Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate WP_013520567.1 ALIDE2_RS20480 MFS transporter
Query= uniprot:D8J257 (457 letters) >NCBI__GCF_000204645.1:WP_013520567.1 Length = 564 Score = 207 bits (528), Expect = 5e-58 Identities = 121/352 (34%), Positives = 198/352 (56%), Gaps = 13/352 (3%) Query: 7 ASTPLSAAEYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLNTAG 66 A P++ E +K IFA +S G + EW+DFY+Y A A FF D + + Sbjct: 14 AHRPMTTEE-KKVIFA---SSLGTVFEWYDFYLYGSLAAIIAKQFFSGLDAGAAFIFALL 69 Query: 67 VFAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAPALL 126 FAAGFL+RP G +FGR+ D GRK + L+++L+M + V V+P YA+IG AP +L Sbjct: 70 AFAAGFLVRPFGALVFGRLGDMIGRKYTFLVTILIMGISTFIVGVLPNYASIGVAAPIIL 129 Query: 127 LLARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQQWL 186 + R+ QGL++GGEYG +ATY++E AP+G+RG + S+ T G L++LV+ G + + Sbjct: 130 IALRMLQGLALGGEYGGAATYVAEHAPHGKRGAYTSWIQTTATLGLFLSLLVILGTRTVM 189 Query: 187 TKAELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTLKGLLQH------ 240 + WGWR+PF++ + V++++R SL+E S A + K + T K L Sbjct: 190 GEPAFNDWGWRIPFLVSILLLAVSVWIRLSLSE-SPAFQKMKAEGKTSKAPLSESFGQWK 248 Query: 241 --KRAFLNVVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIF 298 K L ++G TAG ++++YT Y +L+ +D AN ++ AL + +F Sbjct: 249 NLKIVILALIGLTAGQAVVWYTGQFYALFFLMQQLKVDAVTANLMIAAALLIGTPFFVVF 308 Query: 299 GAISDKIGRRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVS 350 G++SDKIGR+ ++ ++ FP+ L ++P +A A A +++ + Sbjct: 309 GSLSDKIGRKPIIMLGCVLAVLTYFPVFKALTGAANPDLAKAQATAGVSVTA 360 Score = 37.7 bits (86), Expect = 1e-06 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 2/77 (2%) Query: 332 VSSPGVAMALAILALTIVSFYTSISGLIKAEMFPPEVRALGVGLSYAVGNAIFGGSAEFV 391 ++ P + L L + + Y I+ ++ E+FP +R + L Y +GN FGG Sbjct: 461 MNKPMMIAILVYLVILVTMVYGPIAAML-VELFPTRIRYTSMSLPYHIGNGWFGGLLPTT 519 Query: 392 ALSL-KSAGIESAFYWY 407 + +L SAG + WY Sbjct: 520 SFALVASAGNMYSGLWY 536 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: 41 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: 564 Length adjustment: 34 Effective length of query: 423 Effective length of database: 530 Effective search space: 224190 Effective search space used: 224190 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 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