Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate Pf1N1B4_916 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
Query= TCDB::Q8YPM8 (308 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_916 Length = 375 Score = 151 bits (382), Expect = 2e-41 Identities = 81/135 (60%), Positives = 98/135 (72%), Gaps = 1/135 (0%) Query: 175 PEFSALLLGLIFYTGAFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVI 234 PE AL L L YT AFIAEIVR GI+SVS GQ EA SLGL +R VI PQALRVI Sbjct: 241 PELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAAHSLGLRNGPTLRKVIIPQALRVI 300 Query: 235 IPPLTSQYLNLTKNSSLAIAIGYPD-IYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTIS 293 IPPLTSQYLNL KNSSLA IGYP+ + A T NQTG+A+EV+ + M YL++S++IS Sbjct: 301 IPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISIS 360 Query: 294 LIMNAFNRTVQIKER 308 L+MN +N+ + + ER Sbjct: 361 LLMNWYNKRIALIER 375 Score = 140 bits (354), Expect = 4e-38 Identities = 80/195 (41%), Positives = 110/195 (56%), Gaps = 17/195 (8%) Query: 24 LFLAAFVVAI------LLGNLNRNLQRLGIQFGFDFLKQQASFDIGETLIAYKPTDTYSL 77 LF VVA+ L N NLQ GI GFDFL++ A F I + LI Y +D+Y+ Sbjct: 5 LFQIITVVAVVGMGWYLFDNTQTNLQHRGITSGFDFLERSAGFGIAQHLIDYTESDSYAR 64 Query: 78 ALWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLF 137 +GL+N+L + F+G+IL TI+G + G+ARLS NW++ ++ VYVE+FRN P LLQ+LF Sbjct: 65 VFVIGLLNTLLVTFIGVILATILGFIVGVARLSKNWIIAKLATVYVEVFRNIPPLLQILF 124 Query: 138 WYFAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYTGAFIAEIVR 197 WYFAVFL +P N + G +S GL +P A L F+ F+A IV Sbjct: 125 WYFAVFLTMPGPRNSHNFGDTFFVSSRGLNMP---------AALAADGFW--PFVASIVV 173 Query: 198 GGIQSVSKGQWEAGR 212 + V +W R Sbjct: 174 AIVAIVLMSRWATKR 188 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: 332 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: 375 Length adjustment: 28 Effective length of query: 280 Effective length of database: 347 Effective search space: 97160 Effective search space used: 97160 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