Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate GFF2854 PS417_14575 MFS transporter
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__WCS417:GFF2854 Length = 445 Score = 239 bits (611), Expect = 1e-67 Identities = 148/432 (34%), Positives = 228/432 (52%), Gaps = 15/432 (3%) Query: 4 TTQASTPLSAAEYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLN 63 T+ ++ +S RK I+ A GN VEWFDF VY F A A FFP GD ++ LL Sbjct: 2 TSPSTEQVSPQTLRK---VIIAAGIGNFVEWFDFAVYGFLATTIAQQFFPSGDASAALLK 58 Query: 64 TAGVFAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAP 123 T VFA F RP+GG FG + D+ GRK ++ +++L+M G + + ++PTYA IG AP Sbjct: 59 TFAVFAVAFAFRPLGGIFFGMLGDRIGRKRTLAMTILLMAGATTLIGLLPTYAAIGVAAP 118 Query: 124 ALLLLARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQ 183 LL L R QG S GGEY + Y+ E AP+ +R ++ SF V+ A +V + ++ Sbjct: 119 ILLSLIRCAQGFSAGGEYAGACAYLMEHAPSDKRAWYGSFVPVSTFSAFAAAAVVAYALE 178 Query: 184 QWLTKAELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDA---GTLKGLLQH 240 L+ + +WGWR+PF++ A LV +YLR L ET + A K++ LK L++ Sbjct: 179 ASLSAEAMGSWGWRLPFLIAAPLGLVGLYLRWKLDETPAFQAVKEEHTVAHSPLKETLRN 238 Query: 241 KRAFLNVVG-FTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFG 299 A ++ +G F + +L FY FTTY YL G+ +A V AL + P+ G Sbjct: 239 HGAAISCLGAFVSLTALSFYMFTTYFATYLQVAGGLSRAMALLVSLIALIFAAAICPLAG 298 Query: 300 AISDKIGRRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVSFYTS-ISGL 358 SD++GRR +++ MV +P FL S A + ++ L + + ++ Sbjct: 299 LYSDRVGRRATVMTACVLLMVVVYP--SFLMASSGSFAASIVGVMLLAVGAVLCGVVTAA 356 Query: 359 IKAEMFPPEVRALGVGLSYAVGNAIFGGSAEFVA---LSLKSAGIESAFYWYVSALCLVA 415 + +E FP R ++Y + IFGG+A +A +S + + AF Y+ A+ L+A Sbjct: 357 LLSETFPTRTRYTASAITYNLAYTIFGGTAPLMATWLISTTGSNLSPAF--YLIAVALLA 414 Query: 416 LIISLRMPDPQR 427 L L +P+ R Sbjct: 415 LAGGLALPETSR 426 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: 543 Number of extensions: 29 Number of successful extensions: 4 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: 445 Length adjustment: 33 Effective length of query: 424 Effective length of database: 412 Effective search space: 174688 Effective search space used: 174688 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