Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate WP_013089604.1 BC1002_RS08275 MFS transporter
Query= uniprot:D8J257 (457 letters) >NCBI__GCF_000092885.1:WP_013089604.1 Length = 435 Score = 644 bits (1661), Expect = 0.0 Identities = 314/432 (72%), Positives = 369/432 (85%) Query: 1 MSDTTQASTPLSAAEYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQ 60 M+D T A + R+RIFAI+GASSGNLVEWFDFYVYSF A+YFAP+FFP G+ T+Q Sbjct: 1 MNDLTDQPVVTQADDTRRRIFAIVGASSGNLVEWFDFYVYSFTALYFAPSFFPSGNSTTQ 60 Query: 61 LLNTAGVFAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGA 120 LLNTAGVFAAGFLMRPIGGW FGR+ADK GR+T+M++SV MMCGGSL +A++PTYA IGA Sbjct: 61 LLNTAGVFAAGFLMRPIGGWFFGRLADKRGRRTAMMVSVFMMCGGSLVIAMLPTYAQIGA 120 Query: 121 WAPALLLLARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLF 180 APALLL+ARLFQGLSVGGEYGTSATYMSEVA GRRGFFASFQYVTLIGGQL A+LVL Sbjct: 121 LAPALLLIARLFQGLSVGGEYGTSATYMSEVALKGRRGFFASFQYVTLIGGQLFALLVLV 180 Query: 181 GMQQWLTKAELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTLKGLLQH 240 +QQ LT EL AWGWRVPF +GA+ AL+++YLR SL ET++A R++K+AGTL+GL +H Sbjct: 181 VLQQLLTTDELKAWGWRVPFAIGAISALISLYLRKSLDETTTAATRQRKEAGTLRGLWEH 240 Query: 241 KRAFLNVVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFGA 300 K AF+ V+GFTAGGSL+FYTFTTYMQKYLVNTAGM K A+ VMT ALFVYM++QP FGA Sbjct: 241 KAAFMTVLGFTAGGSLIFYTFTTYMQKYLVNTAGMHAKTASSVMTAALFVYMLMQPAFGA 300 Query: 301 ISDKIGRRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVSFYTSISGLIK 360 +SD+IGRRNSMLCF F +GT P+LH LKDV+SP A A ++AL IVSFYTSISGLIK Sbjct: 301 LSDRIGRRNSMLCFGLFATLGTVPLLHALKDVTSPVAAFAFVVVALAIVSFYTSISGLIK 360 Query: 361 AEMFPPEVRALGVGLSYAVGNAIFGGSAEFVALSLKSAGIESAFYWYVSALCLVALIISL 420 AEMFPP+VRALGVGLSYAV NAIFGGSAE+VAL LKSAG+E+ F+WYV+ALC +A I+SL Sbjct: 361 AEMFPPQVRALGVGLSYAVANAIFGGSAEYVALWLKSAGVETMFFWYVTALCALAGIVSL 420 Query: 421 RMPDPQRDGHLK 432 RM DP +G+L+ Sbjct: 421 RMRDPSTEGYLR 432 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: 722 Number of extensions: 29 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: 435 Length adjustment: 32 Effective length of query: 425 Effective length of database: 403 Effective search space: 171275 Effective search space used: 171275 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 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