Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 16032 b1918 predicted transporter subunit: membrane component of ABC superfamily (NCBI)
Query= TCDB::Q8YPM8 (308 letters) >FitnessBrowser__Keio:16032 Length = 222 Score = 122 bits (306), Expect = 8e-33 Identities = 71/223 (31%), Positives = 115/223 (51%), Gaps = 25/223 (11%) Query: 86 SLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLFWYFAVFLG 145 +L+++ G+ ++G + + RLS W VR ++ Y+ IFR TPL+ QL Y+ Sbjct: 22 TLQLSIGGMFFGLLLGFILALMRLSPIWPVRWLARFYISIFRGTPLIAQLFMIYY----- 76 Query: 146 LPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYTGAFIAEIVRGGIQSVSK 205 GL Q G+EL + ++GL T A+ AE +R I S+ K Sbjct: 77 --------------GLPQFGIELD------PIPSAMIGLSLNTAAYAAETLRAAISSIDK 116 Query: 206 GQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNSSLAIAIGYPDIYFVAS 265 GQWEA S+G+ P MR I PQA RV +PPL++ +++L K++SLA I P+++ A Sbjct: 117 GQWEAAASIGMTPWQTMRRAILPQAARVALPPLSNSFISLVKDTSLAATIQVPELFRQAQ 176 Query: 266 TTFNQTGKAVEVMLLLMLTYLSLSLTISLIMNAFNRTVQIKER 308 ++T + + L L Y ++ +S + N F + +ER Sbjct: 177 LITSRTLEVFTMYLAASLIYWIMATVLSTLQNHFENQLNRQER 219 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: 170 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 308 Length of database: 222 Length adjustment: 25 Effective length of query: 283 Effective length of database: 197 Effective search space: 55751 Effective search space used: 55751 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: 47 (22.7 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