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_086511175.1 BZY95_RS17485 EamA/RhaT family transporter
Query= TCDB::Q31PG5 (330 letters) >NCBI__GCF_002151265.1:WP_086511175.1 Length = 293 Score = 93.2 bits (230), Expect = 7e-24 Identities = 87/290 (30%), Positives = 135/290 (46%), Gaps = 23/290 (7%) Query: 21 SLQLAIATALWGGTFTAGRIAVQQLSPLAVACGRY----LLATTVLLLILWQREGWPPLN 76 SL+L + ++LWG +F R+AV + P+++ R LL +LL + + + W Sbjct: 6 SLRLILLSSLWGMSFIFMRVAVPEFGPVSLILVRMGVGALLLLPLLLSLRYLKLVW---E 62 Query: 77 RRQQLLLFGLGVSGIALYNWLFFIGLSL----IPASRAALIIALNPTAIALGAAIWTGDR 132 + LLL GL + + L F+ L+L + A +LI A P AL A+ Sbjct: 63 NKGGLLLLGL------VNHVLPFVLLALATIRLEAGFTSLINATTPIFTALLGAMLFTTP 116 Query: 133 LRSWQWAGVGLSLIGAILLLGSRQAGALTLPGWGDLALVGCVLCWTVYSLLARQALRSLS 192 ++ Q+ G+ L+ G +L +R AL GW LA +G LC+ + S ++ L L Sbjct: 117 IQRQQYLGLALAFFGVYVLSANRLDFALGGDGWFILAALGASLCYGIASNYSKSYLSHLP 176 Query: 193 PLTVTTGACCWGSVLLI--GLWLGQGAQLPVNVSFSTGSAIAFLGLGGTALAFCLYANGI 250 + G+ +++L+ GLWL + + G+A+ L + T LAF LY I Sbjct: 177 VRVLAAGSTAMSALILLIPGLWLWPSEPIG---GLAWGNALG-LAICSTTLAFLLYYGLI 232 Query: 251 ERLGAARAGLFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGVGLGT 300 GA LVPV G LLL E LS L+G + LAG + T Sbjct: 233 SSAGATATSTVTFLVPVSALLWGYLLLDERLSLQVLVGMAITLAGTAIAT 282 Score = 38.5 bits (88), Expect = 2e-07 Identities = 33/128 (25%), Positives = 53/128 (41%), Gaps = 3/128 (2%) Query: 177 WTVYSLLARQALRSLSPLTVTTGACCWGSVLLIGLWLGQGAQLPVNVSFSTGSAIAFLGL 236 W + + R A+ P+++ G++LL+ L L + + + + LGL Sbjct: 16 WGMSFIFMRVAVPEFGPVSLILVRMGVGALLLLPLLLSLRY---LKLVWENKGGLLLLGL 72 Query: 237 GGTALAFCLYANGIERLGAARAGLFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGV 296 L F L A RL A L P+F + +GA+L P+ LG L GV Sbjct: 73 VNHVLPFVLLALATIRLEAGFTSLINATTPIFTALLGAMLFTTPIQRQQYLGLALAFFGV 132 Query: 297 GLGTLQRL 304 + + RL Sbjct: 133 YVLSANRL 140 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: 312 Number of extensions: 16 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: 293 Length adjustment: 27 Effective length of query: 303 Effective length of database: 266 Effective search space: 80598 Effective search space used: 80598 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