Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate PP_3666 PP_3666 Metabolite MFS transporter, MHS family
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__Putida:PP_3666 Length = 444 Score = 249 bits (636), Expect = 1e-70 Identities = 151/448 (33%), Positives = 240/448 (53%), Gaps = 19/448 (4%) Query: 3 NSQTLPLGSAAVPAKEKTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDT 62 +S TL + A PA + K+ + +GN VEW+D+ Y + A FFP+ D Sbjct: 2 SSTTLDPSAIAGPAHNAERQALRKAARASFMGNFVEWFDYAAYGYLATIIAATFFPQTDK 61 Query: 63 TAQLLNTAAIFAVGFLMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYET 122 T LL T A+FA+ FL+RP+GG + G + DR GR+ AL S+ +M + I L PGY Sbjct: 62 TTGLLATFAVFALSFLVRPLGGIVWGHFGDRHGRRNALSWSILIMSVSTFCIGLLPGYAQ 121 Query: 123 IGVGAPILLVFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALG 182 IG+ AP LL+ RL+QG S GEY +A +L+E A RRG ++S + +G L Sbjct: 122 IGLWAPALLLLIRLVQGFSASGEYAGAAAFLAEYAPPGRRGLYTSIVPASTAAGLLFGAA 181 Query: 183 VLIVLQQTLTTEQLYDWGWRIPFAIGALCAIVALYLRRGMEETESFAKKEKSKE------ 236 + VL + L++E L++WGWR+PF + A +V Y+R +++T F + E+ E Sbjct: 182 FVAVLHELLSSEALHEWGWRLPFLLAAPFGLVGRYIRMSLQDTPKFLEMEQRLETKAGMA 241 Query: 237 -SAMRTLL-RHPKELMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLF 294 + +R LL +H + L +G+T +AFY +YM YL + +GMS DS S +L Sbjct: 242 TTPLRELLGQHRRSLAIGMGVTCLNAVAFYLLLSYMPTYLSSEMGMSERDSFIASTVSLA 301 Query: 295 LFMCLQPIIGGLSDKVGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIV 354 ++ L ++G LSD+ GR+ +L+ +L TVP+ L +I+A I+ Sbjct: 302 TYIGLIFLMGRLSDQFGRKTMLVVASLLFLGLTVPLFRLLD-----GQPLLVILAIQILF 356 Query: 355 SGYTSIN----AVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALWFKSI-GMETGY 409 ++N + AE+FPT +R G L + + ++FGGTA +IA W + G + Sbjct: 357 GAMLAMNDGTLPCLLAEIFPTRVRFSGFALSFNVANALFGGTAPFIATWLIQVTGSKLAP 416 Query: 410 YWYVTACIAVSLLVYVTMKDTRKHSRIE 437 Y+ A V+L+ + ++T H+ +E Sbjct: 417 AGYLLAAALVALVAMLMCRET-AHAALE 443 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: 528 Number of extensions: 28 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: 444 Length adjustment: 32 Effective length of query: 407 Effective length of database: 412 Effective search space: 167684 Effective search space used: 167684 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