Align Alpha-ketoglutarate permease (characterized)
to candidate H281DRAFT_00442 H281DRAFT_00442 MFS transporter, MHS family, proline/betaine transporter
Query= SwissProt::P0AEX3 (432 letters) >FitnessBrowser__Burk376:H281DRAFT_00442 Length = 489 Score = 227 bits (579), Expect = 5e-64 Identities = 145/418 (34%), Positives = 232/418 (55%), Gaps = 23/418 (5%) Query: 25 VGASS-GNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTAGVFAAGFLMRPIGGWLF 83 VGA + GN +EWFDF VYS+ ++ +FFPS + + QL+ T G FAA FL+RP+GG +F Sbjct: 35 VGAMALGNAMEWFDFGVYSYIAVTLGKVFFPSSSPSAQLIATFGTFAAAFLVRPVGGMVF 94 Query: 84 GRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPALLLLARLFQGLSVGGEYG 143 G + D+ GR++ + +++ MM G+ I +P Y +IG APALLL+ARL QG S GGEYG Sbjct: 95 GPLGDRIGRQRVLAMTMIMMAIGTFAIGLIPSYGSIGILAPALLLVARLVQGFSTGGEYG 154 Query: 144 TSATYMSEVAVEGRKGFYASF-QYVTLIGGQLLALLVVVVLQHTMEDAALREWGWRIPFA 202 +AT+++E + + R+GF SF ++ TLIG +L V VL T+ + AL WGWR+PF Sbjct: 155 GAATFIAEFSTDKRRGFMGSFLEFGTLIG-YVLGAGTVAVLTATLSNDALLSWGWRVPFL 213 Query: 203 LGAVLAVVALWLRRQLDET----SQQETRALKEAGSLKGLWRNR-----RAFIMVLGFTA 253 + L +V L++R +L+ET Q E R ++ K RN + ++ +G Sbjct: 214 IAGPLGLVGLYIRMKLEETPAFKKQAEQREAEDKAVPKQSLRNLLMQQWKPLLLCVGLVL 273 Query: 254 AGSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQPL---IGALSDKIGRRT 310 ++ Y +Y+ YL +A +H N + G+ L V +L+ P+ G LSD IGR+ Sbjct: 274 IFNVTDYMALSYLPSYL--SATLHFNESHGLF-IVLLVMVLMMPMTLAAGRLSDTIGRKP 330 Query: 311 SML--CFGSLAAIFTVPILSALQNVSSPYAAFGLVMCALLIVSFYTSISGILKAEMFPAQ 368 ML C G A ++P L L + + FG +M +++S +T + +FP + Sbjct: 331 VMLFGCVGLFA--LSIPAL-LLIRMGTLVPVFGGLMILGVLLSCFTGVMPSALPALFPTK 387 Query: 369 VRALGVGLSYAVANAIFGGSAEYVALSLKSIGMETAFFWYVTLMAVVAFLVSLMLHRK 426 +R + + + ++ ++FGG+ V L Y + A + +VS+M R+ Sbjct: 388 IRYGALAIGFNISVSLFGGTTPLVTAWLVDRTGNLMMPAYYLMGASLIGIVSVMALRE 445 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: 546 Number of extensions: 26 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 432 Length of database: 489 Length adjustment: 33 Effective length of query: 399 Effective length of database: 456 Effective search space: 181944 Effective search space used: 181944 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: 51 (24.3 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