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 Pf1N1B4_5004 Permease of the drug/metabolite transporter (DMT) superfamily
Query= TCDB::Q31PG5 (330 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5004 Length = 315 Score = 177 bits (449), Expect = 3e-49 Identities = 118/292 (40%), Positives = 166/292 (56%), Gaps = 17/292 (5%) Query: 19 PVSLQLAIATALWGGTFTAGRIAVQQLSPLAVACGRYLLATTVLLLILWQREGWPPLNR- 77 PV L+LA T +WGGTF AGR LSPL A R+LLA+ LLL L + PL R Sbjct: 15 PVYLKLAAVTMIWGGTFVAGRFLADSLSPLLAASLRFLLASVALLLFLLLAQ--VPLVRP 72 Query: 78 --RQQLLLFGLGVSGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRLRS 135 RQ L L LG GI YN FF GL I ASRA+LI+ALNP I L + + +RL Sbjct: 73 SPRQWLQLTLLGFFGIFFYNLCFFYGLHYINASRASLIVALNPAVIGLASWLLFKERLSR 132 Query: 136 WQWAGVGLSLIGAILLLGSRQAGALT--LPGW-GDLALVGCVLCWTVYSLLARQALRSLS 192 + G+ + + GA L++ SR L W GDL + GCVL W +YSL ++ ++L Sbjct: 133 AKVTGIAICIAGASLVIVSRNPQLLAGGTDAWIGDLLIFGCVLGWGIYSLFSKGLNQTLG 192 Query: 193 PLTVTTGACCWGSVLLIGLWLGQGAQLPVNVSFSTGS------AIAFLGLGGTALAFCLY 246 P+ T + G+++L W+ + ++V+ G ++ +LG+ G+ALA+ Y Sbjct: 193 PVQTVTYSILLGTLML---WVTSAVRGELSVAALAGLGTQQWLSLLYLGVLGSALAYIGY 249 Query: 247 ANGIERLGAARAGLFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGVGL 298 +GI ++GA R+G+FI L P+ GALLL E L+ + LGG L+LAG+ L Sbjct: 250 YDGIRKIGATRSGVFIALNPLTAVLFGALLLGEQLTLVMCLGGGLILAGIFL 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: 296 Number of extensions: 17 Number of successful extensions: 6 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: 315 Length adjustment: 28 Effective length of query: 302 Effective length of database: 287 Effective search space: 86674 Effective search space used: 86674 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