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 3609905 Dshi_3287 protein of unknown function DUF6 transmembrane (RefSeq)
Query= TCDB::Q31PG5 (330 letters) >FitnessBrowser__Dino:3609905 Length = 288 Score = 90.5 bits (223), Expect = 4e-23 Identities = 85/284 (29%), Positives = 133/284 (46%), Gaps = 37/284 (13%) Query: 30 LWGGTFTAGRIAVQQLSPLAVACGRYLLATTVLL-LILWQREGWPPLNRRQQLLLFGLGV 88 +W FT+ RI V PL R+L++ + + + L + W L+R Q F G+ Sbjct: 16 MWSSAFTSARIIVAAAPPLTTLSLRFLISGLIAVGIALALGQTWR-LSRTQWKATFLFGL 74 Query: 89 SGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRLRSWQWAGVGLSLIGA 148 ALY L F+ + + AS AA+I + P +AL + + +RLR G+ + G Sbjct: 75 CQNALYLGLNFVAMQTVQASLAAIIASTMPLVVALASWLVLRERLRPLAMVGLLAGIAGV 134 Query: 149 ILLLGSR-QAGALTLPGWGDLALVGCVLCWTVYSLLARQALRSLSPLTVTTGACCWGSVL 207 +L++G+R QAG + LVG + C LA + L + T + ++ Sbjct: 135 VLIMGARLQAG---------VDLVGVLYCGIGVLALA------FATLALRTASSGGNLLM 179 Query: 208 LIGLWLGQGA------QLP---VNVSFSTGSAIAFL------GLGGTALAFCLYANGIER 252 ++GL + GA LP + V++S +AF GL T + F L ++R Sbjct: 180 VVGLQMLVGAVALALVGLPTETLEVTWSWQLVVAFAYTTLVPGLAATFVWFLL----VDR 235 Query: 253 LGAARAGLFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGV 296 +GA RA F L PVFG AI A LL E L ++G +V G+ Sbjct: 236 IGAVRAATFHFLNPVFGVAIAAALLGEALGARDVVGVAIVTLGI 279 Score = 25.8 bits (55), Expect = 0.001 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 3/69 (4%) Query: 88 VSGIALYNWLFFIGLSLIPASRAALIIALNPT-AIALGAAIWTGDRLRSWQWAGVGLSLI 146 V G+A +++F+ + I A RAA LNP +A+ AA+ G+ L + GV + + Sbjct: 220 VPGLAA-TFVWFLLVDRIGAVRAATFHFLNPVFGVAIAAAL-LGEALGARDVVGVAIVTL 277 Query: 147 GAILLLGSR 155 G + + SR Sbjct: 278 GILAVQLSR 286 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: 264 Number of extensions: 15 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: 288 Length adjustment: 27 Effective length of query: 303 Effective length of database: 261 Effective search space: 79083 Effective search space used: 79083 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