Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate WP_011317597.1 AVA_RS03730 amino acid ABC transporter permease
Query= TCDB::Q8YPM8 (308 letters) >NCBI__GCF_000204075.1:WP_011317597.1 Length = 381 Score = 112 bits (280), Expect = 1e-29 Identities = 73/229 (31%), Positives = 121/229 (52%), Gaps = 31/229 (13%) Query: 79 LWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLFW 138 LW GL+ +L +A + I+L+ +G+L + R S+ +VR S++Y+EI R PL+ Sbjct: 174 LWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIIRGVPLI------ 227 Query: 139 YFAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALL---LGLIFYTGAFIAEI 195 G + L+Q L L +F +L GL+ ++ A++AE Sbjct: 228 ------------------GILFLAQVMLPL-FFAADVRLDRVLRAIAGLVLFSAAYMAEN 268 Query: 196 VRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNSSLAIAI 255 VRGG+Q+VS+GQ EA ++LGLN ++ L++ PQALR +IP + Q++ L K++SL + Sbjct: 269 VRGGLQAVSRGQVEAAKALGLNTFFVVLLIVLPQALRAVIPAVVGQFIGLFKDTSLLSLV 328 Query: 256 GYPDIYFVASTTFNQ---TGKAVEVMLLLMLTYLSLSLTISLIMNAFNR 301 G ++ +A + Q G+ EV L + L Y ++SL R Sbjct: 329 GLVELTGIARSILAQPQFIGRYAEVYLFIGLIYWLFCYSMSLASRRLER 377 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: 369 Number of extensions: 21 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: 381 Length adjustment: 29 Effective length of query: 279 Effective length of database: 352 Effective search space: 98208 Effective search space used: 98208 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 Sep 24 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