjct: 242 D 242 >B1D6K7.1 B1D6K7_9BACL Two component transcriptional regulator, AraC family Length = 245 Score = 159 bits (403), Expect = 2e-37, Method: Compositional matrix adjust. Identities = 86/238 (36%), Positives = 147/238 (61%), Gaps = 9/238 (3%) Query: 3 VLIVDDEPLILNGLVKIIGEAAPLGTEVFKANNAFEALDLMKDYMPDVTVTDLHMPEKNG 62 +LI++D+ +I G+VKI+ + + + +A+N EAL+ ++ +P++ +TD+ MP +G Sbjct: 4 MLIIEDDDIIRRGIVKIVSKMDLPISSIEEASNGQEALEKIRQLVPELIITDIMMPFLDG 63 Query: 63 FELIEAARDSGLCDRFIILTGYDEFEYVRKALRTGVVDYLLKPIDKNEIALLLARIDQEL 122 +L++ R+ L R II++G+DEF Y ++A+ GV YLLKP+ K+++ +L ++ EL Sbjct: 64 LKLLKQIREWELPSRTIIISGFDEFSYAQEAIAYGVSAYLLKPVKKDKLYQVLNKMIHEL 123 Query: 123 PSE-------ADPECSGH-AKRILAYTKTHYMNDLSLDHLAELMKLHPNYISSLFKKVTG 174 E D GH + Y + HY D+ L+ A L+ ++ Y SSLFKK+TG Sbjct: 124 TKENTNRKPLLDGSQYGHDVGFVTRYLEEHYAEDIDLNKAASLVFMNSTYFSSLFKKMTG 183 Query: 175 DTFVSYLNAFRIKEAQKLLRSQRQLSVNAIGKKVGFENKHYFTKVFKKYTGITPGAYR 232 +F+ YL R++E++KLL + QL + + +KVGF ++ YF +VFK TG+TP +R Sbjct: 184 VSFIHYLQKIRVEESKKLLLNH-QLKIYEVAEKVGFSDEKYFFRVFKNTTGLTPNEFR 240 >B1D7W6.1 B1D7W6_9BACL Two component transcriptional regulator, AraC family Length = 255 Score = 158 bits (400), Expect = 4e-37, Method: Compositional matrix adjust. Identities = 90/249 (36%), Positives = 145/249 (58%), Gaps = 17/249 (6%) Query: 2 RVLIVDDEPLILNGLVKIIGEAAPLGTEVFKANNAFEALDLMKDYMPDVTVTDLHMPEKN 61 R LIV+DE L K+ +A V +A + E L ++++ PDV ++D+ MP + Sbjct: 3 RTLIVEDEQHARASLRKLFSKADIPFEIVGEAADGEEGLRMIRELQPDVVISDIFMPVMD 62 Query: 62 GFELIEAARDSGLCDRFIILTGYDEFEYVRKALRTGVVDYLLK-PID-------KNEIAL 113 G L++ AR+ GL RF++LT EFEY R+A+ G YL+K +D ++A Sbjct: 63 GVRLLQLAREEGLECRFVMLTAVSEFEYARQAVEYGASGYLMKLSLDLAGLRQAMEKVAA 122 Query: 114 LLARI------DQELPSEADPECSGHAK--RILAYTKTHYMNDLSLDHLAELMKLHPNYI 165 LAR+ D+ P + E + H + RI+AY + H+ D++L LA+ +++ +Y+ Sbjct: 123 ELARMEKLRKADKWFPEKTAQEPTDHPEMNRIIAYIEEHFAEDITLKSLADWIRMDASYV 182 Query: 166 SSLFKKVTGDTFVSYLNAFRIKEAQKLLRSQRQLSVNAIGKKVGFENKHYFTKVFKKYTG 225 S LFKK TG T Y+ R+ A K+L ++ + +V+ IG+ VGFEN +YF K+FK++ G Sbjct: 183 SDLFKKKTGSTLTHYIQNRRVA-AAKMLLAETERTVSDIGRTVGFENDNYFIKIFKRWCG 241 Query: 226 ITPGAYREE 234 +TP YR+E Sbjct: 242 VTPNEYRKE 250 >Q5WBZ0.1 Q5WBZ0_BACSK Two-component response regulator Length = 249 Score = 155 bits (391), Expect = 4e-36, Method: Compositional matrix adjust. Identities = 85/238 (35%), Positives = 136/238 (57%), Gaps = 8/238 (3%) Query: 2 RVLIVDDEPLILNGLVKIIGEAAPLGTEVFKANNAFEALDLMKDYMPDVTVTDLHMPEKN 61 +V+I +DE +I GLV I+ + T + +A+N AL+L+ PDV +TD+ MP+ + Sbjct: 14 KVVIAEDEKMIRKGLVTIVDQLVTDFTVIGEADNGERALELLAHDCPDVLLTDIRMPKCD 73 Query: 62 GFELIEAARDSGLCDRFIILTGYDEFEYVRKALRTGVVDYLLKPIDKNEIALLLARIDQE 121 G LI AR + +I++G++EF Y ++A++ GV YLLKPID+ E+ L I + Sbjct: 74 GLSLIREARSYYPHVKIVIVSGHEEFAYAQQAIQHGVSRYLLKPIDRTEVVLAFDEIKRG 133 Query: 122 LPSEADPECSGHAKRIL----AYTKTHYMNDLSLDHLAELMKLHPNYISSLFKKVTGDTF 177 L +PE H ++ +Y KTH D++L +A+L+ LHP Y S FK TG F Sbjct: 134 L---VEPEQEDHENHLIQQVDSYIKTHIDQDITLQAVAKLVHLHPTYFSQWFKNETGQNF 190 Query: 178 VSYLNAFRIKEAQKLLRSQRQLSVNAIGKKVGFENKHYFTKVFKKYTGITPGAYREEG 235 +Y+ R++ A+ LL Q L V + + G++N+ +F K+FKK TP +R+ Sbjct: 191 STYVTQKRLERAETLLH-QTNLRVYEVARMSGYQNEKHFMKLFKKEKRCTPTQFRQRA 247 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.319 0.138 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9421015 Number of Hits to DB: 1,509,978,462 Number of extensions: 60792314 Number of successful extensions: 242897 Number of sequences better than 1.0e-05: 10689 Number of HSP's gapped: 256763 Number of HSP's successfully gapped: 11199 Length of query: 250 Length of database: 3,060,696,203 Length adjustment: 132 Effective length of query: 118 Effective length of database: 1,817,122,223 Effective search space: 214420422314 Effective search space used: 214420422314 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 (21.7 bits) S2: 129 (54.3 bits)