Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate AZOBR_RS08660 AZOBR_RS08660 ABC transporter permease
Query= TCDB::Q8YPM8 (308 letters) >FitnessBrowser__azobra:AZOBR_RS08660 Length = 399 Score = 224 bits (570), Expect = 3e-63 Identities = 147/372 (39%), Positives = 203/372 (54%), Gaps = 86/372 (23%) Query: 23 ALFLAAFVVAI-------LLGNLNRNLQRLGIQFGFDFLKQQASFDIGETLIAYKPTDTY 75 A+F VV I L+ N NL + I GF FL ++ASF IGE+LI Y P D+Y Sbjct: 28 AVFYQVLVVGIVIAVGWFLIHNTLDNLSKRSIATGFGFLDREASFGIGESLIDYHPRDSY 87 Query: 76 SLALWVGLINSLRIAFVGIILTTIVGILAGIARLSDNW-----------LVRNISLV--- 121 A VG++N+L+++ +G++L T++G L G+ARLS NW +VRNI + Sbjct: 88 GRAFLVGVLNTLKVSIIGVVLATVLGTLIGVARLSSNWLIAKLASTYVEIVRNIPPLLQL 147 Query: 122 ---YVEIFRNTPLLLQLLFWYFAVFLG-------LPRAD--------------------- 150 Y + + P + Q L VFL +P AD Sbjct: 148 FFWYALVSESMPPVRQALNPIPGVFLSQRGLFVPVPSADPVWGTMGFALAIAVIGVIFLR 207 Query: 151 ----------------NKISLGGFIGL---------SQNGLELP---WFTF------SPE 176 SL IGL + L++P F F +PE Sbjct: 208 RWAKARQERTGQPFPIGTASLSLLIGLPLIAYIAGGAPTALDVPKLQGFNFVGGVVLTPE 267 Query: 177 FSALLLGLIFYTGAFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIP 236 F A+L+GL+ YT AFIAE+VR GI +V+ GQ EA R+LG++ +RLV+ PQALRVI+P Sbjct: 268 FFAILVGLVVYTAAFIAEVVRSGILAVNWGQTEAARALGIDSGKTLRLVVLPQALRVIVP 327 Query: 237 PLTSQYLNLTKNSSLAIAIGYPDIYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIM 296 PLTSQYLNLTKNSSLA+AIGYPD+ +A+TT NQTG+A+E + ++M TYL +SL IS+ M Sbjct: 328 PLTSQYLNLTKNSSLALAIGYPDLVSIANTTLNQTGQAIEGVAMIMGTYLVISLGISIFM 387 Query: 297 NAFNRTVQIKER 308 N +N+ + + ER Sbjct: 388 NWYNKRIALVER 399 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: 358 Number of extensions: 12 Number of successful extensions: 2 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: 399 Length adjustment: 29 Effective length of query: 279 Effective length of database: 370 Effective search space: 103230 Effective search space used: 103230 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