Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate WP_012399532.1 BPHY_RS00535 MFS transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >NCBI__GCF_000020045.1:WP_012399532.1 Length = 440 Score = 253 bits (645), Expect = 1e-71 Identities = 137/416 (32%), Positives = 227/416 (54%), Gaps = 6/416 (1%) Query: 26 KSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFLMRPIGGW 85 +++ + +GN +EWYD+ V+ ++ A+ FFP + +L T A F V F MRP+GG Sbjct: 11 RAVTAAVIGNALEWYDFTVFGFLTVVIAELFFPSSSDYSAILLTTASFGVAFFMRPVGGI 70 Query: 86 LMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQGLSVGGE 145 ++GLYADRAGRKAAL + LM G L++A++P Y IGVGAP+L+V RLLQG S GGE Sbjct: 71 VLGLYADRAGRKAALSLVIALMSLGILLLAVAPPYSAIGVGAPLLIVVGRLLQGFSAGGE 130 Query: 146 YGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLYDWGWRIPF 205 +G+S L E A +RGF+ S+Q + + L+ V ++ + L+ E L WGWR+PF Sbjct: 131 FGSSTALLIEAAPFSKRGFYGSWQMASQAAALLLGAVVGALMTRGLSPEALRSWGWRVPF 190 Query: 206 AIGALCAIVALYLRRGMEETESF--AKKEKSKESAMRTLLRHPKELMTVVGLTMGGTLAF 263 +G + + Y+RR + ++E+F AK+ + + H ++++ +G + T+ Sbjct: 191 ILGLVIGPIGFYIRRNLADSEAFLHAKQTARRATLGELFAHHSRDVLCGLGSVVALTVTI 250 Query: 264 YTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRRPILIAFGILG 323 Y +Y+ + V + + +DS T L L P+ G SD++GR+ + + ++ Sbjct: 251 YVLISYLPTFAVRQLKLPYADSFTAVIVGNLLLTVLSPLTGAWSDRIGRKGLSLWSLVIT 310 Query: 324 TLFTVPILTTLHTIQTWWGAFFLIMAAL-IIVSGYTSINAVVKAELFPTEIRALGVGLPY 382 + P+ L + L+ A L I +SGY + AELFP +R+ G+ L Y Sbjct: 311 LVAIYPLFVWLEEAPS-VSKLILVQAILSIALSGYYGPFGALMAELFPANVRSTGLSLAY 369 Query: 383 ALTVSIFGGTAEYIALW-FKSIGMETGYYWYVTACIAVSLLVYVTMKDTRKHSRIE 437 V +FGG ++I W K+ G +YV + +S +V V ++H+ ++ Sbjct: 370 NFAVMLFGGFGQFIVTWLIKTTGSPLAPTYYVMCGLTIS-IVAVACMPAKRHADLD 424 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: 554 Number of extensions: 27 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: 439 Length of database: 440 Length adjustment: 32 Effective length of query: 407 Effective length of database: 408 Effective search space: 166056 Effective search space used: 166056 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 24 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