Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate GFF355 PS417_01810 ABC transporter permease
Query= TCDB::Q8YPM8 (308 letters) >FitnessBrowser__WCS417:GFF355 Length = 319 Score = 126 bits (317), Expect = 6e-34 Identities = 77/223 (34%), Positives = 122/223 (54%), Gaps = 27/223 (12%) Query: 79 LWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLFW 138 +W GL +L ++ V IL I+G+ G+ RLS N +R++S +YVE+ R TPLL+Q+ + Sbjct: 118 MW-GLWTTLWLSVVSGILGLIIGLATGLCRLSSNPTLRDLSTIYVELVRGTPLLVQIFIF 176 Query: 139 YFAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYTGAFIAEIVRG 198 YF FIG N S EF+ + L +TGA++AEIVR Sbjct: 177 YF-----------------FIGTVLN--------LSREFAGIA-ALSLFTGAYVAEIVRA 210 Query: 199 GIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNSSLAIAIGYP 258 G+QS+++GQ EA RSLGL+ S MR V+ PQA + ++PPL Q+++L K++SL I Sbjct: 211 GVQSITRGQNEAARSLGLSASQSMRHVVLPQAFKRVLPPLAGQFISLVKDTSLVSVIAIT 270 Query: 259 DIYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIMNAFNR 301 ++ + E++ + YL ++L +S + + R Sbjct: 271 ELLKSGREVITTSFSPFEILFCVAGLYLLINLPLSKMASRLER 313 Lambda K H 0.328 0.143 0.430 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: 245 Number of extensions: 16 Number of successful extensions: 2 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: 308 Length of database: 319 Length adjustment: 27 Effective length of query: 281 Effective length of database: 292 Effective search space: 82052 Effective search space used: 82052 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: 48 (23.1 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