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 WP_051305349.1 G494_RS0103735 EamA/RhaT family transporter
Query= TCDB::Q31PG5 (330 letters) >NCBI__GCF_000429965.1:WP_051305349.1 Length = 299 Score = 115 bits (289), Expect = 1e-30 Identities = 86/277 (31%), Positives = 132/277 (47%), Gaps = 2/277 (0%) Query: 21 SLQLAIATALWGGTFTAGRIAVQQLSPLAVACGRYLLATTVLLLILWQREGWPPLNRRQQ 80 +L + A ALWG +F A + + +L+PL V GR L+A+ L L PL R Sbjct: 11 TLAMLTAMALWGSSFVAMKYSFFELNPLVVVLGRLLVASLCFLPFLGAFVK-VPLRRHHL 69 Query: 81 LLLFGLGVSGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRLRSWQWAG 140 L + G+ + LY L AS+A++I + P +AL A ++ G+ + G Sbjct: 70 LPMLGMALCEPCLYFLFEAAALQQTSASQASMITTMLPLLVALTAGLFLGEHVSGKTILG 129 Query: 141 VGLSLIGAI-LLLGSRQAGALTLPGWGDLALVGCVLCWTVYSLLARQALRSLSPLTVTTG 199 L+ +GA+ L P G+ ++C T Y +L + R L P +T Sbjct: 130 FFLAALGALWLTFAGTSTEQAPNPVLGNFLEFMAMVCATGYIILMKYLSRDLPPFFLTAV 189 Query: 200 ACCWGSVLLIGLWLGQGAQLPVNVSFSTGSAIAFLGLGGTALAFCLYANGIERLGAARAG 259 C G++ + + L +LP + S + I +LG + A+ LY GI R+ A++A Sbjct: 190 QCFVGALFFLPVLLLPQVELPSTLPLSGLTIILYLGTFVSVGAYGLYNFGISRIPASQAS 249 Query: 260 LFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGV 296 FINL+PVF +G L L E LS LL +LV GV Sbjct: 250 SFINLIPVFSVVLGFLCLGERLSFWQLLASVLVFCGV 286 Score = 35.8 bits (81), Expect = 1e-06 Identities = 31/92 (33%), Positives = 42/92 (45%), Gaps = 6/92 (6%) Query: 61 VLLLILWQREGWPPLNRRQQLLLFG--LGVSGIALYNWLFFIGLSLIPASRAALIIALNP 118 VLLL + PL+ +L G + V LYN+ G+S IPAS+A+ I L P Sbjct: 201 VLLLPQVELPSTLPLSGLTIILYLGTFVSVGAYGLYNF----GISRIPASQASSFINLIP 256 Query: 119 TAIALGAAIWTGDRLRSWQWAGVGLSLIGAIL 150 + + G+RL WQ L G IL Sbjct: 257 VFSVVLGFLCLGERLSFWQLLASVLVFCGVIL 288 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: 261 Number of extensions: 11 Number of successful extensions: 4 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: 330 Length of database: 299 Length adjustment: 27 Effective length of query: 303 Effective length of database: 272 Effective search space: 82416 Effective search space used: 82416 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 24 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