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 WP_051305635.1 G494_RS23155 EamA family transporter
Query= TCDB::Q31PG5 (330 letters) >NCBI__GCF_000429965.1:WP_051305635.1 Length = 323 Score = 191 bits (484), Expect = 3e-53 Identities = 119/285 (41%), Positives = 164/285 (57%), Gaps = 12/285 (4%) Query: 20 VSLQLAIATALWGGTFTAGRIAVQQLSPLAVACGRYLLATTVLLLILWQREG-WPPLNRR 78 V L+L + WGGTF AGRIA ++ P+ A GR+LLA+ +LLL ++ EG L+ R Sbjct: 15 VYLRLVLTMIFWGGTFVAGRIATAEIHPVTAASGRFLLASLLLLLFIYSTEGRLQRLSLR 74 Query: 79 QQLLLFGLGVSGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRLRSWQW 138 Q + LG+SGI YN FF GL I A R A+IIA NP L A ++ G+R + Sbjct: 75 QWGAMALLGLSGIFAYNLFFFAGLQRIEAGRGAMIIAANPVITTLLAMLFFGERFNLRRS 134 Query: 139 AGVGLSLIGAILLLGSRQAGALTLP-----GWGDLALVGCVLCWTVYSLLARQALRSLSP 193 G+ S GA++++ G L L G G+L +G VL WT Y+L+ ++ LR++SP Sbjct: 135 FGICFSAAGALVVISR---GDLLLLFRGEIGAGELCFLGAVLSWTAYTLVGKRVLRAISP 191 Query: 194 LTVTTGACCWGSVLLIG--LWLGQGAQLPVNVSFSTGSAIAFLGLGGTALAFCLYANGIE 251 LT T +C GS LL+ L +G+G +L + +S G ++ +L GT L F + G+ Sbjct: 192 LTAVTYSCLTGSALLLPTMLLMGKGHEL-LTLSLRGGGSLLYLAFFGTTLGFIWFYQGVR 250 Query: 252 RLGAARAGLFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGV 296 LGA RA LF+NLVPV G G LLL E L L GG LVL G+ Sbjct: 251 ELGAGRAVLFVNLVPVCGVVWGILLLNEGLDLSLLSGGALVLIGL 295 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: 294 Number of extensions: 18 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: 323 Length adjustment: 28 Effective length of query: 302 Effective length of database: 295 Effective search space: 89090 Effective search space used: 89090 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 24 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