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= 0272.0004.p (336 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_00035411.1| COG1175: ABC-type sugar transport systems, pe... 255 1e-66 ref|ZP_00037453.1| COG1175: ABC-type sugar transport systems, pe... 249 9e-65 ref|NP_241984.1| lactose transport system (permease) [Bacillus h... 246 7e-64 ref|NP_357485.1| AGR_L_3390p [Agrobacterium tumefaciens] >gi|252... 243 6e-63 ref|NP_533613.1| ABC transporter, membrane spanning protein [sug... 241 2e-62 >ref|ZP_00035411.1| COG1175: ABC-type sugar transport systems, permease components [Enterococcus faecium] Length = 295 Score = 255 bits (651), Expect = 1e-66, Method: Compositional matrix adjust. Identities = 134/296 (45%), Positives = 193/296 (65%), Gaps = 4/296 (1%) Query: 34 VNRPKTKRSSYKNELYGILFALPAILGLLIFTLGPMIYSLYMSFTDYSGSNSPTFIGLDN 93 + + K KR ++ + G +FA P ILG L+ T+ PMI SLY SFTDY N ++IGLDN Sbjct: 1 MKKEKLKRFLDQDNVVGYVFASPFILGFLLITVIPMILSLYYSFTDYRLGNPVSWIGLDN 60 Query: 94 YTRMFSGEDQYFYKSLGVTLYFVVLSVPTGIIYSFLLAILLNRNIKGKAIFRTVFYLPSI 153 Y +M S D F S+ VT +V SVP +I+ L+A LL RNIKG FR+++Y+PS+ Sbjct: 61 YIKMLS--DARFLNSIRVTFLYVFASVPVKLIFGLLIAYLLTRNIKGTTFFRSLYYVPSL 118 Query: 154 VP-IIAISFIWLWLLNPDLGLANEMLRAIGLPGSQWIFGEKSVVPSLALMNLWTTGGTMI 212 + I+I+ +W L + + GL N L +G P W +K V+ L LM+ W G MI Sbjct: 119 IGGSISIALVWRELFSKN-GLVNIFLERLGAPALSWFSDQKLVMIPLVLMSAWQFGSAMI 177 Query: 213 IFLAGLQDIPRSLYEAIEIDGGSKLHKLRNITIPMMTPTIFFNLIMGIINGFQVFSQAYV 272 IF AG+++IP S YEA EIDG +K IT+P+++P I +NL+M I F F+QA++ Sbjct: 178 IFAAGIKEIPGSYYEAAEIDGANKWQTFYKITLPLLSPIILYNLVMQTIAAFMTFTQAFI 237 Query: 273 MTSGGPNNASLFYVFYLYREAFQFSRMGSASAIAWVLFIIIMLLTYMVFKSSKKWV 328 +T GGPN+A+ FY Y+Y +AF F+ MG ASAI+W++ +I+ +T+++FKSSKKWV Sbjct: 238 ITQGGPNDATNFYALYVYNQAFSFNSMGYASAISWIMLLIMGDVTFLIFKSSKKWV 293 >ref|ZP_00037453.1| COG1175: ABC-type sugar transport systems, permease components [Enterococcus faecium] Length = 274 Score = 249 bits (635), Expect = 9e-65, Method: Compositional matrix adjust. Identities = 123/274 (44%), Positives = 188/274 (68%), Gaps = 4/274 (1%) Query: 66 LGPMIYSLYMSFTDYSGSNSPTFIGLDNYTRMFSGEDQYFYKSLGVTLYFVVLSVPTGII 125 LGPM++S+ SFTDY+ ++ FIGL N+ RMF D F+KSL T+YFV+ +VP I Sbjct: 2 LGPMLFSVIGSFTDYNLTSKMNFIGLANFKRMFV-HDDLFWKSLYNTVYFVIFNVPLTTI 60 Query: 126 YSFLLAILLNRNIKGKAIFRTVFYLPSIVPIIAISFIWLWLLNPDLGLANEMLRAIGLPG 185 +S LA +LN+ IKG ++FRT FYLP+++ +A+ +W+ LL+P GL N L +PG Sbjct: 61 FSVFLATVLNQKIKGISVFRTAFYLPAVLSGVAVYILWMQLLSPSAGLINTFLGWFHIPG 120 Query: 186 SQWIFGEKSVVPSLALMNLWTTGGTMIIFLAGLQDIPRSLYEAIEIDGGSKLHKLRNITI 245 W+F + P+L LM +W++GG M+++LA LQ++PRSLYE+ EIDG K ++IT+ Sbjct: 121 PAWLFDPQWTKPALILMKIWSSGGAMLLYLATLQNVPRSLYESAEIDGAGVWGKFKSITL 180 Query: 246 PMMTPTIFFNLIMGIINGFQVFSQAYVMT---SGGPNNASLFYVFYLYREAFQFSRMGSA 302 P++TP IF+++I I FQ+F +AYVMT +GGP N+ LFY +++ +AF MG A Sbjct: 181 PLITPIIFYDVITSTIGSFQIFQEAYVMTKNGTGGPANSLLFYNLHMWNKAFVAFDMGYA 240 Query: 303 SAIAWVLFIIIMLLTYMVFKSSKKWVYYEGDEAR 336 A++ +LF+I+++LT++ K + KWVYY G + + Sbjct: 241 MAMSMILFLIVLVLTFVNLKLAPKWVYYSGGDGK 274 >ref|NP_241984.1| lactose transport system (permease) [Bacillus halodurans] pir||F83789 lactose transport system (permease) BH1118 [imported] - Bacillus halodurans (strain C-125) dbj|BAB04837.1| lactose transport system (permease) [Bacillus halodurans] Length = 318 Score = 246 bits (627), Expect = 7e-64, Method: Compositional matrix adjust. Identities = 130/303 (42%), Positives = 183/303 (60%), Gaps = 3/303 (0%) Query: 35 NRPKTKRSSYKNELYGILFALPAILGLLIFTLGPMIYSLYMSFTDYSGSNSPTFIGLDNY 94 ++ + +R +K G P +LG +GPMI SLY SFTDY +S ++GL NY Sbjct: 17 SKTRQERKKWKESFVGYAMISPWLLGFFGLVIGPMIASLYFSFTDYDMLSSANWVGLQNY 76 Query: 95 TRMFSGEDQYFYKSLGVTLYFVVLSVPTGIIYSFLLAILLNRNIKGKAIFRTVFYLPSIV 154 +F+ D F +SL VTL FV + P + ++ LA+L N KG +F T++Y+PSI+ Sbjct: 77 IHIFT-SDPRFVQSLKVTLIFVFVPTPLKLAFALFLAMLFNTGRKGSGLFSTIYYIPSII 135 Query: 155 P-IIAISFIWLWLLNPDLGLANEMLRAIGLPGSQWIFGEKSVVPSLALMNLWTTGGTMII 213 +A++ +W L G N L G G WI + L L+ +W G MII Sbjct: 136 GGSVAVAVVWKQLFGSR-GAVNSFLELFGFSGVNWIGSTDYALSILILLVVWQFGSPMII 194 Query: 214 FLAGLQDIPRSLYEAIEIDGGSKLHKLRNITIPMMTPTIFFNLIMGIINGFQVFSQAYVM 273 FLAGL+ IP+ LYEA +DG + K +IT+PM+TP IFFNLIM I GF F+QAY++ Sbjct: 195 FLAGLRQIPQELYEAASVDGANSFRKFFSITLPMLTPVIFFNLIMQTIGGFMTFTQAYLI 254 Query: 274 TSGGPNNASLFYVFYLYREAFQFSRMGSASAIAWVLFIIIMLLTYMVFKSSKKWVYYEGD 333 T GGP +++LFY YLY AF++ RMG ASA+AW+L +II +T++ FKSS WV+YE + Sbjct: 255 TGGGPLDSTLFYAVYLYEVAFEYLRMGYASAMAWILLVIIGGITFVFFKSSSYWVHYESE 314 Query: 334 EAR 336 R Sbjct: 315 GGR 317 >ref|NP_357485.1| AGR_L_3390p [Agrobacterium tumefaciens] pir||D98343 lactose transport system (permease) (AP001511) [imported] - Agrobacterium tumefaciens (strain C58, Cereon) gb|AAK90270.1| AGR_L_3390p [Agrobacterium tumefaciens str. C58 (Cereon)] Length = 309 Score = 243 bits (619), Expect = 6e-63, Method: Compositional matrix adjust. Identities = 133/325 (40%), Positives = 200/325 (61%), Gaps = 22/325 (6%) Query: 11 GRAAAGSSPKKGSMCMEPVPSLSVNRPKTKRSSYKNELYGILFALPAILGLLIFTLGPMI 70 G + + PK+G M R + ++ LF LP ++G TLGP + Sbjct: 2 GESRGAALPKRGGM----------------RRMFDRNIHAYLFLLPWLIGFFGLTLGPAL 45 Query: 71 YSLYMSFTDYSGSNSPTFIGLDNYTRMFSGEDQYFYKSLGVTLYFVVLSVPTGIIYSFLL 130 SLY+SFT+Y SP ++G NY R+ + D F ++ VT +V+LSVP +I++ L+ Sbjct: 46 ASLYLSFTNYDLLQSPDWVGAANYVRI-ATADPKFAAAMQVTFTYVLLSVPLKLIFALLV 104 Query: 131 AILLNRNIKGKAIFRTVFYLPSIV-PIIAISFIWLWLLNPDLGLANEML-RAIGLPGSQW 188 A+ NR I+G ++R +FYLPS++ +AI+ +W L D GL N +L +A G G W Sbjct: 105 ALAFNRGIRGLTLYRAIFYLPSLLGSSVAIAVLWRQLFASD-GLVNMILWQAFGYEGPSW 163 Query: 189 IFGEKSVVPSLALMNLWTTGGTMIIFLAGLQDIPRSLYEAIEIDGGSKLHKLRNITIPMM 248 I + +L ++++W G MIIFLAGL+ IP+ +YEA EIDG SK+ + IT+P++ Sbjct: 164 ISNPDYSIYTLVILSVWQFGSPMIIFLAGLRQIPQDMYEAAEIDGASKVRQFFRITLPLL 223 Query: 249 TPTIFFNLIMGIINGFQVFSQAYVMT--SGGPNNASLFYVFYLYREAFQFSRMGSASAIA 306 TP IFFN ++ I+ F+ F+ A++++ +GGP N++LFY YLY+EAF F RMG ASA+A Sbjct: 224 TPVIFFNAVIQTIDAFKAFTPAFIISEGTGGPINSTLFYTLYLYQEAFGFFRMGYASALA 283 Query: 307 WVLFIIIMLLTYMVFKSSKKWVYYE 331 W+L III L T F S+K WV+Y+ Sbjct: 284 WILVIIISLFTAFSFLSAKYWVHYD 308 >ref|NP_533613.1| ABC transporter, membrane spanning protein [sugar] [Agrobacterium tumefaciens str. C58 (U. Washington)] pir||AC2939 hypothetical protein Atu3113 [imported] - Agrobacterium tumefaciens (strain C58, Dupont) gb|AAL43929.1| ABC transporter, membrane spanning protein [sugar] [Agrobacterium tumefaciens str. C58 (U. Washington)] Length = 295 Score = 241 bits (614), Expect = 2e-62, Method: Compositional matrix adjust. Identities = 128/295 (43%), Positives = 192/295 (65%), Gaps = 6/295 (2%) Query: 41 RSSYKNELYGILFALPAILGLLIFTLGPMIYSLYMSFTDYSGSNSPTFIGLDNYTRMFSG 100 R + ++ LF LP ++G TLGP + SLY+SFT+Y SP ++G NY R+ + Sbjct: 2 RRMFDRNIHAYLFLLPWLIGFFGLTLGPALASLYLSFTNYDLLQSPDWVGAANYVRI-AT 60 Query: 101 EDQYFYKSLGVTLYFVVLSVPTGIIYSFLLAILLNRNIKGKAIFRTVFYLPSIV-PIIAI 159 D F ++ VT +V+LSVP +I++ L+A+ NR I+G ++R +FYLPS++ +AI Sbjct: 61 ADPKFAAAMQVTFTYVLLSVPLKLIFALLVALAFNRGIRGLTLYRAIFYLPSLLGSSVAI 120 Query: 160 SFIWLWLLNPDLGLANEML-RAIGLPGSQWIFGEKSVVPSLALMNLWTTGGTMIIFLAGL 218 + +W L D GL N +L +A G G WI + +L ++++W G MIIFLAGL Sbjct: 121 AVLWRQLFASD-GLVNMILWQAFGYEGPSWISNPDYSIYTLVILSVWQFGSPMIIFLAGL 179 Query: 219 QDIPRSLYEAIEIDGGSKLHKLRNITIPMMTPTIFFNLIMGIINGFQVFSQAYVMT--SG 276 + IP+ +YEA EIDG SK+ + IT+P++TP IFFN ++ I+ F+ F+ A++++ +G Sbjct: 180 RQIPQDMYEAAEIDGASKVRQFFRITLPLLTPVIFFNAVIQTIDAFKAFTPAFIISEGTG 239 Query: 277 GPNNASLFYVFYLYREAFQFSRMGSASAIAWVLFIIIMLLTYMVFKSSKKWVYYE 331 GP N++LFY YLY+EAF F RMG ASA+AW+L III L T F S+K WV+Y+ Sbjct: 240 GPINSTLFYTLYLYQEAFGFFRMGYASALAWILVIIISLFTAFSFLSAKYWVHYD 294 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 0.325 0.141 0.429 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: 531,306,735 Number of extensions: 23176747 Number of successful extensions: 82917 Number of sequences better than 1.0e-05: 1390 Number of HSP's gapped: 80871 Number of HSP's successfully gapped: 1396 Length of query: 336 Length of database: 757,237,578 Length adjustment: 126 Effective length of query: 210 Effective length of database: 415,135,104 Effective search space: 87178371840 Effective search space used: 87178371840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 126 (53.1 bits)