Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate Pf1N1B4_5961 Major facilitator superfamily transporter
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5961 Length = 558 Score = 217 bits (553), Expect = 7e-61 Identities = 128/360 (35%), Positives = 201/360 (55%), Gaps = 14/360 (3%) Query: 1 MSDTTQASTPLSAA--EYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPT 58 + +TT S P E RK IFA +S G + EW+DFY+Y A A FF + T Sbjct: 4 IDNTTTGSAPHHGITREERKVIFA---SSLGTVFEWYDFYLYGSLAAIIAKHFFAGVNET 60 Query: 59 SQLLNTAGVFAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATI 118 + + FAAGF +RP G +FGR+ D GRK + LI++++M + V +P YATI Sbjct: 61 TSFIFALLAFAAGFAVRPFGAIVFGRLGDMIGRKHTFLITIVIMGISTAVVGFLPGYATI 120 Query: 119 GAWAPALLLLARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLV 178 G AP +L+ RL QGL++GGEYG +ATY++E AP G+RG+F S+ T G L++LV Sbjct: 121 GVAAPIILITLRLLQGLALGGEYGGAATYVAEHAPKGKRGYFTSWIQTTATLGLFLSLLV 180 Query: 179 LFGMQQWLTKAELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTLKGLL 238 + + L AWGWR+PF+L + +V++Y+R L+E S + K++ + K L Sbjct: 181 ILACRTILGNEAFEAWGWRIPFLLSILLLIVSVYIRLQLSE-SPVFLKMKEEGKSSKAPL 239 Query: 239 QH--------KRAFLNVVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFV 290 K + ++G TAG ++++YT Y +L+ T +DP+ AN ++ G+L + Sbjct: 240 TESFARWENLKIVIMALLGGTAGQAVVWYTGQFYALFFLLQTLKIDPQTANFLIAGSLLI 299 Query: 291 YMILQPIFGAISDKIGRRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVS 350 IFG++SD+IGR+ ++ + FPI H L + +P V A +T+++ Sbjct: 300 GTPFFIIFGSLSDRIGRKGIIMAGCVIAALTYFPIFHALTEYGNPDVFAAQEKNPVTVIA 359 Score = 40.8 bits (94), Expect = 1e-07 Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 2/85 (2%) Query: 335 PGVAMALAILALTIVSFYTSISGLIKAEMFPPEVRALGVGLSYAVGNAIFGGSAEFVALS 394 P V + L IL + + Y I+ + E+FP +R + L Y +GN FGG VA + Sbjct: 459 PMVLLLLTILVIYVTMVYGPIAAWL-VELFPARIRYTSMSLPYHIGNGWFGGFLPTVAFA 517 Query: 395 LKSAGIESAF-YWYVSALCLVALII 418 + +A + + WY + ++ I+ Sbjct: 518 MVAATGDIYYGLWYPIVIAVMTAIL 542 Lambda K H 0.325 0.138 0.418 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: 665 Number of extensions: 36 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: 2 Length of query: 457 Length of database: 558 Length adjustment: 34 Effective length of query: 423 Effective length of database: 524 Effective search space: 221652 Effective search space used: 221652 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: 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