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 Pf6N2E2_455 Permease of the drug/metabolite transporter (DMT) superfamily
Query= TCDB::Q31PG5 (330 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_455 Length = 314 Score = 179 bits (454), Expect = 8e-50 Identities = 121/296 (40%), Positives = 165/296 (55%), Gaps = 17/296 (5%) Query: 15 PLKFPVSLQLAIATALWGGTFTAGRIAVQQLSPLAVACGRYLLATTVLLLILWQREGWPP 74 P PV L+LA+ T +WGGTF AGRI L+P+ A R+LLA+ LL L P Sbjct: 11 PSDLPVYLKLAMVTMIWGGTFVAGRILSDALAPMFAASLRFLLASIALLAFL--ALAGIP 68 Query: 75 LNR---RQQLLLFGLGVSGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGD 131 L R +Q L L LG GI YN FF GL I ASRA+LI+ALNP I L + + Sbjct: 69 LARPSVKQGLHLAALGFFGIFFYNLCFFYGLQYINASRASLIVALNPAVIGLASWWLFKE 128 Query: 132 RLRSWQWAGVGLSLIGAILLLGSRQAGAL--TLPGW-GDLALVGCVLCWTVYSLLARQAL 188 RL + AG+ L + GA L++ SR L GW GDL + GCVL W +YSL +R+ Sbjct: 129 RLSRLKVAGIVLCIGGAGLVIVSRDPSLLQGAAQGWIGDLLIFGCVLGWGIYSLFSRRLN 188 Query: 189 RSLSPLTVTTGACCWGSVLLIGLWLGQGAQLPVNVS------FSTGSAIAFLGLGGTALA 242 SL PL T + G+++L WL A + V ++ +LG+ G+ALA Sbjct: 189 DSLGPLQTVTWSILLGTLML---WLACAAAGEIRVEALRALDLEQWLSLLYLGVLGSALA 245 Query: 243 FCLYANGIERLGAARAGLFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGVGL 298 + + +GI R+GA R+G+FI L P+ +GALLL E L+ L +GG ++L G+ L Sbjct: 246 YIAWYDGIRRIGATRSGVFIALNPLTAVLLGALLLDERLTALMCVGGGVILVGIFL 301 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: 302 Number of extensions: 22 Number of successful extensions: 5 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: 314 Length adjustment: 28 Effective length of query: 302 Effective length of database: 286 Effective search space: 86372 Effective search space used: 86372 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