Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate N515DRAFT_0011 N515DRAFT_0011 MFS transporter, MHS family, alpha-ketoglutarate permease
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__Dyella79:N515DRAFT_0011 Length = 435 Score = 214 bits (545), Expect = 5e-60 Identities = 132/424 (31%), Positives = 218/424 (51%), Gaps = 18/424 (4%) Query: 22 GRLRKAITAAALGNAMEWFDFGVYGFVAYALGQVFFPGADPGVQMIAALATFSVPFLIRP 81 G+ ++I + ++GN +EW+D+ VY + QVFFP +D Q++ F+V FL+RP Sbjct: 18 GQRLRSIFSGSIGNLVEWYDWYVYSAFSLYFAQVFFPASDQTTQLLNTSGIFAVGFLMRP 77 Query: 82 LGGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFS 141 LGG G D+ GR+ L +++ +MS+ + IGL P Y +IG+ APILL+LA++ QG S Sbjct: 78 LGGWLLGTFADRRGRKAALLLSVFMMSLGSLIIGLSPGYAQIGVAAPILLVLARLLQGLS 137 Query: 142 VGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLG-AGVVVLISTLIGEQAFLAWG 200 +GGEY ++ +++E +P RGF S +AG ++ A +VVL ++ Q WG Sbjct: 138 IGGEYGTSATYLSEMAPRESRGFWSSIQYVTLVAGQLIALALLVVLQHFVLSTQQLHDWG 197 Query: 201 WRLPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWK 260 WR+PF + L +I + +R ++ET +F++ +LE R ++ H + Sbjct: 198 WRIPFLIGALLAVIAVIIRRNMDETASFKK-ARQLESPLRTLMR-------------HPR 243 Query: 261 SLLVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGMLFVQPVMGLLS 320 +L IGL + + +Y TYM +L +S S+ I A + +QP G LS Sbjct: 244 EVLTVIGLTMGGTLAFYTFTTYMQKFLVNSAGMSKADATSISTAALFVYALLQPAFGALS 303 Query: 321 DRFGRKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLA-VILNAFTGVMASTLPA 379 DR GR+P ++ V L P + GL+M A +I++ +T + A Sbjct: 304 DRIGRRPLLIGFGVLGALLTYPILSTLKEAHDWWQAFGLIMAALIIVSGYTSINAVVKAE 363 Query: 380 LFPTHIRYSALASAFNISVLIAGLTPT-VAAWLVESSQNLYMPAYYLMVIAVIGLLTGLF 438 LFPT IR + + +++ + G T VA W + Y +Y+ LL + Sbjct: 364 LFPTEIRAIGVGLPYALALSVFGGTAEYVALWFKKIGHEDYF-YWYVTACIACSLLVYIG 422 Query: 439 MKET 442 M++T Sbjct: 423 MRDT 426 Lambda K H 0.327 0.142 0.427 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: 504 Number of extensions: 24 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: 501 Length of database: 435 Length adjustment: 33 Effective length of query: 468 Effective length of database: 402 Effective search space: 188136 Effective search space used: 188136 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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