Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 1936976 b3269 predicted amino-acid transporter subunit (NCBI)
Query= TCDB::Q8YPM8 (308 letters) >FitnessBrowser__Keio:1936976 Length = 393 Score = 159 bits (402), Expect = 1e-43 Identities = 101/226 (44%), Positives = 131/226 (57%), Gaps = 22/226 (9%) Query: 91 FVGIILTTIVGIL--AGIARLSDNWLVRNISL-----VYVEIFRNTPLLLQLLFWYFAVF 143 F+ IL ++ I+ G+ R + + ++ L + + PLL Q LF A+ Sbjct: 182 FIAFILAVVMAIVLSVGLFRFNKTYQIKTGQLRRTWPIAAVLIIGLPLLAQWLFGA-ALH 240 Query: 144 LGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYTGAFIAEIVRGGIQSV 203 +P GG + + PE +AL L L YT AFIAEI+R GIQ+V Sbjct: 241 WDVPALRGFNFRGGMVLI-------------PELAALTLALSVYTSAFIAEIIRAGIQAV 287 Query: 204 SKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNSSLAIAIGYPD-IYF 262 GQ EA RSLGL + +R VI PQALRVIIPPLTSQYLN+ KNSSLA AIGYPD + Sbjct: 288 PYGQHEAARSLGLPNPVTLRQVIIPQALRVIIPPLTSQYLNIVKNSSLAAAIGYPDMVSL 347 Query: 263 VASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIMNAFNRTVQIKER 308 A T NQTG+A+E + + M YL +SLTISL+MN +NR + I ER Sbjct: 348 FAGTVLNQTGQAIETIAMTMSVYLIISLTISLLMNIYNRRIAIVER 393 Score = 126 bits (316), Expect = 9e-34 Identities = 67/166 (40%), Positives = 94/166 (56%) Query: 20 QLIALFLAAFVVAILLGNLNRNLQRLGIQFGFDFLKQQASFDIGETLIAYKPTDTYSLAL 79 Q++A+ +V L N NL GI GF FL + A F I + LI Y+ DTY Sbjct: 25 QILAVVAVVGIVGWLFHNTVTNLNNRGITSGFAFLDRGAGFGIVQHLIDYQQGDTYGRVF 84 Query: 80 WVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLFWY 139 VGL+N+L ++ + I+ +++G G+ARLSDNWL+R +S +Y+EIFRN P LLQ+ FWY Sbjct: 85 IVGLLNTLLVSALCIVFASVLGFFIGLARLSDNWLLRKLSTIYIEIFRNIPPLLQIFFWY 144 Query: 140 FAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLI 185 FAV LP +S LS GL +P F A +L ++ Sbjct: 145 FAVLRNLPGPRQAVSAFDLAFLSNRGLYIPSPQLGDGFIAFILAVV 190 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: 338 Number of extensions: 16 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: 393 Length adjustment: 29 Effective length of query: 279 Effective length of database: 364 Effective search space: 101556 Effective search space used: 101556 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