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= 0490.0059.p (278 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BH3412 [E] COG0253 Diaminopimelate epimerase 240 2e-63 alr2048 [E] COG0253 Diaminopimelate epimerase 239 3e-63 alr4841 [E] COG0253 Diaminopimelate epimerase 177 2e-44 STM1522 [G] COG2814 Arabinose efflux permease 58 2e-08 >BH3412 [E] COG0253 Diaminopimelate epimerase Length = 286 Score = 240 bits (613), Expect = 2e-63, Method: Compositional matrix adjust. Identities = 131/285 (45%), Positives = 179/285 (62%), Gaps = 16/285 (5%) Query: 1 MEFTKMHGLGNDFIIV------FGEQELPGNASELAVTLCNRFFGIGADGLVYILPSERG 54 M+FTKMHGLGN +I V E+ELP LAV + ++ GIG+DG++ I PS+R Sbjct: 1 MKFTKMHGLGNSYIYVDCFKELLKEEELPA----LAVAVADKNKGIGSDGMILICPSDRA 56 Query: 55 DYMMRIMNSDGTEAEQCGNAIRCVSKYVYEHGLVSSEQIVIETIGAGEQKVSLQVKD-GV 113 MR+ N+DG+EA+ CGN +RCV+K+ +EHG V +ET+G G K ++ D G+ Sbjct: 57 PVKMRVFNNDGSEAKNCGNGLRCVAKFAFEHGYVKETSFDVETLG-GLVKATVHPNDNGL 115 Query: 114 VETVTVDMGEPVLSGTQIP-VAIDAEPVLDQPIEADGRAFRFTAVSMGNPHCVIYVDDAV 172 V+TVTV+MGEP L QIP + +A V+ +P + +R TAVSMGNPH ++++D Sbjct: 116 VDTVTVNMGEPRLGRAQIPMLGEEAAEVVAEPFTIGEKEYRLTAVSMGNPHAIMFIDTIE 175 Query: 173 SFDLAAWGPKLEVHPLFPRKVNVEFATVLDRSHVDMRVWERGAGPTLACGTGACATLVSS 232 + GP LE H FP VNVEF V+ + + RVWERG+G T ACGTGACA +V+S Sbjct: 176 DAPVEQVGPLLEKHEAFPDWVNVEFVQVVSPTEIHFRVWERGSGITQACGTGACAAVVAS 235 Query: 233 VLNGLTDR--SATISLKGGDLFIEWNEADNHVYMTGPAQVVYTGS 275 VLNG T + T+ L GGDL I W E + V MTG A+ + G+ Sbjct: 236 VLNGFTQKGQEVTVHLLGGDLTISWLE-NGDVLMTGAAETICEGT 279 >alr2048 [E] COG0253 Diaminopimelate epimerase Length = 359 Score = 239 bits (611), Expect = 3e-63, Method: Compositional matrix adjust. Identities = 8/248 (3%), Positives = 27/248 (10%), Gaps = 8/248 (3%) Query: 33 LCNRFFGIGADGLVYILPSERG-DYMMRIMNSDGTEAEQCGNAIRCVSKYVYE-HGLVSS 90 A E M + R + + Sbjct: 3 AATVVINRRALRHNLQRLRELAPASKMVAVVKANAYGHGLLETARTLPDADAFGVARLEE 62 Query: 91 EQIVIETIGAGEQKVSLQVKDGVVETVTVDMGEPVLSGTQIPVAIDAE--PVLDQPIEAD 148 + + + + T + Sbjct: 63 ALRLRAGGITKPVLLLE-GFFDARD---LPTISAQHFHTAVHNEEQLAALEEASLDEPVT 118 Query: 149 GRAFRFTAVSMGNPHCVIYVDDAVSFDLAAWGPKLEVHPLFPRKVNVEFATVLDRSHVDM 208 T + + + + ++ Sbjct: 119 VWMKLDTGMHRLGVRPEQAEAFYHRLTQCKNVRQPVNIVSHFARADEPKCGATEKQLAIF 178 Query: 209 RVWERGAGPTLACGTGACATLVSSVLNGLTDRSATISLKGGDLFIEWNEADNHVYMTGPA 268 + G + L + + Sbjct: 179 NTFCEGKPGQRSIAASGGILLWPQSHFDWVRPGIILYGVSPLEDRSTGADFGCQPVMSLT 238 Query: 269 QVVYTGSV 276 + Sbjct: 239 SSLIAVRE 246 >alr4841 [E] COG0253 Diaminopimelate epimerase Length = 359 Score = 177 bits (449), Expect = 2e-44, Method: Compositional matrix adjust. Identities = 17/267 (6%), Positives = 50/267 (18%), Gaps = 8/267 (2%) Query: 1 MEFTKMHGLGNDFIIVFGEQ-ELPGNASELAVTLCNRFFGIGADGLVY-ILPSERGDYMM 58 M+ + EL + +AV + +G G + ++ Sbjct: 1 MQAATVVINRRALRHNLQRLRELAPASKMVAV-VKANAYGHGLLETARTLPDADAFGVAR 59 Query: 59 RIMNSDGTEAEQCGNAIRCVSKYVYEHGLVSSEQIVIETIGAGEQKVSLQVKDGVVETVT 118 + + S Q + + L + Sbjct: 60 LEEALRLRAGGITKPVLLLEGFFDARDLPTISAQHFHTAVHN---EEQLAALEEA-SLDE 115 Query: 119 VDMGEPVLSGTQIPVAIDAEPVLDQPIEADGRAFRFTAVSMGNPHCVIYVDDAVSFDLAA 178 L + + E V++ + + + Sbjct: 116 PVTVWMKLDTGMHRLGVRPEQAEAFYHRLTQCKNVRQPVNIVSHFARADEPKCGATEKQL 175 Query: 179 WGPKLEVHPLFPRKVNVEFATVLDRSHVDMRVWERGAGPTLACGTGACATLVSSVLNGLT 238 ++ +L G +T + Sbjct: 176 AIFNTFCEGKPGQRSIAASGGILLWPQSHFDWVRPGIILYGVSPLEDRSTGADFGCQPVM 235 Query: 239 DRSATISLKGGDLFIEWNEADNHVYMT 265 ++++ E +++ Sbjct: 236 SLTSSLIAVREHKAGEPVG-YGGTWVS 261 >STM1522 [G] COG2814 Arabinose efflux permease Length = 396 Score = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust. Identities = 12/229 (5%), Positives = 32/229 (13%), Gaps = 36/229 (15%) Query: 43 DGLVYILPSERGDYMMRIMNSDGTEAEQCGNAIRCVSKYVYEHGLVSSEQIVIETIGAGE 102 + + + ++ ++ + L+ ++ Sbjct: 37 SDIAESFHMQ-TAQVGIMLTIYAWVVAVMSLPFMLLTSQMERRKLLIYLFVLFIA-SHVL 94 Query: 103 QKVSLQVKDGVVETVTVDMGEPVLSGTQIPVAIDAEPVLDQPIEADGRAFRFTAVSMGNP 162 ++ TV V + P Sbjct: 95 SFLAWN------FTVLVIS--RIGIAF-------------AHAIFWSITASLAIR--LAP 131 Query: 163 HCVIYVDDAVSFDLAAWGPKLEVHPLFPRKVNVEFATVL-DRSHVDMRVWERGA-GPTLA 220 ++ A L P V L Sbjct: 132 AGKRAQALSLIATGTALAMVLG----LPIGRVVGQYFGWRTTFFA--IGMGALITLLCLI 185 Query: 221 CGTGACATLVSSVLNGLTDRSATISLKGGDLFIEWNEADNHVYMTGPAQ 269 + S + + T + Sbjct: 186 KLLPKLPSEH-SGSLKSLPLLFRRPALMSLYVLT--VVVVTAHYTAYSY 231 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 0.410 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: 20,846,114 Number of extensions: 874761 Number of successful extensions: 2814 Number of sequences better than 1.0e-05: 4 Number of HSP's gapped: 2803 Number of HSP's successfully gapped: 4 Length of query: 278 Length of database: 38,378,431 Length adjustment: 105 Effective length of query: 173 Effective length of database: 26,268,361 Effective search space: 4544426453 Effective search space used: 4544426453 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)