Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate AZOBR_RS27070 AZOBR_RS27070 ABC transporter permease
Query= TCDB::Q8YPM8 (308 letters) >FitnessBrowser__azobra:AZOBR_RS27070 Length = 220 Score = 121 bits (303), Expect = 2e-32 Identities = 70/223 (31%), Positives = 125/223 (56%), Gaps = 24/223 (10%) Query: 82 GLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLFWYFA 141 G + ++ + ++L ++G++ G+A+LS ++R IS Y+E+FR TPLL+QLL++Y+A Sbjct: 19 GTLVTIGLTAAVVVLGLLLGLVGGLAQLSRFAVLRWISWAYIELFRCTPLLVQLLWFYYA 78 Query: 142 VFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYTGAFIAEIVRGGIQ 201 LP G+++ T S +L L Y G+F AE++RGG+ Sbjct: 79 ----LPML--------------TGIQIDAVTAS------VLTLSLYGGSFYAEVIRGGVV 114 Query: 202 SVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNSSLAIAIGYPDIY 261 S+ GQ EAG +LG+ P+ +MR ++ PQA++ +IPPL +Q + KN+SL + PD+ Sbjct: 115 SIEAGQTEAGLALGMTPAKVMRRIVLPQAVKRMIPPLMNQSIIQFKNTSLVSVVAVPDLL 174 Query: 262 FVASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIMNAFNRTVQ 304 + T + +EV ++ L Y + + ++ I+ + +Q Sbjct: 175 YQGQVAATDTFRPLEVYTIVALIYFVVLVPLTAIVKRGEKQLQ 217 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: 182 Number of extensions: 11 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: 220 Length adjustment: 24 Effective length of query: 284 Effective length of database: 196 Effective search space: 55664 Effective search space used: 55664 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