Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate H281DRAFT_00442 H281DRAFT_00442 MFS transporter, MHS family, proline/betaine transporter
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__Burk376:H281DRAFT_00442 Length = 489 Score = 503 bits (1295), Expect = e-147 Identities = 245/485 (50%), Positives = 347/485 (71%), Gaps = 10/485 (2%) Query: 6 KRVKPIALDDVTIIDDGRLRKAITAAALGNAMEWFDFGVYGFVAYALGQVFFPGADPGVQ 65 K+ + ++LDD+T++D+ L++A+ A ALGNAMEWFDFGVY ++A LG+VFFP + P Q Sbjct: 13 KQEQRLSLDDITVVDNSLLKRAVGAMALGNAMEWFDFGVYSYIAVTLGKVFFPSSSPSAQ 72 Query: 66 MIAALATFSVPFLIRPLGGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGI 125 +IA TF+ FL+RP+GG+ FG LGD+ GRQ++LA+T+I+M+I TF IGLIPSY IGI Sbjct: 73 LIATFGTFAAAFLVRPVGGMVFGPLGDRIGRQRVLAMTMIMMAIGTFAIGLIPSYGSIGI 132 Query: 126 WAPILLLLAKMAQGFSVGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVV 185 AP LLL+A++ QGFS GGEY GA+ F+AE+S D++RGFMGS+L+FG++ G+VLGAG V Sbjct: 133 LAPALLLVARLVQGFSTGGEYGGAATFIAEFSTDKRRGFMGSFLEFGTLIGYVLGAGTVA 192 Query: 186 LISTLIGEQAFLAWGWRLPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKA 245 +++ + A L+WGWR+PF +A PLGL+GLY+R LEETPAF++ E+ E D KA Sbjct: 193 VLTATLSNDALLSWGWRVPFLIAGPLGLVGLYIRMKLEETPAFKKQAEQREAED----KA 248 Query: 246 GPGVSFREIATHHWKSLLVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAI 305 P S R + WK LL+C+GLV+ NVT YM L+Y+PSYLS +LH++E+HG+ I++ + Sbjct: 249 VPKQSLRNLLMQQWKPLLLCVGLVLIFNVTDYMALSYLPSYLSATLHFNESHGLFIVLLV 308 Query: 306 MIGMLFVQPVMGLLSDRFGRKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVI 365 M+ M+ + G LSD GRKP ++ G V +F L++P+ +LI + +F GL++L V+ Sbjct: 309 MVLMMPMTLAAGRLSDTIGRKPVMLFGCVGLFALSIPALLLIRMGTLVPVFGGLMILGVL 368 Query: 366 LNAFTGVMASTLPALFPTHIRYSALASAFNISV-LIAGLTPTVAAWLVESSQNLYMPAYY 424 L+ FTGVM S LPALFPT IRY ALA FNISV L G TP V AWLV+ + NL MPAYY Sbjct: 369 LSCFTGVMPSALPALFPTKIRYGALAIGFNISVSLFGGTTPLVTAWLVDRTGNLMMPAYY 428 Query: 425 LMVIAVIGLLTGLFMKETANKPLKGATPAASDLSEAKEILQEHHDNIEHKIEDITQQIAE 484 LM ++IG+++ + ++ETA KPL G+ P + +EA +L+ E + E++ ++ A Sbjct: 429 LMGASLIGIVSVMALRETARKPLLGSGPCVATRAEAHAVLRG-----EREAEEMDERYAA 483 Query: 485 LEAKR 489 R Sbjct: 484 TATAR 488 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: 666 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: 489 Length adjustment: 34 Effective length of query: 467 Effective length of database: 455 Effective search space: 212485 Effective search space used: 212485 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: 52 (24.6 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