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= 0545.0008.p (289 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value lin2338 [E] COG0169 Shikimate 5-dehydrogenase 139 6e-33 lin0493 [E] COG0169 Shikimate 5-dehydrogenase 138 1e-32 STM1359 [E] COG0169 Shikimate 5-dehydrogenase 137 3e-32 ZydiB [E] COG0169 Shikimate 5-dehydrogenase 132 7e-31 ydiB [E] COG0169 Shikimate 5-dehydrogenase 132 7e-31 >lin2338 [E] COG0169 Shikimate 5-dehydrogenase Length = 289 Score = 139 bits (349), Expect = 6e-33, Method: Compositional matrix adjust. Identities = 86/271 (31%), Positives = 143/271 (52%), Gaps = 11/271 (4%) Query: 14 LLGVMGDPIAHTKSPLMHTAALKALGIPGAYVPLHIAPGQLGEAIQAIRTLGFRGVNVTI 73 LL ++G P+ H+KSP+M+ + + G+ AY+ I ++ +AI AI+T RG NVT+ Sbjct: 11 LLSLIGTPVDHSKSPIMYNYSFQKAGLDYAYLAFDIPVSKVADAIAAIKTFNLRGSNVTM 70 Query: 74 PHKVAVMEYIDRIDDSAXXXXXXXXXXXXXXXLTGYNTDGIGYVRSLKAEATPDLAGSXX 133 P K V++Y+D + +A LTG+ TDG+G+ +L+ ++ D+AG Sbjct: 71 PCKSEVLKYMDELSPAARMIGAVNTIINEDGKLTGHITDGLGFASNLR-DSGVDVAGKKM 129 Query: 134 XXXXXXXXXXXXXXXXXXEHPAAVVIAN---RTVEKSKQLAEAFQGK--GTVNGIG--ND 186 + + I N EK+KQ + + + + I ND Sbjct: 130 TIIGAGGAATAIQVQCALDGAKEIAIFNIKDDFYEKAKQTIASIKQEVPDCIVHIYDLND 189 Query: 187 EIAAH--IADMDIVINTTSVGMYPHIDAMPI-DPALLREGMIVSDLIYNPLQTRLLTESL 243 H IA DI++N T VGM+PH + P+ D + R+ +IV+D++YNP +TRLL ++ Sbjct: 190 AAKLHEEIATSDILVNATLVGMHPHENETPVKDTTVFRKDLIVTDVVYNPKKTRLLLDAE 249 Query: 244 QRGCRIHGGLGMFVYQGAYSLEYWSGRSAPV 274 G + GGLGM ++QGA + + ++G+ PV Sbjct: 250 AAGSKTIGGLGMLLWQGAEAYKLFTGKDMPV 280 >lin0493 [E] COG0169 Shikimate 5-dehydrogenase Length = 291 Score = 138 bits (347), Expect = 1e-32, Method: Compositional matrix adjust. Identities = 84/282 (29%), Positives = 137/282 (48%), Gaps = 18/282 (6%) Query: 14 LLGVMGDPIAHTKSPLMHTAALKALGIPGAYVPLHIAPGQLGEAIQAIRTLGFRGVNVTI 73 L+G++ PI H+ SP MH A LG+ Y+ + +L + +Q R + RG NV++ Sbjct: 15 LIGLIATPIRHSLSPTMHNEAFAKLGLDYVYLAFEVGDKELKDVVQGFRAMNLRGWNVSM 74 Query: 74 PHKVAVMEYIDRIDDSAXXXXXXXXXXXXXXXLTGYNTDGIGYVRSLKAEATPDLAGSXX 133 P+K + +Y+D++ +A LTG+ TDG GY+R+LK EA D+ G Sbjct: 75 PNKTNIHKYLDKLSPAAELVGAVNTVVNDDGVLTGHITDGTGYMRALK-EAGHDIIGKKM 133 Query: 134 XXXXXXXXXXXXXXXXXXEHPAAVVIANRTVEKSKQLAEAFQGKGTVNGIGN-------- 185 + + I NR K A A + +N N Sbjct: 134 TICGAGGAATAICIQAALDGVKEISIFNR---KDDFYANAEKTVEKINTKTNCKAQLFDM 190 Query: 186 ---DEIAAHIADMDIVINTTSVGMYPHIDAMPIDPA--LLREGMIVSDLIYNPLQTRLLT 240 +++ IA+ I N T VGM P + + P+ +LR +IVSD++Y P +TRLL Sbjct: 191 EDHEQLRKEIAESVIFTNATGVGMKP-FEGETLLPSADMLRPELIVSDVVYKPTKTRLLE 249 Query: 241 ESLQRGCRIHGGLGMFVYQGAYSLEYWSGRSAPVDIMRQTII 282 + ++GC+ GLGM ++QGA + E W+ + PVD +++ + Sbjct: 250 IAEEQGCQTLNGLGMMLWQGAKAFEIWTHKEMPVDYIKEILF 291 >STM1359 [E] COG0169 Shikimate 5-dehydrogenase Length = 288 Score = 137 bits (344), Expect = 3e-32, Method: Compositional matrix adjust. Identities = 83/277 (29%), Positives = 134/277 (48%), Gaps = 10/277 (3%) Query: 14 LLGVMGDPIAHTKSPLMHTAALKALGIPGAYVPLHIAPGQLGEAIQAIRTLGFRGVNVTI 73 L+G+M PI H+ SP M AL+ G+P Y+ + AI+ ++ L RG V++ Sbjct: 9 LIGLMAYPIRHSLSPEMQNKALEKAGLPYTYMAFEVDNTTFASAIEGLKALKMRGTGVSM 68 Query: 74 PHKVAVMEYIDRIDDSAXXXXXXXXXXXXXXXLTGYNTDGIGYVRSLKAEATPDLAGSXX 133 P+K EY+D + +A L GYNTDG G++R++K E+ D+ G Sbjct: 69 PNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIK-ESGFDMRGKTM 127 Query: 134 XXXXXXXXXXXXXXXXXXEHPAAVVIANRT-------VEKSKQLAEAFQGKGTVNGIGND 186 E + + NR V +K++ E TV + + Sbjct: 128 VLLGAGGAATAIGAQAAIEGIKEIKLFNRKDDFFEKAVAFAKRVNENTDCVVTVTDLADQ 187 Query: 187 E-IAAHIADMDIVINTTSVGMYPHIDAMPI-DPALLREGMIVSDLIYNPLQTRLLTESLQ 244 +A DI+ N T VGM P + I D +LLR ++V++ +YNP T+LL ++ Q Sbjct: 188 HAFTEALASADILTNGTKVGMKPLENESLIGDVSLLRPELLVTECVYNPHMTKLLQQAQQ 247 Query: 245 RGCRIHGGLGMFVYQGAYSLEYWSGRSAPVDIMRQTI 281 GC+ G GM ++QGA E W+G++ P+D ++Q + Sbjct: 248 AGCKTIDGYGMLLWQGAEQFELWTGKAFPLDYVKQVM 284 >ZydiB [E] COG0169 Shikimate 5-dehydrogenase Length = 288 Score = 132 bits (332), Expect = 7e-31, Method: Compositional matrix adjust. Identities = 80/277 (28%), Positives = 135/277 (48%), Gaps = 10/277 (3%) Query: 14 LLGVMGDPIAHTKSPLMHTAALKALGIPGAYVPLHIAPGQLGEAIQAIRTLGFRGVNVTI 73 L+G+M PI H+ SP M AL+ G+P Y+ + AI+ ++ L RG V++ Sbjct: 9 LIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALKMRGTGVSM 68 Query: 74 PHKVAVMEYIDRIDDSAXXXXXXXXXXXXXXXLTGYNTDGIGYVRSLKAEATPDLAGSXX 133 P+K EY+D + +A L GYNTDG G++R++K E+ D+ G Sbjct: 69 PNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIK-ESGFDIKGKTM 127 Query: 134 XXXXXXXXXXXXXXXXXXEHPAAVVIANRTVE-------KSKQLAEAFQGKGTVNGIGND 186 E + + NR E ++++ E TV + + Sbjct: 128 VLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQ 187 Query: 187 E-IAAHIADMDIVINTTSVGMYP-HIDAMPIDPALLREGMIVSDLIYNPLQTRLLTESLQ 244 + A +A DI+ N T VGM P +++ D +LL G++V++ +YNP T+LL ++ Q Sbjct: 188 QAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQ 247 Query: 245 RGCRIHGGLGMFVYQGAYSLEYWSGRSAPVDIMRQTI 281 GC+ G GM ++QGA W+G+ P++ ++Q + Sbjct: 248 AGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVM 284 >ydiB [E] COG0169 Shikimate 5-dehydrogenase Length = 288 Score = 132 bits (332), Expect = 7e-31, Method: Compositional matrix adjust. Identities = 80/277 (28%), Positives = 135/277 (48%), Gaps = 10/277 (3%) Query: 14 LLGVMGDPIAHTKSPLMHTAALKALGIPGAYVPLHIAPGQLGEAIQAIRTLGFRGVNVTI 73 L+G+M PI H+ SP M AL+ G+P Y+ + AI+ ++ L RG V++ Sbjct: 9 LIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALKMRGTGVSM 68 Query: 74 PHKVAVMEYIDRIDDSAXXXXXXXXXXXXXXXLTGYNTDGIGYVRSLKAEATPDLAGSXX 133 P+K EY+D + +A L GYNTDG G++R++K E+ D+ G Sbjct: 69 PNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIK-ESGFDIKGKTM 127 Query: 134 XXXXXXXXXXXXXXXXXXEHPAAVVIANRTVE-------KSKQLAEAFQGKGTVNGIGND 186 E + + NR E ++++ E TV + + Sbjct: 128 VLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQ 187 Query: 187 E-IAAHIADMDIVINTTSVGMYP-HIDAMPIDPALLREGMIVSDLIYNPLQTRLLTESLQ 244 + A +A DI+ N T VGM P +++ D +LL G++V++ +YNP T+LL ++ Q Sbjct: 188 QAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQ 247 Query: 245 RGCRIHGGLGMFVYQGAYSLEYWSGRSAPVDIMRQTI 281 GC+ G GM ++QGA W+G+ P++ ++Q + Sbjct: 248 AGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVM 284 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 0.319 0.137 0.401 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: 19,703,791 Number of extensions: 744226 Number of successful extensions: 2700 Number of sequences better than 1.0e-05: 309 Number of HSP's gapped: 2084 Number of HSP's successfully gapped: 315 Length of query: 289 Length of database: 38,378,431 Length adjustment: 105 Effective length of query: 184 Effective length of database: 26,268,361 Effective search space: 4833378424 Effective search space used: 4833378424 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: 115 (48.9 bits)