Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate SMc03865 SMc03865 amino-acid transport system permease ABC transporter protein
Query= TCDB::Q8YPM8 (308 letters) >FitnessBrowser__Smeli:SMc03865 Length = 273 Score = 117 bits (292), Expect = 4e-31 Identities = 75/227 (33%), Positives = 129/227 (56%), Gaps = 11/227 (4%) Query: 82 GLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLFWYFA 141 GL ++ + VG +L T++G+ + LS++ ++R I+ Y E+ R P+L+ L ++ Sbjct: 49 GLGVTVFVTLVGFVLATVLGLGVALMALSEHVVLRQIARFYTEVIRGVPILVLL---FYI 105 Query: 142 VFLGLPRADNKISLGGFIG--LSQNGLELPWFT--FSPEFSALLLGLIFYTGAFIAEIVR 197 F+G P +++ F+ L G P+ S + A++ +I Y+ AFIAE+ R Sbjct: 106 AFVGAPAL---VTVANFVAAPLISAGWIEPFVVRDVSLMWRAIMALMIGYS-AFIAEVFR 161 Query: 198 GGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNSSLAIAIGY 257 GIQSV KGQ EA ++LGL+ RLV+FPQA+RVI+PPL + ++ + K+SSL +G Sbjct: 162 AGIQSVDKGQVEAAKALGLSRYQRFRLVVFPQAIRVILPPLGNDFVAMVKDSSLVSVLGV 221 Query: 258 PDIYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIMNAFNRTVQ 304 DI + + + + E ++ YL L++ +SL + A R ++ Sbjct: 222 ADITQMGKVYASGSFRFFETYSIVAYVYLVLTIGLSLALRAVERRLR 268 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: 194 Number of extensions: 7 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: 273 Length adjustment: 26 Effective length of query: 282 Effective length of database: 247 Effective search space: 69654 Effective search space used: 69654 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