Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate WP_057507667.1 ABB28_RS05485 proline/glycine betaine transporter ProP
Query= SwissProt::Q47421 (501 letters) >NCBI__GCF_001431535.1:WP_057507667.1 Length = 495 Score = 514 bits (1324), Expect = e-150 Identities = 254/461 (55%), Positives = 340/461 (73%), Gaps = 7/461 (1%) Query: 6 KRVKPIALDDVTIIDDGRLRKAITAAALGNAMEWFDFGVYGFVAYALGQVFFPGADPGVQ 65 KR + + ++++T++D LR+A+ AAALGNAMEWFDFGVYG++A LGQVFFP ++P Q Sbjct: 15 KRRRQMDVEEITVVDKPMLRRAVGAAALGNAMEWFDFGVYGYLAVTLGQVFFPASNPTAQ 74 Query: 66 MIAALATFSVPFLIRPLGGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGI 125 +IA ATF+V FL+RPLGG+ FG LGD+YGRQK+LA T+I+M++ TF IGLIPSYERIGI Sbjct: 75 LIATFATFTVAFLVRPLGGLVFGPLGDRYGRQKVLAFTMILMALGTFSIGLIPSYERIGI 134 Query: 126 WAPILLLLAKMAQGFSVGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVV 185 WAP+LLLLA++ QGFS GGEY GA+ F+AEY+ DR RG MGSWL+FG++ G++ GA V Sbjct: 135 WAPVLLLLARLVQGFSTGGEYGGAATFIAEYATDRNRGLMGSWLEFGTLGGYIAGAATVT 194 Query: 186 LISTLIGEQAFLAWGWRLPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKA 245 + L+ L WGWR+PF +A PLGL+GLY+R LEETPAFR + E+ + D + Sbjct: 195 TLHLLLSGAQMLDWGWRIPFLVAGPLGLLGLYMRMRLEETPAFRAYAEEAAKRDHE---- 250 Query: 246 GPGVSFREIATHHWKSLLVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAI 305 PG+ E+ H + LL+C+GLV+ NVT YMLLTYMPSYL+ +L Y+E+ G+L+II + Sbjct: 251 RPGLG--ELLRVHGRQLLICMGLVLVFNVTDYMLLTYMPSYLTVTLGYAESKGLLLIIIV 308 Query: 306 MIGMLFVQPVMGLLSDRFGRKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVI 365 M+ M+ + V GL SDR GR+P ++ +A+ LA+P +L+ S GLIFLGL++L + Sbjct: 309 MLVMMPLNIVGGLFSDRLGRRPMIIGACIALLLLAIPCLLLVRSGEDGLIFLGLMLLGIA 368 Query: 366 LNAFTGVMASTLPALFPTHIRYSALASAFNISV-LIAGLTPTVAAWLVESSQNLYMPAYY 424 L FT M STLPALF T +RYSAL+ AFN+SV L G TP V AWLVE S + +PAYY Sbjct: 369 LVCFTSSMPSTLPALFYTPVRYSALSIAFNVSVSLFGGTTPLVTAWLVERSGDPMVPAYY 428 Query: 425 LMVIAVIGLLTGLFMKETANKPLKGATPAASDLSEAKEILQ 465 LM AVIGL+T LF++ETA PL+G+ PA + EA+ +L+ Sbjct: 429 LMGAAVIGLVTMLFVRETAGLPLRGSPPAVASDQEARALLR 469 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: 705 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: 501 Length of database: 495 Length adjustment: 34 Effective length of query: 467 Effective length of database: 461 Effective search space: 215287 Effective search space used: 215287 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 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