Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate N515DRAFT_3073 N515DRAFT_3073 Arabinose efflux permease
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__Dyella79:N515DRAFT_3073 Length = 551 Score = 211 bits (537), Expect = 5e-59 Identities = 123/354 (34%), Positives = 194/354 (54%), Gaps = 12/354 (3%) Query: 7 ASTPLSAAEY---RKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLN 63 A+T + AA +R+ IL +S G + EW+DFY+Y A+ FF + TS + Sbjct: 2 ATTAMGAANIGTGHRRV--ILASSLGTVFEWYDFYLYGSLAVLIGKHFFSGLNETSAFIF 59 Query: 64 TAGVFAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAP 123 FAAGF +RP G +FGR+ D GRK + LI++++M + V V+P+Y+T+G AP Sbjct: 60 ALLAFAAGFAVRPFGAIVFGRLGDLVGRKYTFLITIIIMGLSTFLVGVLPSYSTVGMIAP 119 Query: 124 ALLLLARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQ 183 LL++ RL QGL++GGEYG +ATY++E AP+G+RG + SF +T G L++LV+ G + Sbjct: 120 VLLIVLRLLQGLALGGEYGGAATYVAEHAPDGKRGLYTSFIQITATFGLFLSLLVILGTR 179 Query: 184 QWLTKAELMAWGWRVPFVLGAVGALVAMYLRSSLAET---SSAGARKKKDAGTLKGLLQH 240 L WGWR+PF++ +V V++Y+R L E+ A K L H Sbjct: 180 MALGDKVFEDWGWRIPFLISSVLVAVSVYIRLQLQESPVFQQMKAEGKHSKAPLTEAFGH 239 Query: 241 ----KRAFLNVVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQP 296 K L ++G TAG ++++YT Y +L + +D AN ++ AL + Sbjct: 240 WKNLKVVILALLGATAGQAVVWYTGQFYALYFLTQSLKIDGTTANLLIAAALIIGTPFFV 299 Query: 297 IFGAISDKIGRRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVS 350 FG +SD+IGR++ +L + FPI L +P + A A +T+++ Sbjct: 300 FFGWLSDRIGRKSIVLAGCLLAALTYFPIFKGLTHFGNPAIETAAASAPVTVIA 353 Score = 37.0 bits (84), Expect = 2e-06 Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 1/59 (1%) Query: 337 VAMALAILALTIVSFYTSISGLIKAEMFPPEVRALGVGLSYAVGNAIFGGSAEFVALSL 395 + + LAIL L + Y I+ + EMFP +R + L Y +GN FGG + L Sbjct: 455 LVILLAILVLYVTMVYGPIAAWL-VEMFPTRIRYTSMSLPYHIGNGWFGGFVPTIGFML 512 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: 742 Number of extensions: 42 Number of successful extensions: 6 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: 551 Length adjustment: 34 Effective length of query: 423 Effective length of database: 517 Effective search space: 218691 Effective search space used: 218691 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 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