Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit
Query= TCDB::Q8YPM8 (308 letters) >NCBI__GCF_000016765.1:WP_012048835.1 Length = 374 Score = 148 bits (373), Expect = 2e-40 Identities = 70/133 (52%), Positives = 96/133 (72%) Query: 172 TFSPEFSALLLGLIFYTGAFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQAL 231 T +PEF A+L G + Y AF AEIVRGG+ V +GQWEA R+LGL+ +RLVI PQAL Sbjct: 238 TLTPEFVAVLWGSVIYASAFAAEIVRGGLDGVPRGQWEASRALGLSKRQSLRLVIVPQAL 297 Query: 232 RVIIPPLTSQYLNLTKNSSLAIAIGYPDIYFVASTTFNQTGKAVEVMLLLMLTYLSLSLT 291 R+I+PP+ SQ++ + KNS+LA+ +GYPD+ FVA+T N TG+ +E + +LML + +L+ Sbjct: 298 RMIVPPMNSQFITILKNSTLALVVGYPDLNFVANTAINHTGQGLEGVAILMLVFFTLASA 357 Query: 292 ISLIMNAFNRTVQ 304 ISL MN N VQ Sbjct: 358 ISLAMNRLNARVQ 370 Score = 90.1 bits (222), Expect = 7e-23 Identities = 46/135 (34%), Positives = 79/135 (58%), Gaps = 1/135 (0%) Query: 15 WYIAGQLIALFLAAFVVAILLGNLNRNLQRLGIQFGFDFLKQQASFDIGETLIAYKPTDT 74 W++ + L LA V+ ++ ++ N++R + FL+ A F I E+ +AY P DT Sbjct: 12 WWLPQVALLLALAGLVL-VVARTVSDNMERQDMVLSLGFLRSTAEFPIAESFLAYAPGDT 70 Query: 75 YSLALWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQ 134 + A VGL NS+ + + I+L+T+ G+ +AR S + L R ++ +V++ RN PL++Q Sbjct: 71 IAWAFVVGLGNSIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRNVPLVVQ 130 Query: 135 LLFWYFAVFLGLPRA 149 LLFWY + + P A Sbjct: 131 LLFWYGVILMAFPPA 145 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: 291 Number of extensions: 15 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 308 Length of database: 374 Length adjustment: 28 Effective length of query: 280 Effective length of database: 346 Effective search space: 96880 Effective search space used: 96880 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: 49 (23.5 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