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= 0005.0011.p (200 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3K385.1 B3K385_9BACI Response regulator receiver 293 6e-78 A6TNE3.1 A6TNE3_ALKMQ Two component transcriptional regulator, w... 270 6e-71 B1DL05.1 B1DL05_9BACL Two component transcriptional regulator, w... 266 6e-70 C3II98.1 C3II98_BACTU DNA-binding response regulator 262 1e-68 B7IT74.1 B7IT74_BACC2 DNA-binding response regulator 262 1e-68 >B3K385.1 B3K385_9BACI Response regulator receiver Length = 226 Score = 293 bits (750), Expect = 6e-78, Method: Compositional matrix adjust. Identities = 140/200 (70%), Positives = 160/200 (80%) Query: 1 MEEVFGASDGIEALRLLEDNGVDLAVIDVMMPNMDGWELCKELRRSYDIPILMLTAKGET 60 ME V ASDG+EAL ++E VDL V+D+MMPNMDGWELC+E+RR+ IP+LMLTAKGET Sbjct: 26 MEGVMEASDGVEALSVMEQVSVDLVVMDIMMPNMDGWELCREIRRNTGIPVLMLTAKGET 85 Query: 61 SQIVKGFELGTDDYLVKPFEPPVLIARVKALLKRYQISAAQSVNVGGLRMNRKTYEVTAD 120 QIVKGFELGTDDYLVKPFEP L+ RVKALLKRYQ++A+Q+V +G L+MNRKTYE A Sbjct: 86 RQIVKGFELGTDDYLVKPFEPAELVVRVKALLKRYQVAASQTVTIGNLQMNRKTYEAKAG 145 Query: 121 QGSITLPXXXXXXXXXXASYPGQTLTRDRLIEEVWGYDFEGNERTLDVHVGRLRDRFPRE 180 TLP ASYPG TLTRDRLIE++WGYDFEGNERTLDVHV RLR+RFP E Sbjct: 146 DEVFTLPLKEFELLFKLASYPGSTLTRDRLIEDIWGYDFEGNERTLDVHVNRLRERFPEE 205 Query: 181 DYGFAIRTVRGLGYRLEVGK 200 Y F IRTVRGLGYRLE G+ Sbjct: 206 KYRFRIRTVRGLGYRLEAGE 225 >A6TNE3.1 A6TNE3_ALKMQ Two component transcriptional regulator, winged helix family Length = 224 Score = 270 bits (689), Expect = 6e-71, Method: Compositional matrix adjust. Identities = 126/197 (63%), Positives = 152/197 (77%) Query: 3 EVFGASDGIEALRLLEDNGVDLAVIDVMMPNMDGWELCKELRRSYDIPILMLTAKGETSQ 62 +V A DG+EAL LE VD+ ++DVMMPNMDGW+LC+ELR YD+P+LMLTAKGETSQ Sbjct: 27 DVHEAFDGVEALSKLETIKVDMVILDVMMPNMDGWQLCRELREHYDLPLLMLTAKGETSQ 86 Query: 63 IVKGFELGTDDYLVKPFEPPVLIARVKALLKRYQISAAQSVNVGGLRMNRKTYEVTADQG 122 VKGF+LGTDDYLVKPFEP L+ RVKALLKRYQI +Q+V +G L MN+K Y+VT Sbjct: 87 KVKGFQLGTDDYLVKPFEPMELVVRVKALLKRYQIITSQTVRIGELVMNQKNYKVTVGSE 146 Query: 123 SITLPXXXXXXXXXXASYPGQTLTRDRLIEEVWGYDFEGNERTLDVHVGRLRDRFPREDY 182 S TLP ASYP +T +R++LIE++WGYDF GNERTLDVH+ RLR RFP E++ Sbjct: 147 SFTLPLKEFELLFKMASYPEKTFSREQLIEDIWGYDFAGNERTLDVHINRLRQRFPEENH 206 Query: 183 GFAIRTVRGLGYRLEVG 199 F IRT+RGLGYRLEV Sbjct: 207 SFKIRTIRGLGYRLEVS 223 >B1DL05.1 B1DL05_9BACL Two component transcriptional regulator, winged helix family Length = 224 Score = 266 bits (681), Expect = 6e-70, Method: Compositional matrix adjust. Identities = 126/196 (64%), Positives = 152/196 (77%) Query: 3 EVFGASDGIEALRLLEDNGVDLAVIDVMMPNMDGWELCKELRRSYDIPILMLTAKGETSQ 62 EV ASDG+EAL +L+ DL ++DVMMPNMDGWELC E+R YD+P LMLTAKGET+Q Sbjct: 27 EVLEASDGVEALTILDSAKADLVIMDVMMPNMDGWELCAEIRDHYDLPRLMLTAKGETAQ 86 Query: 63 IVKGFELGTDDYLVKPFEPPVLIARVKALLKRYQISAAQSVNVGGLRMNRKTYEVTADQG 122 +KGFELG DDYLVKPFEP LIARVKALLKRY+I+++Q+V G L ++RKTY V + Sbjct: 87 KLKGFELGADDYLVKPFEPLELIARVKALLKRYRIASSQTVQAGDLILDRKTYVVQVNGQ 146 Query: 123 SITLPXXXXXXXXXXASYPGQTLTRDRLIEEVWGYDFEGNERTLDVHVGRLRDRFPREDY 182 S+TLP ASYPGQ+ +R +LIEE+WGYDFEGNERTLDVH+ RLR+RFP + Sbjct: 147 SMTLPLKEFELLFKLASYPGQSFSRGQLIEEIWGYDFEGNERTLDVHINRLRERFPESQH 206 Query: 183 GFAIRTVRGLGYRLEV 198 F I T+RGLGYRLEV Sbjct: 207 TFRISTIRGLGYRLEV 222 >C3II98.1 C3II98_BACTU DNA-binding response regulator Length = 234 Score = 262 bits (670), Expect = 1e-68, Method: Compositional matrix adjust. Identities = 119/198 (60%), Positives = 157/198 (79%) Query: 3 EVFGASDGIEALRLLEDNGVDLAVIDVMMPNMDGWELCKELRRSYDIPILMLTAKGETSQ 62 + + A DG++ALR ++D VD+ ++D+MMPNMDG+++C ELR+ YDIP+LMLTAKGETSQ Sbjct: 37 QTYEAIDGVDALRKMDDVKVDMVILDIMMPNMDGFDVCFELRKYYDIPVLMLTAKGETSQ 96 Query: 63 IVKGFELGTDDYLVKPFEPPVLIARVKALLKRYQISAAQSVNVGGLRMNRKTYEVTADQG 122 VKGF LGTDDYLVKPF+P L+ RVKALLKRYQI+ +QS+ VG + +NRKT+EVT+ + Sbjct: 97 KVKGFHLGTDDYLVKPFDPIELVVRVKALLKRYQITVSQSIQVGNVLLNRKTFEVTSGEQ 156 Query: 123 SITLPXXXXXXXXXXASYPGQTLTRDRLIEEVWGYDFEGNERTLDVHVGRLRDRFPREDY 182 ++TLP S G+T +R++LIEE+WGYDFEGNERTLDVH+ RLR++F E Sbjct: 157 TVTLPLKEFELLFTLGSKSGRTCSREQLIEEIWGYDFEGNERTLDVHINRLREKFQEEQS 216 Query: 183 GFAIRTVRGLGYRLEVGK 200 F+I+T+RGLGYRLEV K Sbjct: 217 KFSIKTIRGLGYRLEVSK 234 >B7IT74.1 B7IT74_BACC2 DNA-binding response regulator Length = 225 Score = 262 bits (670), Expect = 1e-68, Method: Compositional matrix adjust. Identities = 119/198 (60%), Positives = 157/198 (79%) Query: 3 EVFGASDGIEALRLLEDNGVDLAVIDVMMPNMDGWELCKELRRSYDIPILMLTAKGETSQ 62 + + A DG++ALR ++D VD+ ++D+MMPNMDG+++C ELR+ YDIP+LMLTAKGETSQ Sbjct: 28 QTYEAIDGVDALRKMDDVKVDMVILDIMMPNMDGFDVCFELRKYYDIPVLMLTAKGETSQ 87 Query: 63 IVKGFELGTDDYLVKPFEPPVLIARVKALLKRYQISAAQSVNVGGLRMNRKTYEVTADQG 122 VKGF LGTDDYLVKPF+P L+ RVKALLKRYQI+ +QS+ VG + +NRKT+EVT+ + Sbjct: 88 KVKGFHLGTDDYLVKPFDPIELVVRVKALLKRYQITVSQSIQVGNVLLNRKTFEVTSGEQ 147 Query: 123 SITLPXXXXXXXXXXASYPGQTLTRDRLIEEVWGYDFEGNERTLDVHVGRLRDRFPREDY 182 ++TLP S G+T +R++LIEE+WGYDFEGNERTLDVH+ RLR++F E Sbjct: 148 TVTLPLKEFELLFTLGSKSGRTCSREQLIEEIWGYDFEGNERTLDVHINRLREKFQEEQS 207 Query: 183 GFAIRTVRGLGYRLEVGK 200 F+I+T+RGLGYRLEV K Sbjct: 208 KFSIKTIRGLGYRLEVSK 225 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 0.320 0.140 0.410 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: 1,117,133,892 Number of extensions: 41845137 Number of successful extensions: 196109 Number of sequences better than 1.0e-05: 24229 Number of HSP's gapped: 180139 Number of HSP's successfully gapped: 24319 Length of query: 200 Length of database: 3,060,696,203 Length adjustment: 129 Effective length of query: 71 Effective length of database: 1,845,385,268 Effective search space: 131022354028 Effective search space used: 131022354028 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: 128 (53.9 bits)