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= 0303.0020.p (228 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|ZP_00098268.1| COG0745: Response regulators consisting of a ... 351 8e-96 ref|NP_349364.1| Response regulator (CheY receiver domain and HT... 249 5e-65 ref|NP_601808.1| two-component system, response regulator [Coryn... 202 6e-51 gb|AAR04621.1| PhoP [Rhodococcus equi] 201 7e-51 ref|NP_739104.1| conserved hypothetical protein [Corynebacterium... 200 2e-50 >ref|ZP_00098268.1| COG0745: Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Desulfitobacterium hafniense] Length = 227 Score = 351 bits (900), Expect = 8e-96, Method: Compositional matrix adjust. Identities = 162/228 (71%), Positives = 203/228 (89%), Gaps = 1/228 (0%) Query: 1 MKAAQGVKLLLVDDEPHILQFLELGLINEGFEVRTAPDGASAIAVAADFKPHVAILDVMM 60 M+ +G+K+L++DDEP+IL+FLE+GL+NEGFEV+TA DG + + +A PH+ ILD+MM Sbjct: 1 MQKLKGIKILIIDDEPNILEFLEMGLLNEGFEVQTAADGMTGVTLAKQLHPHLVILDIMM 60 Query: 61 PGMDGFELCRYLRSEESELAVIMLTAKDEVDDRVKGLSIGADDYMVKPFSFDELLARIQA 120 PGMDGFE+CR L+ E+ +++IMLTAKDEV+DRVKGL+IGADDYM KPFSF+ELLARI A Sbjct: 61 PGMDGFEVCRMLKKSEN-VSIIMLTAKDEVEDRVKGLTIGADDYMAKPFSFEELLARIHA 119 Query: 121 RLRNQFPGLLGEVRCGPFRIDGRRKEIRHKDEVLELSPTEYELLQYLVINHGLVLSKPMI 180 R+RNQFP LLGEV GPFR+D RRKEI+ +D+VLELSPTEYELL++L++N GLVLSK MI Sbjct: 120 RIRNQFPTLLGEVVMGPFRLDDRRKEIQFQDKVLELSPTEYELLKFLILNQGLVLSKTMI 179 Query: 181 LDKVWGYDFGGEENIVEVYIRSLREKLGDKDHRIIRTLRGAGYRVDLV 228 LDKVWGYDF G++NIVEVYIRSLREKLGDK+HR+IRTLRG+GYR+DL+ Sbjct: 180 LDKVWGYDFAGDDNIVEVYIRSLREKLGDKEHRLIRTLRGSGYRMDLI 227 >ref|NP_349364.1| Response regulator (CheY receiver domain and HTH-type DNA-binding domain) [Clostridium acetobutylicum] pir||E97239 response regulator (CheY receiver domain and HTH-type DNA-binding domain) [imported] - Clostridium acetobutylicum gb|AAK80704.1| Response regulator (CheY receiver domain and HTH-type DNA-binding domain) [Clostridium acetobutylicum] Length = 228 Score = 249 bits (635), Expect = 5e-65, Method: Compositional matrix adjust. Identities = 126/223 (56%), Positives = 168/223 (75%), Gaps = 1/223 (0%) Query: 3 AAQGVKLLLVDDEPHILQFLELGLINEGFEVRTAPDGASAIAVAADFKPHVAILDVMMPG 62 +++VDDE HI++FL++GL EGF V TA +G A+ + P++ ILDVM+P Sbjct: 5 TKNNFSIMVVDDEEHIVEFLKMGLEAEGFTVYTAFNGNDAVIYSRKLNPNLIILDVMLPY 64 Query: 63 MDGFELCRYLRSEESELAVIMLTAKDEVDDRVKGLSIGADDYMVKPFSFDELLARIQARL 122 M+G+E+C ++ + S + +IMLTAKDE+DD+V GL++GADDYM+KPFSF ELLARI ARL Sbjct: 65 MNGYEVCSLIK-KASNIPIIMLTAKDEIDDKVLGLNLGADDYMIKPFSFKELLARINARL 123 Query: 123 RNQFPGLLGEVRCGPFRIDGRRKEIRHKDEVLELSPTEYELLQYLVINHGLVLSKPMILD 182 RN F L +V GPF I EI +KD++L LSPTEY LL+YL++N+G+ LSK IL+ Sbjct: 124 RNSFSETLNKVVIGPFLIKDSAHEIIYKDDILSLSPTEYNLLKYLLLNNGIALSKDQILE 183 Query: 183 KVWGYDFGGEENIVEVYIRSLREKLGDKDHRIIRTLRGAGYRV 225 KVWGYDF GE+NIVEVYIR LR+K+ DK+H IIRT+RG GY+V Sbjct: 184 KVWGYDFTGEKNIVEVYIRYLRDKISDKNHTIIRTVRGVGYKV 226 >ref|NP_601808.1| two-component system, response regulator [Corynebacterium glutamicum ATCC 13032] dbj|BAC00001.1| Two-component system, response regulators consisting of a CheY-like receiver domain and a HTH DNA-binding domain [Corynebacterium glutamicum ATCC 13032] emb|CAF21269.1| putative two component response regulator [Corynebacterium glutamicum ATCC 13032] Length = 235 Score = 202 bits (513), Expect = 6e-51, Method: Compositional matrix adjust. Identities = 104/222 (46%), Positives = 150/222 (67%), Gaps = 7/222 (3%) Query: 7 VKLLLVDDEPHILQFLELGLINEGFEVRTAPDGASAIAVAADFKPHVAILDVMMPGMDGF 66 +++L+VDDEP+I++ L + L +GF V TA DG A+ +A +F+P ILDVMMPGMDGF Sbjct: 9 IRVLVVDDEPNIVELLTVSLKFQGFAVMTANDGNEALKIAREFRPDAYILDVMMPGMDGF 68 Query: 67 ELCRYLRSEESELAVIMLTAKDEVDDRVKGLSIGADDYMVKPFSFDELLARIQARLRNQF 126 EL LR E + V+ LTAKD V+ R+ GL+IGADDY+ KPFS +E++ R++ LR Sbjct: 69 ELLTKLRGEGLDSPVLYLTAKDAVEHRIHGLTIGADDYVTKPFSLEEVITRLRVILRRG- 127 Query: 127 PGLLGE-----VRCGPFRIDGRRKEIRHKDEVLELSPTEYELLQYLVINHGLVLSKPMIL 181 G + E ++ ++ E+ E+++LSPTE+ LL+YL++N +VLSK IL Sbjct: 128 -GAVEEDTSTSLQYADLTLNDETHEVTKAGELIDLSPTEFNLLRYLMLNAEVVLSKAKIL 186 Query: 182 DKVWGYDFGGEENIVEVYIRSLREKLGDKDHRIIRTLRGAGY 223 D VW YDFGG+ N+VE YI LR K+ +D ++I+T+RG GY Sbjct: 187 DNVWHYDFGGDGNVVESYISYLRRKVDTQDPQLIQTVRGVGY 228 >gb|AAR04621.1| PhoP [Rhodococcus equi] Length = 242 Score = 201 bits (512), Expect = 7e-51, Method: Compositional matrix adjust. Identities = 103/220 (46%), Positives = 143/220 (65%), Gaps = 3/220 (1%) Query: 7 VKLLLVDDEPHILQFLELGLINEGFEVRTAPDGASAIAVAADFKPHVAILDVMMPGMDGF 66 V++L+VDDEP +++ L + L +GFEV TA +GA + A F+P ILDVMMPGMDGF Sbjct: 17 VRVLIVDDEPSLVELLSVSLRFQGFEVETAANGAEGLDKARAFRPDALILDVMMPGMDGF 76 Query: 67 ELCRYLRSEESELAVIMLTAKDEVDDRVKGLSIGADDYMVKPFSFDELLARIQARLR--- 123 + R LR++ + V+ LTA+D V+D+V GL+IGADDY+ KPFS +E++ R++ LR Sbjct: 77 GMLRRLRADGVDAPVLFLTARDAVEDKVTGLTIGADDYVTKPFSLEEVVTRLRVILRRAG 136 Query: 124 NQFPGLLGEVRCGPFRIDGRRKEIRHKDEVLELSPTEYELLQYLVINHGLVLSKPMILDK 183 + V +D +E+ E + LSPTE+ LL+Y ++N G VLSKP ILD Sbjct: 137 HSDDKQSARVTFADLELDDDTREVWKAGEPVSLSPTEFTLLRYFMVNAGTVLSKPRILDH 196 Query: 184 VWGYDFGGEENIVEVYIRSLREKLGDKDHRIIRTLRGAGY 223 VW YDFGGE +VE Y+ LR K+ + R+I TLRG GY Sbjct: 197 VWNYDFGGEVGVVESYVSYLRRKIDTTEPRLIHTLRGVGY 236 >ref|NP_739104.1| conserved hypothetical protein [Corynebacterium efficiens YS-314] dbj|BAC19304.1| conserved hypothetical protein [Corynebacterium efficiens YS-314] Length = 240 Score = 200 bits (509), Expect = 2e-50, Method: Compositional matrix adjust. Identities = 102/221 (46%), Positives = 147/221 (66%), Gaps = 4/221 (1%) Query: 7 VKLLLVDDEPHILQFLELGLINEGFEVRTAPDGASAIAVAADFKPHVAILDVMMPGMDGF 66 VK+L+VDDEP+I++ L + L +GF V TA DG + +A +F+P ILDVMMPGMDGF Sbjct: 13 VKVLVVDDEPNIVELLTVSLKFQGFNVMTASDGNEGLKIAREFRPDAYILDVMMPGMDGF 72 Query: 67 ELCRYLRSEESELAVIMLTAKDEVDDRVKGLSIGADDYMVKPFSFDELLARIQARLRN-- 124 EL LR+E + V+ LTAKD V++R+ GL+IGADDY+ KPFS +E++ R++ LR Sbjct: 73 ELLTKLRAEGLDGPVLYLTAKDAVENRIHGLTIGADDYVTKPFSLEEVITRLRVILRRGG 132 Query: 125 --QFPGLLGEVRCGPFRIDGRRKEIRHKDEVLELSPTEYELLQYLVINHGLVLSKPMILD 182 + + ++ E+ E+++LSPTE+ LL+YL++N +VLSK ILD Sbjct: 133 SVESESNDATLTYADLTLNDETHEVTKAGELVDLSPTEFNLLRYLMLNAEVVLSKAKILD 192 Query: 183 KVWGYDFGGEENIVEVYIRSLREKLGDKDHRIIRTLRGAGY 223 VW YDFGG+ N+VE YI LR K+ + ++I+T+RG GY Sbjct: 193 NVWHYDFGGDGNVVESYISYLRRKVDTHEPQLIQTVRGVGY 233 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 0.323 0.144 0.416 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: 342,874,985 Number of extensions: 14164722 Number of successful extensions: 61382 Number of sequences better than 1.0e-05: 5810 Number of HSP's gapped: 56697 Number of HSP's successfully gapped: 5859 Length of query: 228 Length of database: 757,237,578 Length adjustment: 121 Effective length of query: 107 Effective length of database: 428,710,599 Effective search space: 45872034093 Effective search space used: 45872034093 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 124 (52.4 bits)