Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate WP_017597434.1 D471_RS0103990 MFS transporter
Query= SwissProt::Q47421 (501 letters) >NCBI__GCF_000341125.1:WP_017597434.1 Length = 433 Score = 243 bits (619), Expect = 1e-68 Identities = 144/418 (34%), Positives = 229/418 (54%), Gaps = 19/418 (4%) Query: 23 RLRKAITAAALGNAMEWFDFGVYGFVA-YALGQVFFPG-ADPGVQMIAALATFSVPFLIR 80 R +A AA +G +EWFDF VY A G +FFPG DP V ++A+ ATF+V F R Sbjct: 11 RPARAAVAAFVGTTIEWFDFYVYATAAGLVFGTLFFPGDIDPMVGLMASFATFAVGFFAR 70 Query: 81 PLGGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGF 140 PLGGV FG GD+ GR+ L T+++M ++TFC+GL+P+Y ++G AP+LL++ + QG Sbjct: 71 PLGGVVFGHFGDRLGRKSALVTTLLMMGVATFCVGLLPTYAQVGFVAPLLLVVLRFVQGI 130 Query: 141 SVGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWG 200 +VGGE+ GA + E +P+ ++ F GS+ G+ AG +L G LI T WG Sbjct: 131 AVGGEWGGAVLMAVESAPEERKTFYGSFAQLGNPAGALLATGSFGLI-TAWDSDLLYTWG 189 Query: 201 WRLPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGP-GVSFREIATHHW 259 WRLPF + L L+GL +R +EE+P F + R+ A P G RE W Sbjct: 190 WRLPFLASCLLVLVGLVVRLKVEESPVF--------EAARENRAAEPEGPPLRETLRTSW 241 Query: 260 KSLLVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGM---LFVQPVM 316 +++L+ IG++ YY++ T++ +Y SE LI+ + + LF Sbjct: 242 RAVLLGIGVLPVAVGGYYVVTTFLQAYGVTEAGISEQ---LILSGLTLAAFVELFATLAT 298 Query: 317 GLLSDRFGRKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVILNAFTGVMAST 376 L DRFG V +G A+ LA+P F+++ + LI L L ++ V + A G +A Sbjct: 299 AWLGDRFGTARIVTVGLAAVAVLALPQFLVLETGSAVLIVLMLCLMRVAMAAVYGPIARV 358 Query: 377 LPALFPTHIRYSALASAFNIS-VLIAGLTPTVAAWLVESSQNLYMPAYYLMVIAVIGL 433 L ++P +RY+ ++ ++ ++ L GL+P L + ++ A L+V+A++ + Sbjct: 359 LAQMYPPRVRYTGISVSYQVAGALFGGLSPLACTALFALTGSILSVAVLLVVMALVSI 416 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: 480 Number of extensions: 29 Number of successful extensions: 5 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: 433 Length adjustment: 33 Effective length of query: 468 Effective length of database: 400 Effective search space: 187200 Effective search space used: 187200 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 Apr 09 2024. 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