Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate AO353_17220 AO353_17220 alpha-ketoglutarate permease
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__pseudo3_N2E3:AO353_17220 Length = 431 Score = 592 bits (1525), Expect = e-173 Identities = 294/417 (70%), Positives = 350/417 (83%), Gaps = 2/417 (0%) Query: 9 TPLSAAEYR-KRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLNTAGV 67 T L AE R KRIFAI+GASSGNLVEWFDFYVY+FCAIYFAPAFFP +PT QL+NTAGV Sbjct: 5 TSLYTAEERGKRIFAIVGASSGNLVEWFDFYVYAFCAIYFAPAFFPSDNPTVQLVNTAGV 64 Query: 68 FAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAPALLL 127 FAAGFLMRPIGGWLFGR+ADKHGRK SM+ISVLMMC GSL +A +PTY IG WAP LLL Sbjct: 65 FAAGFLMRPIGGWLFGRVADKHGRKNSMMISVLMMCAGSLLIACLPTYKDIGVWAPLLLL 124 Query: 128 LARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQQWLT 187 +ARL QG+SVGGEYGT+ATYMSEVA G+RGFFASFQYVTLIGGQLLAV ++ +QQ+LT Sbjct: 125 VARLIQGVSVGGEYGTTATYMSEVALKGQRGFFASFQYVTLIGGQLLAVSLVVILQQFLT 184 Query: 188 KAELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTLKGLLQHK-RAFLN 246 + +L AWGWR+PFV+GA AL++++LR SL ET+S R+ KDAG++ L ++ AF+ Sbjct: 185 EDDLRAWGWRIPFVVGAAAALISLFLRRSLKETTSKEMRENKDAGSMAALFRNNTAAFIT 244 Query: 247 VVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFGAISDKIG 306 V+GFTAGGSL+FYTFTTYMQKYLVNTAGM K A+ +MTGALF+YM +QP+FG ++DKIG Sbjct: 245 VLGFTAGGSLIFYTFTTYMQKYLVNTAGMPAKTASYIMTGALFLYMCMQPLFGTLADKIG 304 Query: 307 RRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVSFYTSISGLIKAEMFPP 366 RRNSML F G + T PIL LK V++P +A L +AL IVSFYTSISGL+KAEMFPP Sbjct: 305 RRNSMLWFGALGTLFTVPILLTLKSVTNPFLAFGLITVALAIVSFYTSISGLVKAEMFPP 364 Query: 367 EVRALGVGLSYAVGNAIFGGSAEFVALSLKSAGIESAFYWYVSALCLVALIISLRMP 423 +VRALGVGL+YAV NAIFGGSAE+VALSLKS GIE++FYWYV+A+ +A + SLR+P Sbjct: 365 QVRALGVGLAYAVANAIFGGSAEYVALSLKSVGIENSFYWYVTAMMAIAFLFSLRLP 421 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: 700 Number of extensions: 35 Number of successful extensions: 4 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: 457 Length of database: 431 Length adjustment: 32 Effective length of query: 425 Effective length of database: 399 Effective search space: 169575 Effective search space used: 169575 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