Align Alpha-ketoglutarate permease (characterized)
to candidate WP_051790058.1 EZMO1_RS17450 MFS transporter
Query= SwissProt::P0AEX3 (432 letters) >NCBI__GCF_001583435.1:WP_051790058.1 Length = 434 Score = 201 bits (511), Expect = 4e-56 Identities = 126/398 (31%), Positives = 203/398 (51%), Gaps = 10/398 (2%) Query: 28 SSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTAGVFAAGFLMRPIGGWLFGRIA 87 S G ++E +DF VY+ + Y A FFPS + T LL T FA G+L RP+GG+ FG + Sbjct: 24 SLGGMLEMYDFMVYAMMASYIAESFFPSSDPMTSLLGTFATFAVGYLSRPLGGFFFGHLG 83 Query: 88 DKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPALLLLARLFQGLSVGGEYGTSAT 147 D++GRK + L++ +M + +I C+P Y++IG APALL+L RLFQG S+GGE + T Sbjct: 84 DRYGRKSTFTLTISIMALTTALIGCMPTYDSIGILAPALLVLLRLFQGFSLGGELPGAMT 143 Query: 148 YMSEVAVEGRKGFYASFQYVTLIGGQLLALLVVVVLQHTMEDAALREWGWRIPFALGAVL 207 Y+SE GR G +++ G LA V +L + A+ WGWR+PF +G +L Sbjct: 144 YVSE-TTPGRSGLVIGILFMSFTLGFSLATFVHGLLTLILSPEAMSGWGWRVPFWVGGLL 202 Query: 208 AVVALWLRRQLDET----SQQETRALKEAGSLKGLWRNRRAFIMVLGFTAAGSLCFYTFT 263 ++ ++R + DE+ + R + L+ + ++RR F G A Sbjct: 203 GGLSYYIRLRFDESGLFMALNLVRQRQMIPMLELVRKHRRGFFCGFGIAAVCGSAVTLLG 262 Query: 264 TYMQKYLVNTAGMHANVASGIMTAALFVFMLIQPLIGALSDKIGRRTSMLCFGSLAAIFT 323 YM YL G + + A +F + L+G ++D+ + + C L A Sbjct: 263 AYMPGYLTTLHGFSRAEVAWHSSLAYIMFAPLCLLMGLVTDRCSHKKLLFCSIVLIAGVC 322 Query: 324 VPILSALQNVSSPYAAFG-LVMCALLIVSFYTSISGILKAEMFPAQVRALGVGLSYAVAN 382 +P Q VSS A ++M A ++ SF + +FP++VR GV SY + Sbjct: 323 LPY---YQYVSSHEAELSRIMMVAAILSSFVIGTLPPMLVRLFPSEVRYTGVATSYNLGM 379 Query: 383 AIFGGSAEY-VALSLKSIGMETAFFWYVTLMAVVAFLV 419 A+FGG A + +K+ G+ Y+ ++++V L+ Sbjct: 380 ALFGGLAPVSITPLIKAYGLALGPALYLIIISLVTLLI 417 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: 454 Number of extensions: 33 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 432 Length of database: 434 Length adjustment: 32 Effective length of query: 400 Effective length of database: 402 Effective search space: 160800 Effective search space used: 160800 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 24 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