Align Possible transporter of polar amino acids including glutamate, glutamine and aspartate, DmeA. It complements a sepJ mutation in Anabaena (TC# 2.A.7.23.2), and SepJ complements a dmeA mutation. Alternatively, and less likely, it could be an activator of an ABC transporter catalyzing uptake of these amino acids (characterized)
to candidate SMa1945 SMa1945 hypothetical protein
Query= TCDB::Q31PG5 (330 letters) >FitnessBrowser__Smeli:SMa1945 Length = 286 Score = 78.2 bits (191), Expect = 2e-19 Identities = 57/188 (30%), Positives = 87/188 (46%), Gaps = 6/188 (3%) Query: 12 AGLPLK-FPVSLQLAIATALWGGTFTAGRIAVQQLSPLAVACGRYLLATTVLLL-ILWQR 69 A +P+ F +L +A W +F A A++++ PL +A R+ LA + I W+R Sbjct: 23 ADIPMTPFLPALAIAGTVITWSFSFAAIGYALREVEPLPLAAIRFALAAVFAIAWIAWRR 82 Query: 70 EGWPPLNRRQQLLLFGLGVSGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWT 129 W R ++L G+ GIA YN L +G + + A A I+ P + L A ++ Sbjct: 83 PRW--FLPRDFVVLAISGLLGIAAYNVLLNLGQAAVSAGAAGFIVNTQPLFMVLLAVLFL 140 Query: 130 GDRLRSWQWAGVGLSLIGAILLLGSRQAGALTLPGWGDLALVGCVLCWTVYSLLARQALR 189 +R W W G + G + L+ S Q G L+ G G +V C YS+L R Sbjct: 141 KERFGRWNWVGTIVGFSG-VALIASGQPGGLSF-GTGSTLIVLAAACAAAYSILQRPLFA 198 Query: 190 SLSPLTVT 197 PL VT Sbjct: 199 RAEPLDVT 206 Lambda K H 0.325 0.142 0.454 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: 229 Number of extensions: 18 Number of successful extensions: 1 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: 330 Length of database: 286 Length adjustment: 27 Effective length of query: 303 Effective length of database: 259 Effective search space: 78477 Effective search space used: 78477 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 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