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= 0534.0002.p (256 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value CAC1581 [KT] COG3279 Response regulator of the LytR/AlgR family 81 1e-15 lin0801 [KT] COG3279 Response regulator of the LytR/AlgR family 75 1e-13 BS_lytT [KT] COG3279 Response regulator of the LytR/AlgR family 66 5e-11 VCA0850 [KT] COG3279 Response regulator of the LytR/AlgR family 64 3e-10 ypdB [KT] COG3279 Response regulator of the LytR/AlgR family 60 4e-09 >CAC1581 [KT] COG3279 Response regulator of the LytR/AlgR family Length = 234 Score = 81.3 bits (199), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 64/238 (26%), Positives = 111/238 (46%), Gaps = 32/238 (13%) Query: 7 LFHVGVCDDEAGVRNELQRYFSQLSVATNYSFDVHYFPSGEKLLQHYKAMQGEYAYHLLI 66 + + VCDD R E+ ++ F + F E++L+ + L Sbjct: 1 MLKIAVCDDNDIEREEIVHIINKHLKYNQKDFTILKFEQAEQVLK------SIIKFDLYF 54 Query: 67 LDVEMTGISGLETARQIRSLPDRDVQIIFLTSYPEYMMESFDVQTFQYLLKPVTYELFKK 126 LD++M ++G+E A+ IR++ +D IIF+TSY +Y+ ++FDV+ F Y++KP+ E K Sbjct: 55 LDIKMEKMNGIELAKNIRNIS-KDAVIIFVTSYRDYVFDAFDVRAFNYIIKPIDQERI-K 112 Query: 127 KTLKLCSYLISSSNRFFTIKV--EDGQIVLRKPEIIAMVKIKHSLAQNKLKVITAAQEYI 184 K L +RF K + ++ LR I K K+K+ T Sbjct: 113 KILNEALAEFEKQDRFIITKTISKSTKVFLRDITYIEAEK-------RKIKIHTTYD--- 162 Query: 185 INGTLQEYSDKLGSL--------FLMIHRSIIVNLEHVRRFTATSVVMSNDEEYPIGR 234 + EY +K+ L F H+S IVNL +V+ + TS+ + N+++ I + Sbjct: 163 ----VIEYYNKISQLEEELREYNFFRCHKSYIVNLGYVKSYDNTSITLENNDKIYISK 216 >lin0801 [KT] COG3279 Response regulator of the LytR/AlgR family Length = 240 Score = 74.7 bits (182), Expect = 1e-13, Method: Compositional matrix adjust. Identities = 57/247 (23%), Positives = 121/247 (48%), Gaps = 31/247 (12%) Query: 10 VGVCDDEAGVRNELQRYFSQLSVATNYSFDVHYFPSGEKLLQHYKAMQGEYAYHLLILDV 69 + +CDD+ V +++ Q + + + +H F G L++ +Q + + L+ LD+ Sbjct: 5 IAICDDDKVVCAQIESMILQYAQESGFDVTIHIFYDGSSLME---GIQNDDNFDLIYLDI 61 Query: 70 EMTGISGLETARQIRS-LPDRDVQIIFLTSYPEYMMESFDVQTFQYLLKPV-------TY 121 EM GI+G++ IR L D +QI++++ +Y + FDVQ ++ KP+ + Sbjct: 62 EMDGINGVDVGMTIRDKLRDHKMQIVYVSGKGQYDRQLFDVQPLLFIPKPIEESKLVKSI 121 Query: 122 ELFKKK---TLKLCSYLISSSNRFFTIKVEDGQIVLRKPEIIAMVKIKHSLAQNKLKVIT 178 L ++K T KL Y +F++ +ED ++ ++S K+ I Sbjct: 122 NLAREKLALTPKLYHY--KKRKEYFSVWMED------------IIYFENSGRNVKIMTID 167 Query: 179 AAQEYIINGTLQEYSDK-LGSLFLMIHRSIIVNLEHVRRFTATSVVMSNDEEYPIGRSQS 237 ++ G +++ + + L F+ I +SIIVN V +++ +++ N E+ I +++ Sbjct: 168 GTDLFV--GNIKDIAKEVLPYGFIQISQSIIVNYNFVSKYSREEIILINKEKIAIPKNKR 225 Query: 238 KTIKDVY 244 +K+ + Sbjct: 226 NGVKEQF 232 >BS_lytT [KT] COG3279 Response regulator of the LytR/AlgR family Length = 241 Score = 66.2 bits (160), Expect = 5e-11, Method: Compositional matrix adjust. Identities = 63/250 (25%), Positives = 117/250 (46%), Gaps = 29/250 (11%) Query: 7 LFHVGVCDDEAGVRNELQRYFSQLSVATNYSFDVHYFPSGEKLLQHYKAMQGEYAYHLLI 66 + V + DDE R+EL + TN +++ E + + M + LL Sbjct: 1 MLRVLIVDDEMLARDELAYLLKR----TNDEMEIN---EAENIESAFDQMMDQKP-DLLF 52 Query: 67 LDVEMTGISGLETARQIRSLPDRDVQIIFLTSYPEYMMESFDVQTFQYLLKPVTYELFK- 125 LDV+++G +G + A++++ + I+F T+Y +Y +++F+V YL KP E + Sbjct: 53 LDVDLSGENGFDIAKRLKKMK-HPPAIVFATAYDQYALKAFEVDALDYLTKPFDEERIQQ 111 Query: 126 --KKTLKLCSYLISSSNRFFTIKVEDGQ--IVLRKPEIIAMVKIKHSL----AQNKLKVI 177 KK K+ ++ + GQ + L E I +V K + + V Sbjct: 112 TLKKYKKVNRDIVETEQNSHA-----GQHKLALSVGESIVIVDTKDIIYAGTEDGHVNVK 166 Query: 178 TAAQEYIINGTLQEYSDKL-GSLFLMIHRSIIVNLEHVRR----FTAT-SVVMSNDEEYP 231 T Y ++ TL KL S F+ +HRS +VN E+++ F +T +++M + + P Sbjct: 167 TFDHSYTVSDTLVVIEKKLPDSDFIRVHRSFVVNTEYIKEIQPWFNSTYNLIMKDGSKIP 226 Query: 232 IGRSQSKTIK 241 + R+ +K +K Sbjct: 227 VSRTYAKELK 236 >VCA0850 [KT] COG3279 Response regulator of the LytR/AlgR family Length = 261 Score = 63.5 bits (153), Expect = 3e-10, Method: Compositional matrix adjust. Identities = 63/252 (25%), Positives = 112/252 (44%), Gaps = 36/252 (14%) Query: 12 VCDDEAGVRNELQRYFSQLSVATNYSFDVHYFPSGEKLLQHYKAMQGEYAYHLLILDVEM 71 + DDE +R+ L + ++L A V +G+ LQ + Q + + LD+ M Sbjct: 10 LADDEPLLRHHLNKLLAELWPALEI---VASAENGQIALQAIEQHQPDVVF----LDIRM 62 Query: 72 TGISGLETARQIRSLPDRDVQIIFLTSYPEYMMESFDVQTFQYLLKPVTYELFKKKTLKL 131 + G+E AR++ P + ++F+T+Y EY + +F+ YLLKP++ KL Sbjct: 63 PKMDGIEVARRLLQQPKVPL-VVFITAYDEYAVSAFETHAIDYLLKPLSSSRLASCCEKL 121 Query: 132 CSYL---ISSSNRFFTIKVEDGQIVLR-KPEIIAMVKIK-----HSLAQNKLKVITA--- 179 L ++ SN + + Q+ KP+ +K H +A N+L + A Sbjct: 122 QQQLRRNVAPSNDLAQLMSQFEQLTRTVKPQYQVWLKASKGEEIHLIAVNELLYVKAEDK 181 Query: 180 -----------AQEYIINGTLQEYSDKLG-SLFLMIHRSIIVNLEHV----RRFTATSVV 223 EY++ +L+E +L + F IHRSI+VN+ + R F V Sbjct: 182 YLSLYKVHGATTHEYLLRSSLKELLAQLDPNQFWQIHRSIVVNVGKIDKVTRDFGGKMWV 241 Query: 224 MSNDEEYPIGRS 235 + + P+ R+ Sbjct: 242 HIDRLQLPVSRA 253 >ypdB [KT] COG3279 Response regulator of the LytR/AlgR family Length = 244 Score = 59.7 bits (143), Expect = 4e-09, Method: Compositional matrix adjust. Identities = 56/208 (26%), Positives = 96/208 (46%), Gaps = 22/208 (10%) Query: 48 KLLQHYKAMQGEYAYHLLILDVEMTGISGLETARQIRSLPDRDVQIIFLTSYPEYMMESF 107 K LQH + + LD+ + + G+ A+ I + I+F+T++ E+ +E+F Sbjct: 40 KFLQHNRV-------DAIFLDINIPSLDGVLLAQNISQFAHKPF-IVFITAWKEHAVEAF 91 Query: 108 DVQTFQYLLKPVTYELFKKKTLKLCSYL---ISSSNRFFTIKVEDGQIVLRKPEIIAMVK 164 +++ F Y+LKP KL + +SS T+ E+ I L K E I + Sbjct: 92 ELEAFDYILKPYQESRITGMLQKLEAAWQQQQTSSTPAATVTRENDTINLVKDERIIVTP 151 Query: 165 IK---HSLAQNKLK-VITAAQEYIINGTLQEYSDKL-GSLFLMIHRSIIVNLEHVRR--- 216 I ++ A K+ V T + Y++ + E+ KL S F HRS VNL +R Sbjct: 152 INDIYYAEAHEKMTFVYTRRESYVMPMNITEFCSKLPPSHFFRCHRSFCVNLNKIREIEP 211 Query: 217 -FTATSVVMSNDEEY--PIGRSQSKTIK 241 F T ++ D ++ P+ RS+ K + Sbjct: 212 WFNNTYILRLKDLDFEVPVSRSKVKEFR 239 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.322 0.137 0.383 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 17,427,210 Number of extensions: 661207 Number of successful extensions: 1652 Number of sequences better than 1.0e-05: 20 Number of HSP's gapped: 1643 Number of HSP's successfully gapped: 20 Length of query: 256 Length of database: 38,378,431 Length adjustment: 104 Effective length of query: 152 Effective length of database: 26,383,695 Effective search space: 4010321640 Effective search space used: 4010321640 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: 114 (48.5 bits)