Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate CA265_RS19920 CA265_RS19920 MFS transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__Pedo557:CA265_RS19920 Length = 507 Score = 216 bits (550), Expect = 1e-60 Identities = 116/313 (37%), Positives = 177/313 (56%), Gaps = 9/313 (2%) Query: 26 KSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFLMRPIGGW 85 K I + S+G ++EWYD+Y++ + ++ FP+ + L+NT AIFA GF++RP G Sbjct: 12 KVIGASSLGTLIEWYDFYIFGSLAVIIGHQLFPEDAGASALINTLAIFAAGFIVRPFGAL 71 Query: 86 LMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQGLSVGGE 145 + G D GRK + ++ LM + I L P Y++IG APIL++ RL+QGL++GGE Sbjct: 72 VFGRLGDLIGRKYTFLLTLVLMGGSTFFIGLIPSYKSIGYAAPILVLILRLIQGLALGGE 131 Query: 146 YGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLYDWGWRIPF 205 YG +ATY++E A K +RGFF+S+ T G ++LG++++ + L E DWGWRIPF Sbjct: 132 YGGAATYVAEHAPKNKRGFFTSWIQTTATLGLFLSLGIIVITKNILGAETFGDWGWRIPF 191 Query: 206 AIGALCAIVALYLRRGMEETESFAK--------KEKSKESAMRTLLRHPKELMTVVGLTM 257 + + +V++Y+R M E+ F+K K KES L+ + G TM Sbjct: 192 LLSIVLVVVSIYIRMKMHESPMFSKLKAEGNVSKNPLKES-FNNKANFKMVLLALFGATM 250 Query: 258 GGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRRPILI 317 G + +YT Y Q +L NT + +DS I + I G SDKVGR+ I++ Sbjct: 251 GQGVIWYTGQFYAQSFLENTCKLDFNDSRYILLWGIAFATPFFVIFGAWSDKVGRKWIML 310 Query: 318 AFGILGTLFTVPI 330 + +LG LF PI Sbjct: 311 SGMLLGILFYRPI 323 Score = 43.9 bits (102), Expect = 1e-08 Identities = 27/86 (31%), Positives = 40/86 (46%), Gaps = 2/86 (2%) Query: 340 WWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALW 399 +W LI +++V+ A ELFPT+IR + LPY + +FGG +IA Sbjct: 407 FWKFVGLIFFQILLVTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPFIATL 466 Query: 400 FKSIGMET--GYYWYVTACIAVSLLV 423 S T WY A+SL++ Sbjct: 467 IASFSGSTPLSGLWYPIGIAALSLVI 492 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: 631 Number of extensions: 32 Number of successful extensions: 4 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: 439 Length of database: 507 Length adjustment: 33 Effective length of query: 406 Effective length of database: 474 Effective search space: 192444 Effective search space used: 192444 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