Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate SMc04407 SMc04407 transport transmembrane protein
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__Smeli:SMc04407 Length = 629 Score = 198 bits (503), Expect = 5e-55 Identities = 117/343 (34%), Positives = 191/343 (55%), Gaps = 10/343 (2%) Query: 15 EYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLNTAGVFAAGFLM 74 E +K IFA +S G + EW+DFY+Y A+Y FF + T++ + FAAGFL+ Sbjct: 18 EEKKVIFA---SSLGTVFEWYDFYLYGSLAVYIGATFFSQYPETTRNIFALLAFAAGFLV 74 Query: 75 RPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAPALLLLARLFQG 134 RP G +FGR+ D GRK + L+++L+M + V V+P A+IG AP +L+ RL QG Sbjct: 75 RPFGALVFGRLGDLVGRKYTFLVTILIMGVSTFLVGVLPGAASIGIAAPIILIALRLLQG 134 Query: 135 LSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQQWLTKAELMAW 194 L++GGEYG +ATY++E AP+GRRG+F S+ T G L+++V+ +Q L K W Sbjct: 135 LALGGEYGGAATYVAEHAPHGRRGYFTSWIQTTATLGLFLSLVVILLVQYMLGKEAFAEW 194 Query: 195 GWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTLKGLLQ-------HKRAFLNV 247 GWR+PF+L V V++++R + E+ + K++ G+ L + K A L + Sbjct: 195 GWRIPFLLSFVLLGVSVWIRLKMNESPAFKKMKEEGKGSKAPLTEAFGQWRNAKIAVLAL 254 Query: 248 VGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFGAISDKIGR 307 G G ++++Y+ Y +L + +D + AN ++ +L + FG +SDKIGR Sbjct: 255 FGAVVGQAVVWYSGQFYALFFLQSILKVDGQSANLMVAASLLLGTGFFVFFGWLSDKIGR 314 Query: 308 RNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVS 350 + ++ M+ FP+ L +P +A A + T+ + Sbjct: 315 KPIIMAGLLLAMLTYFPLFKALTWAGNPALAEAQQSVRATVTA 357 Score = 43.5 bits (101), Expect = 2e-08 Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 2/85 (2%) Query: 337 VAMALAILALTIVSFYTSISGLIKAEMFPPEVRALGVGLSYAVGNAIFGGSAEFVALSLK 396 + L +L + + Y I+ L+ E+FP +R G+ L Y +GN FGG A ++ Sbjct: 531 IIAVLTVLVIYVTMVYGPIAALL-VELFPTRIRYTGMSLPYHIGNGWFGGLLPATAFAMS 589 Query: 397 SAGIESAF-YWYVSALCLVALIISL 420 +A + + WY + L+I L Sbjct: 590 AAKGDIYYGLWYPIVFAGITLVIGL 614 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: 770 Number of extensions: 44 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: 629 Length adjustment: 35 Effective length of query: 422 Effective length of database: 594 Effective search space: 250668 Effective search space used: 250668 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