Align Alpha-ketoglutarate permease (characterized)
to candidate CCNA_01031 CCNA_01031 transporter, major facilitator superfamily
Query= SwissProt::P0AEX3 (432 letters) >FitnessBrowser__Caulo:CCNA_01031 Length = 550 Score = 206 bits (524), Expect = 1e-57 Identities = 121/338 (35%), Positives = 186/338 (55%), Gaps = 8/338 (2%) Query: 10 SKLTSSDTRRRIWAIVGASS-GNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTAGV 68 +K ++ + R +VGASS G + EW+DFY+Y + FF N TT + Sbjct: 3 AKGQAAPAKGRDTMVVGASSLGTVFEWYDFYLYGSLAPIITSHFFSGVNETTGFILALLA 62 Query: 69 FAAGFLMRPIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPALLL 128 FAAGF +RP+G +FGR+ D GRK + L+++ +M + V+ LP Y IG AP L+ Sbjct: 63 FAAGFAIRPLGALIFGRLGDLWGRKNTFLITMLLMGVSTFVVGLLPSYAQIGVAAPIALV 122 Query: 129 LARLFQGLSVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVVVVLQHTME 188 L RL QGL++GGEYG +ATY++E A G++GFY S+ T G L+L V++V + + Sbjct: 123 LMRLVQGLALGGEYGGAATYVAEHAPPGKRGFYTSWIQTTATIGLFLSLAVILVARIQLG 182 Query: 189 DAALREWGWRIPFALGAVLAVVALWLRRQLDETSQQETRALKEAGSLK------GLWRNR 242 + A + WGWRIPF + +L V+LW+R +L E+ E + GS K G W N Sbjct: 183 EEAFKAWGWRIPFLVSLLLLGVSLWIRLKLHESPTFERMIAEGKGSKKPLTEAFGNWPNL 242 Query: 243 RAFIMVL-GFTAAGSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQPLIGA 301 + ++ L G T ++ +YT Y +L T + +A+ ++ AL + + G Sbjct: 243 KIVLLALVGLTMGQAVVWYTGQFYALFFLEKTLKLDGALANTLVAVALLIGTPFFVICGW 302 Query: 302 LSDKIGRRTSMLCFGSLAAIFTVPILSALQNVSSPYAA 339 LSDKIGR+ ++ LAA+ PI A+ ++P A Sbjct: 303 LSDKIGRKPIIILGCLLAALTYFPIFKAITTYANPALA 340 Score = 37.0 bits (84), Expect = 2e-06 Identities = 24/101 (23%), Positives = 46/101 (45%), Gaps = 2/101 (1%) Query: 333 VSSPYAAFGLVMCALLIVSFYTSISGILKAEMFPAQVRALGVGLSYAVANAIFGGSAEYV 392 V+ P L + + + Y I+ +L E+FP ++R + L Y + N FGG Sbjct: 449 VNKPAVIGLLALLVIYVTMVYGPIAAML-VELFPTRIRYTAMSLPYHIGNGWFGGFLPTT 507 Query: 393 ALSL-KSIGMETAFFWYVTLMAVVAFLVSLMLHRKGKGMRL 432 A ++ + G + WY ++A + +V + + + RL Sbjct: 508 AFAIVAATGDIYSGLWYPVIIAAITAVVGGLFLKDTRHNRL 548 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: 576 Number of extensions: 32 Number of successful extensions: 3 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: 550 Length adjustment: 34 Effective length of query: 398 Effective length of database: 516 Effective search space: 205368 Effective search space used: 205368 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