Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate BPHYT_RS11175 BPHYT_RS11175 alpha-ketoglutarate transporter
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__BFirm:BPHYT_RS11175 Length = 434 Score = 649 bits (1674), Expect = 0.0 Identities = 323/432 (74%), Positives = 370/432 (85%), Gaps = 1/432 (0%) Query: 1 MSDTTQASTPLSAAEYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQ 60 M+D T T SA + R+RIFAI+GASSGNLVEWFDFYVYSFCA+YFAPAFFP G+ T+Q Sbjct: 1 MTDLTD-QTVASAHDTRRRIFAIVGASSGNLVEWFDFYVYSFCALYFAPAFFPSGNTTTQ 59 Query: 61 LLNTAGVFAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGA 120 LLNTAGVFAAGFLMRPIGGW FGR+ADKHGR+T+M++SV MMCGGSL +AV+PTYA IGA Sbjct: 60 LLNTAGVFAAGFLMRPIGGWFFGRLADKHGRRTAMMVSVFMMCGGSLVIAVLPTYAQIGA 119 Query: 121 WAPALLLLARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLF 180 APALLL+ARLFQGLSVGGEYGTSATYMSEVA GRRGFFASFQYVTLIGGQL A+LVL Sbjct: 120 LAPALLLVARLFQGLSVGGEYGTSATYMSEVALKGRRGFFASFQYVTLIGGQLCALLVLV 179 Query: 181 GMQQWLTKAELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTLKGLLQH 240 +QQ L+ EL AWGWRVPF +GAV ALVA+YLR SL ET++A R++K+AGTL+GL H Sbjct: 180 VLQQTLSNDELKAWGWRVPFAIGAVAALVALYLRKSLDETTTAETRQRKEAGTLRGLWLH 239 Query: 241 KRAFLNVVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFGA 300 K AF+ V+GFTAGGSL+FYTFTTYMQKYLVNTAGM K A+ VMT ALFVYM++QP FGA Sbjct: 240 KGAFMTVLGFTAGGSLIFYTFTTYMQKYLVNTAGMHAKTASNVMTAALFVYMVMQPAFGA 299 Query: 301 ISDKIGRRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVSFYTSISGLIK 360 +SD+IGRR SML F FF +GT P+LH LKDV+SP A L ++AL IVSFYTSISGLIK Sbjct: 300 LSDRIGRRRSMLFFGFFATIGTVPLLHALKDVTSPYAAFGLVVVALAIVSFYTSISGLIK 359 Query: 361 AEMFPPEVRALGVGLSYAVGNAIFGGSAEFVALSLKSAGIESAFYWYVSALCLVALIISL 420 AEMFPPEVRALGVGLSYAV NAIFGGSAE+VAL LKS G ES FYWYV+ALC +A I+SL Sbjct: 360 AEMFPPEVRALGVGLSYAVANAIFGGSAEYVALWLKSVGNESIFYWYVTALCAIAGIVSL 419 Query: 421 RMPDPQRDGHLK 432 RM DP ++G+L+ Sbjct: 420 RMRDPSKEGYLR 431 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: 748 Number of extensions: 28 Number of successful extensions: 3 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: 457 Length of database: 434 Length adjustment: 32 Effective length of query: 425 Effective length of database: 402 Effective search space: 170850 Effective search space used: 170850 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