Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate GFF1323 PS417_06725 alpha-ketoglutarate permease
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__WCS417:GFF1323 Length = 431 Score = 603 bits (1554), Expect = e-177 Identities = 300/420 (71%), Positives = 350/420 (83%), Gaps = 1/420 (0%) Query: 5 TQASTPLSAAEYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLNT 64 T ++ + E KRIFAI+GASSGNLVEWFDFYVY+FCAIYFAPAFFP DPT QLLNT Sbjct: 2 TTTTSHYTGEERSKRIFAIVGASSGNLVEWFDFYVYAFCAIYFAPAFFPSDDPTVQLLNT 61 Query: 65 AGVFAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAPA 124 AGVFAAGFLMRPIGGWLFGR+ADKHGRK SM+ISVLMMC GSL +A +PTY IGAWAPA Sbjct: 62 AGVFAAGFLMRPIGGWLFGRVADKHGRKNSMMISVLMMCAGSLVIAFLPTYKDIGAWAPA 121 Query: 125 LLLLARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQQ 184 LLL+ARLFQGLSVGGEYGT+ATYMSEVA G+RGFFASFQYVTLIGGQLLAVLV+ +QQ Sbjct: 122 LLLVARLFQGLSVGGEYGTTATYMSEVALKGQRGFFASFQYVTLIGGQLLAVLVVVILQQ 181 Query: 185 WLTKAELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTLKGLLQ-HKRA 243 LT+ EL AWGWR+PFV+GA+ A++++ LR +L ET+S R+ KDAG++ L + HK A Sbjct: 182 ILTEEELRAWGWRIPFVIGAIAAVISLLLRRTLKETTSKETRQDKDAGSVAALFRNHKAA 241 Query: 244 FLNVVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFGAISD 303 F+ V+G+TAGGSL+FYTFTTYMQKYLVNTAGM K A+ +MTGALFVYM +QP+FG +SD Sbjct: 242 FITVLGYTAGGSLIFYTFTTYMQKYLVNTAGMHAKTASYIMTGALFVYMCMQPLFGMLSD 301 Query: 304 KIGRRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVSFYTSISGLIKAEM 363 KIGRRNSML F G + T PIL LK V++P +A L LAL IVSFYTSISGL+KAEM Sbjct: 302 KIGRRNSMLWFGALGTLCTVPILLTLKTVTNPFLAFVLISLALAIVSFYTSISGLVKAEM 361 Query: 364 FPPEVRALGVGLSYAVGNAIFGGSAEFVALSLKSAGIESAFYWYVSALCLVALIISLRMP 423 FPP VRALGVGL+YAV NAIFGGSAE+VAL LKS G+E+ FYWYV+ + VA + SLR+P Sbjct: 362 FPPHVRALGVGLAYAVANAIFGGSAEYVALGLKSMGMENTFYWYVTGMMAVAFLFSLRLP 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: 705 Number of extensions: 34 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