Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate PP_1298 PP_1298 putative amino acid ABC transporter - permease subunit
Query= TCDB::Q8YPM8 (308 letters) >FitnessBrowser__Putida:PP_1298 Length = 392 Score = 154 bits (389), Expect = 3e-42 Identities = 82/135 (60%), Positives = 99/135 (73%), Gaps = 1/135 (0%) Query: 175 PEFSALLLGLIFYTGAFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVI 234 PE AL L L YT AFIAEIVR GI+SVS GQ EA RSLGL +R VI PQALRVI Sbjct: 258 PELLALTLALTIYTAAFIAEIVRSGIRSVSHGQTEAARSLGLREGPTLRKVIIPQALRVI 317 Query: 235 IPPLTSQYLNLTKNSSLAIAIGYPD-IYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTIS 293 IPPLTSQYLNL KNSSLA IGYP+ + A T NQTG+A+EV+ + M YL++S++IS Sbjct: 318 IPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISIS 377 Query: 294 LIMNAFNRTVQIKER 308 L+MN +N+ + + ER Sbjct: 378 LLMNWYNKRIALIER 392 Score = 141 bits (355), Expect = 3e-38 Identities = 76/180 (42%), Positives = 106/180 (58%), Gaps = 4/180 (2%) Query: 21 LIALFLAAFVVAI---LLGNLNRNLQRLGIQFGFDFLKQQASFDIGETLIAYKPTDTYSL 77 L + FVV + L N NLQ GI GFDFL + A F I + LI Y +D+Y+ Sbjct: 22 LFQILTIVFVVGLGWYLFHNTQTNLQHRGITSGFDFLDRSAGFGIAQHLIPYVESDSYAR 81 Query: 78 ALWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLF 137 +GL+N+L + F+G+IL TI+G + G+ARLS NW++ ++ VYVE FRN P LLQ+LF Sbjct: 82 VFVIGLLNTLLVTFIGVILATILGFIIGVARLSPNWMINKLATVYVETFRNIPPLLQILF 141 Query: 138 WYFAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYTGAFIAEIVR 197 WYFAVFL LP I++ +S GL +P + + F ++ L A IA +VR Sbjct: 142 WYFAVFLTLPGPRGSINIEDMFFISNRGLNMPGASIADGFWPFVVALALAIAA-IALMVR 200 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: 348 Number of extensions: 22 Number of successful extensions: 3 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: 392 Length adjustment: 29 Effective length of query: 279 Effective length of database: 363 Effective search space: 101277 Effective search space used: 101277 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 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