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= 0128.0025.p (379 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BS_ykfB [MR] COG4948 L-alanine-DL-glutamate epimerase and relate... 197 3e-50 lin0197 [MR] COG4948 L-alanine-DL-glutamate epimerase and relate... 136 5e-32 Cgl2350 [MR] COG4948 L-alanine-DL-glutamate epimerase and relate... 135 2e-31 STM0006 [E] COG1115 Na+/alanine symporter 127 4e-29 VNG1837G [MR] COG4948 L-alanine-DL-glutamate epimerase and relat... 125 8e-29 >BS_ykfB [MR] COG4948 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily Length = 252 Score = 197 bits (500), Expect = 3e-50, Method: Compositional matrix adjust. Identities = 0/364 (0%), Positives = 0/364 (0%), Gaps = 13/364 (3%) Query: 1 MLISQIDVFRYDLPLSPPFTHSSSGTVTHLKEIYLRITADSGVCGWSEVRGNCEYVTGDT 60 M ++ + L+ + G + + + Sbjct: 1 MSDWNPSLYLHFSAERSRP-AVELLARVPLENVEYVADLGCGPGNSTALLQQR-WPAARI 58 Query: 61 PERVAAVLTHTLGPALLGKPVMNRNRINAGLDRLINGNSAARAAVDIALLDLTGKLLKVS 120 ++ + L I A A++ VS Sbjct: 59 TGIDSSPAMIAEARSALPDCQFVEADIRNWQPVQALDLIFANASLQWLPDHYELFPHLVS 118 Query: 121 AAELLGGRMRDSIPSDATIAFGTPDEAEEEAARYLQDGFRTIKLRVGPDR-AGDLERVRR 179 G + +P + Y G + + Sbjct: 119 LLNPQGV-LAVQMPDNWLEPTHVLMREVAWEQNYPDRGREPLAGVHAYYDILSEAGCEVD 177 Query: 180 ARAVIESFGLGGEVLLCVDANQGWTPKQAVLRLREFE--ALGVEWVEQPVPADDFSGLKQ 237 + A W + + + ++++ + Q Sbjct: 178 IWRTT-----YYHQMPSHQAIIDWVTATGLRPWLQDLTESEQQLFLKRYHQMLEEQYPLQ 232 Query: 238 VRQQTRAXXXXVADESCRTCADVARIAAEGAADIVHLKLVKAGSVVNLQRMMAVAESFGI 297 Q Sbjct: 233 ENGQILL-- 290 Query: 298 PYMLGQMDEGRLATAALLQIASASRASHFEVWGFQRVRPEDDPAGVLTVLNGAVSVPVGF 357 Sbjct: 291 350 Query: 358 GLGV 361 Sbjct: 351 354 >lin0197 [MR] COG4948 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily Length = 252 Score = 136 bits (343), Expect = 5e-32, Method: Compositional matrix adjust. Identities = 0/308 (0%), Positives = 0/308 (0%), Gaps = 11/308 (3%) Query: 1 MLISQIDVFRYDLPLSPPFTHSSSGTVTHLKEIYLRITADSGVCGWSEVRGNCEYVTGDT 60 M ++ + L+ + G + + + Sbjct: 1 MSDWNPSLYLHFSAERSRPA-VELLARVPLENVEYVADLGCGPGNSTAL-LQQRWPAARI 58 Query: 61 PERVAAVLTHTLGPALLGKPVMNRNRINAGLDRLINGNSAARAAVDIALLDLTGKLLKVS 120 ++ + L I A A++ VS Sbjct: 59 TGIDSSPAMIAEARSALPDCQFVEADIRNWQPVQALDLIFANASLQWLPDHYELFPHLVS 118 Query: 121 AAELLGGRMRDSIPSDATIAFGTPDEAEEEAARYLQDGFRTIKLRVGPDRAG-DLERVRR 179 G +P + Y G + + Sbjct: 119 LLNPQGVLAV-QMPDNWLEPTHVLMREVAWEQNYPDRGREPLAGVHAYYDILSEAGCEVD 177 Query: 180 ARAVIESFGLGGEVLLCVDANQGWTPKQAVLRLREFEALGVEWVEQPVPADDFSGLKQVR 239 + A W + + + + ++ Sbjct: 178 IWR-----TTYYHQMPSHQAIIDWVTATGLRPWLQDLTESEQQLFLKRYHQMLEEQYPLQ 232 Query: 240 QQTRAXXXXVADESCRTCADVARIAAEGAADIVHLKLVKAGSVVNLQRMMAVAESFGIPY 299 + + Sbjct: 233 ENGQ-- 290 Query: 300 MLGQMDEG 307 Sbjct: 291 298 >Cgl2350 [MR] COG4948 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily Length = 252 Score = 135 bits (339), Expect = 2e-31, Method: Compositional matrix adjust. Identities = 0/377 (0%), Positives = 0/377 (0%), Gaps = 20/377 (5%) Query: 1 MLISQIDVFRYDLPLSPPFTHSSSGTVTHLKEIYLRITADSGVCGWSE-VRGNCEYVTGD 59 ++ + + R A S Sbjct: 18 RPAVELLARVPLENVEYVADLGCG-PGNSTALLQQRWPAARITGIDSSPAMIAEARSALP 76 Query: 60 TPERVAAVLTHTLGPALLGKPVMNRNRINAGLDRLINGNSAARAAVDIALLDLTGKLLKV 119 + V A + + L N + + + + L Sbjct: 77 DCQFVEADIRNWQPVQALDLIFANASLQWLPDHYELFPHLVSLLNPQGVLAVQMPDNWLE 136 Query: 120 SAAELLGGRMRDSIPSDATIAFGT--PDEAEEEAARYLQD-GFRTIKLRVGP-DRAGDLE 175 L+ + A + + Sbjct: 137 PTHVLMREVAWEQN--YPDRGREPLAGVHAYYDILSEAGCEVDIWRTTYYHQMPSHQAII 194 Query: 176 RVRR-ARAVIESFGLGGEVLLCVDANQGWTPKQAVLRLREFEALGVEWVEQPVPADDFSG 234 L Q + + + ++ + P Sbjct: 195 DWVTATGLR------PWLQDLTESEQQLFLKRYHQMLEEQYPLQENGQILLAFPRLFIVA 248 Query: 235 LKQVRQQTRAXXXXVADESCRTCADVARIAAEGAADIVHLKLVKAGSVVNLQRMMAVAES 294 Sbjct: 249 -- 306 Query: 295 FGIPYMLGQMDEGRLATAALLQIASASRASHF--EVWGFQRVRPEDDPAGVLTVLNGAVS 352 Sbjct: 307 - 365 Query: 353 VPVGFGLGVTVDESRLT 369 Sbjct: 366 382 >STM0006 [E] COG1115 Na+/alanine symporter Length = 476 Score = 127 bits (318), Expect = 4e-29, Method: Compositional matrix adjust. Identities = 20/321 (6%), Positives = 51/321 (15%), Gaps = 22/321 (6%) Query: 10 RYDLPLSPPFTHSSSGTVTHLKEIYLRITADSGVCGWSEVRGNCEYVTGDTPERVAAVLT 69 + +G + +++ + + + G L Sbjct: 13 WGSV--MIYL-LLGAGCWFTWRTGFIQFRYIRQFSRSLKGSLSPQ-PGG---LTSFQALC 65 Query: 70 --HTLGPALLGKPVMNRNRINAGLDRLINGNSAARAAVDIALLDLTGKLLKVSAAELLGG 127 + G + + + G Sbjct: 66 TSLAARIGSGNLAGVALAIAAGGPGAVF-WMWVSAIIGMATSFAECSLAQLYKERDPTGQ 124 Query: 128 RMRDSIPSDATIAFGTPDEAEEEAARYLQDGFRTIKLRVGPDRAGDLERVRRARAVIESF 187 R G A L + L +I Sbjct: 125 F-RGGPAWYMARGLGMRWMGVVFALFLLVAYGLIFNSVQANAVSRALHFAFNIPPLIS-- 181 Query: 188 GLGGEVLLCVDANQGWTPKQAVLRLREFEALGVEW--VEQPVPADDFSGLKQVRQQTRAX 245 G + A + + + ++Q+ Sbjct: 182 --GIALA--FCALLIIIRGIKGVARLMQWLIPLIALLWVAGSVFICLWHIEQMP--GVIA 235 Query: 246 XXXVADESCRTCADVARIAAEGAADIVHLKLVKAGSVVNLQRMMAVAESFGIPYMLGQMD 305 + + A A A + A + Y + Sbjct: 236 SIVKSAFGWQEAAAGAAGYTLTQAITSGFQRGMFS-NEAGMGSTPNAAAAATSYPPHPVA 294 Query: 306 EGRLATAALLQIASASRASHF 326 +G + + + Sbjct: 295 QGIVQMIGVFSDTIIICTASA 315 >VNG1837G [MR] COG4948 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily Length = 252 Score = 125 bits (315), Expect = 8e-29, Method: Compositional matrix adjust. Identities = 0/302 (0%), Positives = 0/302 (0%), Gaps = 15/302 (4%) Query: 5 QIDVFRYDLPLSPPFTHSSSGTVTHLKEIYLRITADSGVCGWSEVRGNCEYVTGDTPERV 64 L S + + + + CG + R+ Sbjct: 2 SDWNPSLYLHFSAERS-RPAVELLARVPLENVEYVADLGCGPGNSTALLQQ--RWPAARI 58 Query: 65 AAVLTHTLGPALLGKPVMNRNRINAGLDRLINGNSAARAAVDIALLDLTGKLLKVSAAEL 124 + + A + + + A + + + +L L Sbjct: 59 TGIDSSPAMIAEARSALPDCQFVEADIRNWQPVQALDLIFANASLQWLPDHYELFPHLVS 118 Query: 125 LGGRMRDSIPSDATIAFGTPDEAEEEAARYLQDGFRTIKLRVGPDRAGDLERVRRARAVI 184 L E A R + G + + A Sbjct: 119 LLNPQGVLAVQMPDNWLEPTHVLMREVAWEQNYPDRGREPLAGVHA--YYDILSEAGCE- 175 Query: 185 ESFGLGGEVLLCVDANQGWTPKQAVLRLREFEALGVEWVEQPVPADDFSGLKQVRQQTRA 244 ++ + + Q+ + Sbjct: 176 -----VDIWRTTYYHQMPSHQAIIDWVTATGLRPWLQDLTESEQQLFLKRYHQMLE--EQ 228 Query: 245 XXXXVADESCRTCADVARIAAEGAADIVHLKLVKAGSVVNLQRMMAVAESFGIPYMLGQM 304 + + +A Sbjct: 229 YPLQENGQILLAFPRLFIVARR-- 286 Query: 305 DE 306 Sbjct: 287 288 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 0.320 0.135 0.394 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: 27,402,965 Number of extensions: 1119360 Number of successful extensions: 2238 Number of sequences better than 1.0e-05: 61 Number of HSP's gapped: 2151 Number of HSP's successfully gapped: 61 Length of query: 379 Length of database: 38,378,431 Length adjustment: 108 Effective length of query: 271 Effective length of database: 25,922,359 Effective search space: 7024959289 Effective search space used: 7024959289 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: 117 (49.7 bits)