Align Alpha-ketoglutarate permease (characterized)
to candidate Ga0059261_2720 Ga0059261_2720 Arabinose efflux permease
Query= SwissProt::P0AEX3 (432 letters) >FitnessBrowser__Korea:Ga0059261_2720 Length = 558 Score = 211 bits (538), Expect = 4e-59 Identities = 125/355 (35%), Positives = 194/355 (54%), Gaps = 14/355 (3%) Query: 6 VTADSKLTSSDTRRRIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQT 65 +TA + + R+ I+ +S G + EW+DFY+Y + + FF N TT + Sbjct: 1 MTAQPAVAGRNERK---VIIASSLGTVFEWYDFYLYGLLATVISAKFFSGVNETTAFILA 57 Query: 66 AGVFAAGFLMRPIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPA 125 G FAAGF +RP G +FGR+ D GRK + L+++ +M + + LP Y +IG AP Sbjct: 58 LGAFAAGFAVRPFGALVFGRLGDVVGRKYTFLVTMGLMGLSTFAVGILPSYASIGVAAPI 117 Query: 126 LLLLARLFQGLSVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVVVVLQH 185 +L+ RL QGL++GGEYG +ATY++E A EG++G + S+ T G ALLVV+ ++ Sbjct: 118 ILVALRLVQGLALGGEYGGAATYVAEHAPEGKRGLFTSWIQTTATLGLFAALLVVIGIRT 177 Query: 186 TMEDAALREWGWRIPFALGAVLAVVALWLRRQLDETSQQETRALKEAGSLK--------G 237 + +AA +WGWR+PF + +L V+LW+R QL E+ + +KE G+ G Sbjct: 178 AIGEAAFADWGWRLPFLVSILLLAVSLWIRLQLAES--PVFQKMKEEGTTSKAPFTEAFG 235 Query: 238 LWRN-RRAFIMVLGFTAAGSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQ 296 WRN R I++LG A ++ +YT Y +L T + A+ ++ AL + Sbjct: 236 QWRNLRTVLIVLLGAVAGQAVVWYTGQFYALFFLEKTLKVDGATANILIAIALALATPFF 295 Query: 297 PLIGALSDKIGRRTSMLCFGSLAAIFTVPILSALQNVSSPYAAFGLVMCALLIVS 351 + GALSD+IGR+ +L +LAAI P AL ++P A + I+S Sbjct: 296 VIFGALSDRIGRKKIILTGCALAAISYFPTFHALTQAANPALAAAQRQAPVTIMS 350 Score = 42.0 bits (97), Expect = 5e-08 Identities = 23/91 (25%), Positives = 46/91 (50%), Gaps = 2/91 (2%) Query: 333 VSSPYAAFGLVMCALLIVSFYTSISGILKAEMFPAQVRALGVGLSYAVANAIFGGSAEYV 392 ++ P L LL+ + Y I+ +L E+FP ++R + L Y + N FGG + Sbjct: 454 MNKPLIVALLFWLVLLVTAVYGPIAALL-VEIFPTRIRYTAMSLPYHIGNGWFGGFLPTI 512 Query: 393 ALSLKSIGMETAF-FWYVTLMAVVAFLVSLM 422 A ++ + + + WY ++AV+ ++ L+ Sbjct: 513 AFAMVAATGDIYYGLWYPIIVAVLTLILGLL 543 Lambda K H 0.328 0.138 0.419 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 532 Number of extensions: 32 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 432 Length of database: 558 Length adjustment: 34 Effective length of query: 398 Effective length of database: 524 Effective search space: 208552 Effective search space used: 208552 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory