Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate AO356_30335 AO356_30335 MFS transporter
Query= reanno::pseudo5_N2C3_1:AO356_17790 (439 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30335 Length = 456 Score = 209 bits (533), Expect = 1e-58 Identities = 135/429 (31%), Positives = 225/429 (52%), Gaps = 21/429 (4%) Query: 17 RERTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKV-FFPKGDTTAQLLNTAAIFAV 75 + +TT+SR +S+ +G++GN E YD+ V+ FS+ V FFP D TA LL+T A++AV Sbjct: 3 KTKTTSSR-RSLAAGAIGNFGEIYDFAVFG-FSIPILSVHFFPGSDRTAALLSTFAVYAV 60 Query: 76 GFLMRPIGGWLMGLYADRAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPILLVFAR 135 F+ RP+GG + G ADR GR R + +V+LM G+ II L P+Y TIG+ AP+LL+ R Sbjct: 61 AFVARPLGGLMFGYLADRLGRIRVMAMTVWLMALGTAIIGLLPTYATIGIAAPLLLLLCR 120 Query: 136 LLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQFLTTEQ 195 + QGL++GGE S +Y+ E A + RRG++ F + + G+++ LQ + Sbjct: 121 IAQGLALGGETTGSTSYIVESAPENRRGYWLGFTLIFSHLPNAVVAGLVVALQLGAGDQA 180 Query: 196 LYAWGWRIPFAIGALCAVVALYLRRGMEETESF------TKKEKSKESAMRTLLR--HPK 247 W WRIPF +G + VV +LRR ++E E + +K K K++ + +R + Sbjct: 181 YSDWAWRIPFLLGGIIGVVGFWLRRNIDEPEEYKQARQASKASKIKKNPLIAAIRCGGLR 240 Query: 248 ELMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPVIGGLS 307 ++ V + ++ Y +M +L+ + + + +A + + L P+ G LS Sbjct: 241 GMLHVFMVQPVFSVGAYLLLGFMYTFLIEVGKLDSTSALISNAIAVIVLSALLPLGGLLS 300 Query: 308 DKIGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSG----YTSINAV 363 D+ GR+ +L L P + + G+F +A +++ Y + + V Sbjct: 301 DRFGRKRVLTFGAAWIALSAYPAMYLAAS-----GSFASAVAGQTLLAAGLGIYGAASFV 355 Query: 364 VKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALWF-KSIGMETGYYWYVTACIAVSLL 422 AE FPT RA G + Y +V++FGGT IA + ++ G +YVT + L+ Sbjct: 356 AAAEFFPTSFRATGHAISYQTSVAMFGGTCPLIAAYLSQAFGSPLAPAFYVTLIAVLCLI 415 Query: 423 VYITMKDTR 431 + +TR Sbjct: 416 TTQFVPETR 424 Lambda K H 0.326 0.138 0.416 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: 573 Number of extensions: 30 Number of successful extensions: 5 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: 456 Length adjustment: 33 Effective length of query: 406 Effective length of database: 423 Effective search space: 171738 Effective search space used: 171738 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 (21.7 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