Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate PfGW456L13_4771 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
Query= TCDB::Q8YPM8 (308 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4771 Length = 248 Score = 119 bits (299), Expect = 6e-32 Identities = 81/239 (33%), Positives = 122/239 (51%), Gaps = 22/239 (9%) Query: 72 TDTYSLALWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPL 131 ++TY GL ++ IA I+ +G + G+ R N +V I+ YVE+FRN PL Sbjct: 18 SETYFDWYVTGLAWTIGIAIAAWIIALTLGSILGVMRTVPNRIVSGIATCYVELFRNVPL 77 Query: 132 LLQLLFWYFAVFLGLPRADNKISLGGFIGLSQNGLELPWFT--FSPEFSALLLGLI---F 186 L+QL WYF V LP AD + W+ +P SA L ++ Sbjct: 78 LVQLFIWYFLVPDLLP-ADLQ----------------EWYKQDLNPTTSAFLSVVVCLGL 120 Query: 187 YTGAFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLT 246 +T A + E VR GIQ++ KGQ A R++G I V+ PQA R+IIPPLTS++LN+ Sbjct: 121 FTTARVCEQVRTGIQALPKGQESAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVF 180 Query: 247 KNSSLAIAIGYPDIYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIMNAFNRTVQI 305 KN+S+A IG ++ T + E L L Y +L++++ L+M + V + Sbjct: 181 KNTSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRVVEKKVAV 239 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: 208 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: 248 Length adjustment: 25 Effective length of query: 283 Effective length of database: 223 Effective search space: 63109 Effective search space used: 63109 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