Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate AO356_29600 AO356_29600 MFS transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29600 Length = 432 Score = 237 bits (604), Expect = 6e-67 Identities = 144/412 (34%), Positives = 231/412 (56%), Gaps = 12/412 (2%) Query: 24 RIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFLMRPIG 83 R++S+ + +VGN +EW+DW +YA FS+Y A+ F K D + +L T A+FA GF+ RP+G Sbjct: 10 RLRSLRAAAVGNALEWFDWTLYATFSVYLARNLFDKTDPRSAMLATLAVFAAGFIARPLG 69 Query: 84 GWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQGLSVG 143 G+ G +D GR+A ++ ++ L+ SL IAL P Y+ IG+ A L+ RL+QGL+ G Sbjct: 70 GFFFGRLSDVLGRRAIMVITMMLLAASSLGIALIPNYQDIGLYASSALLVFRLIQGLAHG 129 Query: 144 GEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLYDWGWRI 203 GE G S TY++E+A + RG +SS YV + G + A V L L T+ D+GWRI Sbjct: 130 GETGVSYTYVAEIAPAKHRGLWSSSVYVGVTLGVMGATAVAAALTWLLGTQATGDYGWRI 189 Query: 204 PFAIGALCAIVALYLRRGMEETESFAKKEKSKESAMRTLLRHPKELMT--VVGLTMGGTL 261 FAIG + I AL+LRR +E+ F ++++ + R L + MT +V L + Sbjct: 190 GFAIGGVLGIYALFLRRSAQESHVF-EQQRQQAQPPRKLSKGEVLRMTRNIVMLAAAANV 248 Query: 262 AFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRRPILIAFGI 321 +Y + T+ + GM + + S + +C P+ G LSD+VGR+P++IA+GI Sbjct: 249 TYYAWVTFGAASAI-AQGMDATGAYLASLLAQVICVCWLPVCGMLSDRVGRKPMVIAWGI 307 Query: 322 LGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAV---VKAELFPTEIRALGV 378 + T PI + T + L +A + + + SI A+ V +E PT+ RA V Sbjct: 308 GVVVLTYPISIIVTT-----EPYTLFLAQALALLAWASIAAIFPAVLSEQVPTQARAQSV 362 Query: 379 GLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVSLLVYVTMKDT 430 G +++V+IFGGTA Y+ + +E Y Y+ + V++ +++T Sbjct: 363 GFVSSVSVAIFGGTAPYLHSYLVGAHLEYLYIGYLISLGLVTVAAGYFIEET 414 Lambda K H 0.325 0.138 0.414 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: 537 Number of extensions: 31 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: 439 Length of database: 432 Length adjustment: 32 Effective length of query: 407 Effective length of database: 400 Effective search space: 162800 Effective search space used: 162800 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