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= 0350.0029.p (442 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_357748.1| Response regulator [Streptococcus pneumoniae R6... 97 8e-19 ref|NP_344698.1| DNA-binding response regulator [Streptococcus p... 96 2e-18 ref|ZP_00180754.1| hypothetical protein Mther123301 [Moorella th... 93 1e-17 ref|NP_465534.1| similar to two-component response regulator [Li... 87 8e-16 ref|NP_623880.1| AraC-type DNA-binding domain-containing protein... 86 2e-15 >ref|NP_357748.1| Response regulator [Streptococcus pneumoniae R6] pir||B97891 response regulator [imported] - Streptococcus pneumoniae (strain R6) gb|AAK98958.1| Response regulator [Streptococcus pneumoniae R6] Length = 428 Score = 97.1 bits (240), Expect = 8e-19, Method: Compositional matrix adjust. Identities = 109/458 (23%), Positives = 207/458 (45%), Gaps = 52/458 (11%) Query: 1 MFNVLVVDDEPLICKXXXXXXXXXXXEIGHIYTANSGFEALDVIRMEEVDLLVTDIQMGA 60 M+ VL+VDDE ++ + ++ + TA+ EAL+ ++ VD++++D+ M Sbjct: 1 MYKVLLVDDEYMVTEGLKRLIPFDKWDMEVVATASHADEALEYVQENPVDVIISDVNMPD 60 Query: 61 MSGIELMQHAKLAKPWVQTIIISAHETFQYAQMAVRLGAKDYLIKPLNS---EHFLDSVR 117 +G+++++ K P I++S ++ F Y + A+ L DYL+KP++ + L+ + Sbjct: 61 KTGLDMIREMKEILPDAAYILLSGYQEFDYVKRAMNLSVVDYLVKPVDKVELGNLLEKIA 120 Query: 118 NVLLKMDKPSPEL------ATFMAGIGESFRLEEPLPEYSRLLNALIEEPASVLGDEQKL 171 L + K S L A F++ +G+ E S+ P VLG ++ Sbjct: 121 GQLGERGKKSQTLSQELDEAGFVSYLGDK---ENWWIGLSKEKQGSFTIPYYVLGQAWQI 177 Query: 172 RKLDELKLQGPFFSVIKIKLPLPEEDGEKKYTFRDRELLRYAALNIAKELLDQEWSTVAF 231 D+ P ++ P ++ +++ + L Y ++N L Q S A+ Sbjct: 178 FISDQ-----PLDGLVVTPFEAPYQEHFERWKLNAEKTLFYGSVN-----LQQSESLFAY 227 Query: 232 YSPEEEITVVIQWDEKTYEESAAGQINRLD--VLGRTLHLNIHKYLHLNAVIGISQILKG 289 Y P V+IQ + E ++N L+ VL T + I K L + V+ + + + Sbjct: 228 YEP--IYRVIIQGNLNQIVE----ELNLLEKVVLENTPRIPITKQLFIQFVMDVFHLFEH 281 Query: 290 LSFMDVLN-RQASKAIQWNKEHSDY----YVFYYGDFNWSSYAADPSAEELHTHSNLIVQ 344 L D+ + + AIQ E Y + ++G + + N++ Sbjct: 282 LKADDMTDIVKTIHAIQSFDELVSYIKETLISFFGQY--------------RMNENVV-- 325 Query: 345 KAKEYIDENYAQKGLTIHEVAKKNHVSPNYLSYLFKKNTGHNLWEYVIKLRMEDSREMLL 404 E I +Y QK L++ +++K ++P YL L K+ T E + K R++ ++++LL Sbjct: 326 SVLEVIGRDY-QKELSLKDISKALFINPVYLGQLIKRETDSTFAELLNKQRIKAAQQLLL 384 Query: 405 HTDLRRYEIAERVGYESPEHFSKIFKKYYGISPSELKK 442 T +I VGY + +F K+F+K G SP +K Sbjct: 385 STSDSIEDICYAVGYSNLGYFYKVFRKLCGKSPKAYRK 422 >ref|NP_344698.1| DNA-binding response regulator [Streptococcus pneumoniae TIGR4] pir||A95018 DNA-binding response regulator [imported] - Streptococcus pneumoniae (strain TIGR4) emb|CAB54577.1| response regulator [Streptococcus pneumoniae] gb|AAK74338.1| DNA-binding response regulator [Streptococcus pneumoniae TIGR4] Length = 428 Score = 95.9 bits (237), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 110/459 (23%), Positives = 207/459 (45%), Gaps = 54/459 (11%) Query: 1 MFNVLVVDDEPLICKXXXXXXXXXXXEIGHIYTANSGFEALDVIRMEEVDLLVTDIQMGA 60 M+ VL+VDDE ++ + ++ + TA+ EAL+ ++ VD++++D+ M Sbjct: 1 MYKVLLVDDEYMVTEGLKRLIPFDKWDMEVVATASHADEALEYVQENPVDVIISDVNMPD 60 Query: 61 MSGIELMQHAKLAKPWVQTIIISAHETFQYAQMAVRLGAKDYLIKPLNS---EHFLDSVR 117 +G+++++ K P I++S ++ F Y + A+ L DYL+KP++ + L+ + Sbjct: 61 KTGLDMIREMKEILPDAAYILLSGYQEFDYVKRAMNLSVVDYLVKPVDKVELGNLLEKIA 120 Query: 118 NVLLKMDKPSPEL------ATFMAGIGESFRLEEPLPEYSRLLNALIEEPASVLGDEQKL 171 L + K S L A F++ +G+ E S+ P VLG + ++ Sbjct: 121 GQLGERGKKSQTLSQELDEAGFVSYLGDK---ENWWIGLSKEKQGSFTIPYYVLGQDWQI 177 Query: 172 RKLDELKLQG-PFFSVIKIKLPLPEEDGEKKYTFRDRELLRYAALNIAKELLDQEWSTVA 230 + G P ++ P ++ +++ + L Y ++N L Q S A Sbjct: 178 F------ISGHPLDGLVVTPFEAPYQEHFERWKLNAEKTLFYGSVN-----LQQSESLFA 226 Query: 231 FYSPEEEITVVIQWDEKTYEESAAGQINRLD--VLGRTLHLNIHKYLHLNAVIGISQILK 288 +Y P V+IQ + E ++N L+ VL T ++I K L + V+ + + + Sbjct: 227 YYEP--IYRVIIQGNLNQIVE----ELNLLEKVVLENTPRVSITKQLFIQFVMDVFHLFE 280 Query: 289 GLSFMDVLN-RQASKAIQWNKEHSDY----YVFYYGDFNWSSYAADPSAEELHTHSNLIV 343 L D+ + + AIQ E Y + ++G + N V Sbjct: 281 HLKADDMTDIVKTIHAIQSFDELVSYIKETLISFFGQY----------------RMNENV 324 Query: 344 QKAKEYIDENYAQKGLTIHEVAKKNHVSPNYLSYLFKKNTGHNLWEYVIKLRMEDSREML 403 E I +Y QK L++ +++K ++P YL L K+ T E + K R++ ++++L Sbjct: 325 VSVLEVIGRDY-QKELSLKDISKALFINPVYLGQLIKRETDSTFAELLNKQRIKAAQQLL 383 Query: 404 LHTDLRRYEIAERVGYESPEHFSKIFKKYYGISPSELKK 442 L T +I VGY + +F K+F+K G SP +K Sbjct: 384 LSTSDSIEDICYAVGYSNLGYFYKVFRKLCGKSPKAYRK 422 >ref|ZP_00180754.1| hypothetical protein Mther123301 [Moorella thermoacetica ATCC 39073] Length = 439 Score = 93.2 bits (230), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 45/111 (40%), Positives = 73/111 (65%), Gaps = 1/111 (0%) Query: 332 AEELHTHSNLIVQKAKEYIDENYAQKGLTIHEVAKKNHVSPNYLSYLFKKNTGHNLWEYV 391 AE ++ ++ +A +YI+ N++Q LT+ EVA++ ++SP Y S LFK+ G N +Y+ Sbjct: 319 AETREQRNSSLIDRASKYIEANFSQD-LTLEEVARQVYLSPCYFSKLFKQFKGLNFIDYL 377 Query: 392 IKLRMEDSREMLLHTDLRRYEIAERVGYESPEHFSKIFKKYYGISPSELKK 442 K+R++ +RE+LL+T L EIA RVGY +F ++FKK G +PS +K Sbjct: 378 TKVRLKAARELLLNTKLPVAEIATRVGYRDARYFGQVFKKQEGYTPSVFRK 428 >ref|NP_465534.1| similar to two-component response regulator [Listeria monocytogenes EGD-e] pir||AB1326 two-component response regulator homolog lmo2010 [imported] - Listeria monocytogenes (strain EGD-e) emb|CAD00088.1| lmo2010 [Listeria monocytogenes] Length = 494 Score = 87.0 bits (214), Expect = 8e-16, Method: Compositional matrix adjust. Identities = 44/116 (37%), Positives = 69/116 (59%) Query: 1 MFNVLVVDDEPLICKXXXXXXXXXXXEIGHIYTANSGFEALDVIRMEEVDLLVTDIQMGA 60 M +++VDDEPLI K I I TA +G ALD+ +EVD+L+TDI+M Sbjct: 1 MLKIVLVDDEPLILKGLESIIPEFEQSIEIIGTAKNGAVALDLFANQEVDVLLTDIEMPV 60 Query: 61 MSGIELMQHAKLAKPWVQTIIISAHETFQYAQMAVRLGAKDYLIKPLNSEHFLDSV 116 M+G+EL+ K +P +TI++S E F Y + + G ++YL+KPLN + +++ Sbjct: 61 MNGLELIDEWKKRQPATKTIVLSGFEDFHYVKRGLSAGIENYLLKPLNEQELKETL 116 Score = 54.7 bits (130), Expect = 4e-06, Method: Compositional matrix adjust. Identities = 31/101 (30%), Positives = 56/101 (55%), Gaps = 1/101 (0%) Query: 342 IVQKAKEYIDENYAQKGLTIHEVAKKNHVSPNYLSYLFKKNTGHNLWEYVIKLRMEDSRE 401 I+Q YI E++A+ G+++ + H++ YL LF+K G + +Y+ + R+ ++E Sbjct: 392 IIQNVLSYITEHFAE-GMSLKTLGNDFHINAVYLGQLFQKEMGEHFTDYLNRYRVNYAKE 450 Query: 402 MLLHTDLRRYEIAERVGYESPEHFSKIFKKYYGISPSELKK 442 LL T IA + GY +F + FKK+ G +P+ +K Sbjct: 451 ELLQTKDNLTIIAGKSGYTDMAYFYRQFKKHTGETPNRYRK 491 >ref|NP_623880.1| AraC-type DNA-binding domain-containing proteins [Thermoanaerobacter tengcongensis] gb|AAM25484.1| AraC-type DNA-binding domain-containing proteins [Thermoanaerobacter tengcongensis] Length = 519 Score = 85.9 bits (211), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 43/108 (39%), Positives = 71/108 (65%), Gaps = 1/108 (0%) Query: 334 ELHTHSNLIVQKAKEYIDENYAQKGLTIHEVAKKNHVSPNYLSYLFKKNTGHNLWEYVIK 393 E N I++ A EYID+NY K +++ VAK+ +V+P YLS LFKK N Y+ K Sbjct: 410 ERAGDKNPIIKDAVEYIDKNY-DKDISLESVAKEVYVTPAYLSILFKKEMNINFVSYLHK 468 Query: 394 LRMEDSREMLLHTDLRRYEIAERVGYESPEHFSKIFKKYYGISPSELK 441 +R+E ++++L L+ Y++A VG+ ++FS++FKKY G++PS+ + Sbjct: 469 VRVEKAKKLLEDRSLKTYQVANMVGFGDEKYFSQVFKKYTGLTPSQYR 516 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.318 0.135 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 659,468,198 Number of extensions: 28166205 Number of successful extensions: 84486 Number of sequences better than 1.0e-05: 775 Number of HSP's gapped: 86323 Number of HSP's successfully gapped: 817 Length of query: 442 Length of database: 757,237,578 Length adjustment: 129 Effective length of query: 313 Effective length of database: 406,989,807 Effective search space: 127387809591 Effective search space used: 127387809591 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: 127 (53.5 bits)