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 GFF3374 PGA1_c34270 putative integral membrane protein
Query= TCDB::Q31PG5 (330 letters) >FitnessBrowser__Phaeo:GFF3374 Length = 294 Score = 80.9 bits (198), Expect = 4e-20 Identities = 81/283 (28%), Positives = 130/283 (45%), Gaps = 15/283 (5%) Query: 21 SLQLAIATA-LWGGTFTAGRIAVQQLSPLAVACGRYLLATTVLLLIL-WQREGWPPLNRR 78 +L + +A A +W FT+ RI V SPL R+L++ + + + + + W L R Sbjct: 5 ALAMGLAFAFMWSSAFTSARIIVADASPLYSLAFRFLISGLIGVAVARYMGQSWR-LTRG 63 Query: 79 QQLLLFGLGVSGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRLRSWQW 138 Q G+ ALY L F+ + I AS AA+I + P +A+ + G+RL Sbjct: 64 QLKATVIFGICQNALYLGLNFVAMETIEASLAAIIASTMPMLVAIALWLVYGERLPRLGV 123 Query: 139 AGVGLSLIGAILLLGSRQAGALTLPGWGDLALVGC-VLCWTVYSLLARQALRSLSPLTVT 197 G+ ++G L++G+R + + L G + L G VL T+ +L R A + + V Sbjct: 124 VGLLAGVLGVALIMGTRISAGVDLFG---VLLCGIGVLALTLATLALRGATSGGNYMMVV 180 Query: 198 TGACCWGSVLLIGLWLGQGAQLPVNVSFSTGSAIAFLGLGGTALAFCLYANGIERLGAAR 257 GS +L + + S+ A + L A ++ + R+GA R Sbjct: 181 GLQMLIGSAVLF-VVAPMVETFRLTPSWPLALAFVYTTLVPGLTATFIWVLLLNRIGAVR 239 Query: 258 AGLFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGVGLGT 300 A F L PVFG A+ ++LL E L GLL + GVG+ T Sbjct: 240 AATFHFLNPVFGVAVASVLLGEQL-------GLLDIVGVGIVT 275 Score = 28.5 bits (62), Expect = 2e-04 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 2/70 (2%) Query: 92 ALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRLRSWQWAGVGLSLIGAILL 151 A + W+ L+ I A RAA LNP A++ G++L GVG+ G + + Sbjct: 224 ATFIWVLL--LNRIGAVRAATFHFLNPVFGVAVASVLLGEQLGLLDIVGVGIVTFGILAV 281 Query: 152 LGSRQAGALT 161 +RQ+ T Sbjct: 282 QLARQSAQRT 291 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: 262 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 330 Length of database: 294 Length adjustment: 27 Effective length of query: 303 Effective length of database: 267 Effective search space: 80901 Effective search space used: 80901 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