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 209342 DVU0406 membrane protein, putative
Query= TCDB::Q31PG5 (330 letters) >MicrobesOnline__882:209342 Length = 312 Score = 202 bits (515), Expect = 7e-57 Identities = 117/280 (41%), Positives = 165/280 (58%), Gaps = 5/280 (1%) Query: 22 LQLAIATALWGGTFTAGRIAVQQLSPLAVACGRYLLATTVLLLILWQREGWPPL--NRRQ 79 L+L +A WGGTF AGRI P A+A R+ LAT +L+ + +REG P R Sbjct: 28 LKLLLAAFFWGGTFVAGRIGAAHAGPFALAFLRFTLATAILVWHIRRREGALPQVSGSRN 87 Query: 80 QLLLFGLGVSGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRLRSWQWA 139 L + LG +GI YN LFF L IPA RAA+++A NP IALGAA++ G+ L + Sbjct: 88 ILFVLLLGATGIFAYNALFFTALQTIPAGRAAVVVANNPIVIALGAALFLGEPLTRRKCI 147 Query: 140 GVGLSLIGAILLLGSRQAGALTLPG--WGDLALVGCVLCWTVYSLLARQALRSLSPLTVT 197 G+ +S+ GA++ + + G WGD+ALVGC+ W YSLL ++A+ SLSPL Sbjct: 148 GIAISVCGALVAVTRGDPVSFLQGGVSWGDVALVGCLASWAAYSLLGKKAMSSLSPLAAV 207 Query: 198 TGACCWGSVLLIGLWLGQGAQLPVNV-SFSTGSAIAFLGLGGTALAFCLYANGIERLGAA 256 T +C G+ +L+ L +G + + ++I +LG+ GTAL F + G++R+GAA Sbjct: 208 TWSCASGACMLLPFALHEGMLDAITTYTPDVWASIFYLGMFGTALGFTWFYEGVDRIGAA 267 Query: 257 RAGLFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGV 296 +AG+FIN VP+ G L L EPLS +LG LVL GV Sbjct: 268 KAGVFINFVPITAILSGWLFLGEPLSPSLILGAALVLTGV 307 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: 336 Number of extensions: 21 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: 312 Length adjustment: 28 Effective length of query: 302 Effective length of database: 284 Effective search space: 85768 Effective search space used: 85768 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