Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate WP_086509148.1 BZY95_RS06445 amino acid ABC transporter permease
Query= TCDB::Q8YPM8 (308 letters) >NCBI__GCF_002151265.1:WP_086509148.1 Length = 396 Score = 157 bits (397), Expect = 4e-43 Identities = 84/138 (60%), Positives = 101/138 (73%), Gaps = 1/138 (0%) Query: 172 TFSPEFSALLLGLIFYTGAFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQAL 231 T PEF AL L L YT +FIAEIVR GIQ++ GQ EA ++L L L++RLV+ PQAL Sbjct: 259 TIIPEFLALWLALSIYTASFIAEIVRSGIQAIPHGQTEAAQALSLPQKLVLRLVVVPQAL 318 Query: 232 RVIIPPLTSQYLNLTKNSSLAIAIGYPDIYFV-ASTTFNQTGKAVEVMLLLMLTYLSLSL 290 RVIIPPLTSQYLNL KNSSLA AIGYPD+ V A TT NQTG+A+EV+ + M YL +SL Sbjct: 319 RVIIPPLTSQYLNLIKNSSLATAIGYPDLVSVFAGTTLNQTGQAIEVISMTMAVYLIISL 378 Query: 291 TISLIMNAFNRTVQIKER 308 +S+ MN FN V + ER Sbjct: 379 LVSMFMNWFNARVALVER 396 Score = 153 bits (387), Expect = 6e-42 Identities = 81/192 (42%), Positives = 111/192 (57%) Query: 5 KPPFWRDNRFWYIAGQLIALFLAAFVVAILLGNLNRNLQRLGIQFGFDFLKQQASFDIGE 64 KPPFWRD + Q++ + A + ++GN NL GI GF FL + A F IG+ Sbjct: 13 KPPFWRDRAKRALLFQVLLIAAVAAFLLYIIGNTQDNLAARGITTGFGFLDRTAGFGIGQ 72 Query: 65 TLIAYKPTDTYSLALWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVE 124 +LI Y TY VGL+N+L ++ +G+I TI+G + GIARLS NWL+ ++ Y+E Sbjct: 73 SLIEYSSQSTYGRTFVVGLLNTLLVSALGVIAATIIGFIVGIARLSPNWLIARLASGYIE 132 Query: 125 IFRNTPLLLQLLFWYFAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGL 184 IFRN PLLLQ+ FWYFAV +P A + SLG I L+ GL LP F F + L Sbjct: 133 IFRNIPLLLQIFFWYFAVLRAMPAARDSYSLGEVIFLNVRGLYLPEPLFESGFGLIPLTF 192 Query: 185 IFYTGAFIAEIV 196 + A IA ++ Sbjct: 193 VVAIVASIALVI 204 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: 344 Number of extensions: 19 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: 396 Length adjustment: 29 Effective length of query: 279 Effective length of database: 367 Effective search space: 102393 Effective search space used: 102393 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