Align Alpha-ketoglutarate permease (characterized)
to candidate Ga0059261_0987 Ga0059261_0987 MFS/sugar transport protein/Sugar (and other) transporter
Query= SwissProt::P0AEX3 (432 letters) >FitnessBrowser__Korea:Ga0059261_0987 Length = 533 Score = 185 bits (469), Expect = 3e-51 Identities = 114/352 (32%), Positives = 187/352 (53%), Gaps = 28/352 (7%) Query: 4 STVTADSKLTSSDTRRRIWAIVGASS-GNLVEWFDFYVYSF--CSLYFAHIFFPSGNTTT 60 +T D + ++ + +V ASS G + EW+DF++Y S FF +GN Sbjct: 2 ATTVEDIRPEHEPSKSEMRQVVTASSLGTVFEWYDFFIYGTLAASGVIGRTFFATGNPVL 61 Query: 61 QLLQTAGVFAAGFLMRPIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIG 120 + L FA GF RP+G LFG + DK GRK + L+++ +M + + +P Y +IG Sbjct: 62 ETLYAWAGFAVGFGFRPLGAVLFGYLGDKLGRKYTFLVTITLMGVATAGVGFVPSYASIG 121 Query: 121 TWAPALLLLARLFQGLSVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVV 180 APA+++ R+ QGL++GGEYG +A Y+SE + G+ G++ SF ++ G +L+L VV Sbjct: 122 AAAPAIVIGLRILQGLALGGEYGGAAIYVSEHSPTGQAGYHTSFIQASVSAGFILSLAVV 181 Query: 181 VVLQHTMEDAALREWGWRIPFALGAVLAVVALWLRRQLDETSQQETRALKEAGSLKGLWR 240 ++ + TM A+ +WGWR+PF L ++LW+R +L E+ +A+KEAG + R Sbjct: 182 LITRFTMPQASFDDWGWRLPFIFSIALLAISLWMRVKLSES--PVFKAMKEAGEVA---R 236 Query: 241 N------------RRAFIMVLGFTAAGSLCFYTFTTYMQKYLVNTAGMH----ANVASGI 284 N RR F+ + G A ++ +YT T + +L T + +A+G Sbjct: 237 NPLKESFTYPGNLRRLFVALFGIAAGLTVIWYTATFSVLSFLQGTMRVEPVAAQLLAAGG 296 Query: 285 MTAALFVFMLIQPLIGALSDKIGRRTSMLCFGSLAAIFTVPILSALQNVSSP 336 A LF F+ L G LSD+IGR+ ++ + PI A+ + ++P Sbjct: 297 AAAGLFWFI----LFGKLSDRIGRKKPIVIGYGFTLLLLFPIFWAMGHAANP 344 Score = 35.4 bits (80), Expect = 4e-06 Identities = 21/86 (24%), Positives = 41/86 (47%), Gaps = 2/86 (2%) Query: 342 LVMCALLIVSFYTSISGILKAEMFPAQVRALGVGLSYAVANAIFGGSAEYVA-LSLKSIG 400 +V A L + Y ++ +L E+FP ++R + + Y + FGG ++ + G Sbjct: 442 IVALAALSGATYGPVAALL-TELFPPRIRYSSMSIPYHIGTGYFGGFLPLISQYMVAKSG 500 Query: 401 METAFFWYVTLMAVVAFLVSLMLHRK 426 + WY ++ +A LV+L R+ Sbjct: 501 NAYSGLWYTWIVVAMALLVTLFFLRE 526 Score = 24.6 bits (52), Expect = 0.008 Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 1/77 (1%) Query: 346 ALLIVSFYTSISGILKAEMFPAQVRALGVGLSYAVANAIFGGSAEYVALSLKSIGMETAF 405 ALL +S + + + ++ +F A A V + + + G+ + ++L I Sbjct: 207 ALLAISLWMRVK-LSESPVFKAMKEAGEVARNPLKESFTYPGNLRRLFVALFGIAAGLTV 265 Query: 406 FWYVTLMAVVAFLVSLM 422 WY +V++FL M Sbjct: 266 IWYTATFSVLSFLQGTM 282 Lambda K H 0.328 0.138 0.419 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: 580 Number of extensions: 49 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 432 Length of database: 533 Length adjustment: 34 Effective length of query: 398 Effective length of database: 499 Effective search space: 198602 Effective search space used: 198602 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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