Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate Ga0059261_3091 Ga0059261_3091 Sugar (and other) transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__Korea:Ga0059261_3091 Length = 430 Score = 569 bits (1467), Expect = e-167 Identities = 276/424 (65%), Positives = 331/424 (78%), Gaps = 2/424 (0%) Query: 18 EKTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGF 77 E T R+KSI GS GN+VEWYDWY YAAF+LYFA FFPKGD T QLLNTAA+FAVGF Sbjct: 7 EAGTRQRLKSILGGSAGNLVEWYDWYAYAAFTLYFAPHFFPKGDQTTQLLNTAAVFAVGF 66 Query: 78 LMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLL 137 LMRPIGGWLMG+YAD+ GRKA L SV LMC GSL+IA++PGYETIG AP LLVFARL+ Sbjct: 67 LMRPIGGWLMGVYADKYGRKAGLTLSVSLMCAGSLLIAVTPGYETIGALAPALLVFARLM 126 Query: 138 QGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLY 197 QGLS+GGEYG SATYLSEMA ++RRGFFSSFQYVTLISGQLIALGVL++LQ +++ L Sbjct: 127 QGLSIGGEYGASATYLSEMAGRKRRGFFSSFQYVTLISGQLIALGVLLILQASMSEAALE 186 Query: 198 DWGWRIPFAIGALCAIVALYLRRGMEETESF--AKKEKSKESAMRTLLRHPKELMTVVGL 255 WGWRIPF IG A++ +LRRG+ ET+SF AK E K A+ L HP E + V+ L Sbjct: 187 SWGWRIPFFIGGALAVIVFWLRRGLSETQSFENAKAEGRKTGALALLREHPGEFLLVMAL 246 Query: 256 TMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRRPI 315 T GGTLAFY Y+ Y+QK+LVNT G ++ I+AA LF+FMC+QP+ G LSD++GR+P+ Sbjct: 247 TAGGTLAFYAYSIYLQKFLVNTSGFDRETASEINAAALFVFMCIQPLAGALSDRIGRKPL 306 Query: 316 LIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRA 375 +I FG+LG L T PI T L + + W AF L++ AL+IV+GYTSINAVVKAELFP IR Sbjct: 307 MIGFGVLGVLCTYPIFTALEQVSSAWAAFGLMLGALVIVTGYTSINAVVKAELFPAHIRT 366 Query: 376 LGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVSLLVYVTMKDTRKHSR 435 LGV LPYAL +IFGGTAEY+ALWFK GME G+YWYVT I +SL+VY+ M+DTR HS+ Sbjct: 367 LGVALPYALANAIFGGTAEYVALWFKDQGMERGFYWYVTGMIGISLIVYLRMRDTRTHSK 426 Query: 436 IETD 439 I D Sbjct: 427 ILED 430 Lambda K H 0.325 0.138 0.414 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: 699 Number of extensions: 39 Number of successful extensions: 2 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: 439 Length of database: 430 Length adjustment: 32 Effective length of query: 407 Effective length of database: 398 Effective search space: 161986 Effective search space used: 161986 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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