Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 207828 DVU2341 amino acid ABC transproter, permease protein, His/Glu/Gln/Arg/opine family
Query= TCDB::Q8YPM8 (308 letters) >MicrobesOnline__882:207828 Length = 233 Score = 138 bits (347), Expect = 1e-37 Identities = 83/224 (37%), Positives = 125/224 (55%), Gaps = 20/224 (8%) Query: 80 WV--GLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLF 137 W+ G+I + +++ + ++L ++G L + RLS S+ + E FRNTPLL+Q+ F Sbjct: 18 WIVQGVITTCQLSGLSLVLAMLLGTLIAVMRLSGVRPFVWFSVAFTEFFRNTPLLVQIFF 77 Query: 138 WYFAVFLGLPRADNKISLGGFIGLSQNGLELPW-FTFSPEFSALLLGLIFYTGAFIAEIV 196 WYF LP A N+ W + + EF+A ++ L YT AFIAE + Sbjct: 78 WYFGSDAVLPDAVNQ-----------------WLYKQNFEFAAGVISLTVYTAAFIAEEI 120 Query: 197 RGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNSSLAIAIG 256 R GI S+ + Q EA R+ GL+ M V+ PQA R+I+PPL SQ LNL KNSSL + IG Sbjct: 121 RSGIFSIPRTQLEASRACGLSFMQAMSYVVLPQAFRIIVPPLISQALNLFKNSSLCMTIG 180 Query: 257 YPDIYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIMNAFN 300 ++ ++A + T E + L YL +SL +SL++N +N Sbjct: 181 VMELTYMARQIESYTFHGFEAFTVSTLIYLCISLMVSLLINLYN 224 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: 162 Number of extensions: 9 Number of successful extensions: 3 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: 233 Length adjustment: 25 Effective length of query: 283 Effective length of database: 208 Effective search space: 58864 Effective search space used: 58864 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: 47 (22.7 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