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 Dsui_0634 Dsui_0634 putative permease, DMT superfamily
Query= TCDB::Q31PG5 (330 letters) >FitnessBrowser__PS:Dsui_0634 Length = 303 Score = 68.9 bits (167), Expect = 1e-16 Identities = 79/246 (32%), Positives = 103/246 (41%), Gaps = 24/246 (9%) Query: 74 PLNRRQQLLLFGLGVSGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRL 133 PL RR L LGV G + L F+GL I A LI+ PT L ++ G L Sbjct: 68 PLTRRDWGTLVVLGVLGYYASSMLDFLGLQYISAGLERLILFTYPTLTVLIGVLFMGQSL 127 Query: 134 RSWQ-------WAGVGLSLIGAILLLGSRQAGALTLPGWGDLALVGCVLCWTVYSLLARQ 186 Q +AG+GL+ L LG A LT G + G L + +YS A Sbjct: 128 EKRQVGALLLSYAGIGLAFAHD-LQLGGDVATLLT----GAAFVFGSALTYAIYSAGAEP 182 Query: 187 ALRSLSPLTVTTGACCWGSVLLIGLWLGQGAQLPVNVS------FSTGSAIAFLGLGGTA 240 A+R L A V L A P++ + G+A+A L T Sbjct: 183 AIRRLGSARFAALAML---VSTTATQLHFFATQPLSALVQPLPIYLYGAAMA---LFSTV 236 Query: 241 LAFCLYANGIERLGAARAGLFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGVGLGT 300 L + I R+GAAR+ L L PV LLQEP+S L G LVLAGV L + Sbjct: 237 LPILWQSAAIRRIGAARSVLIGTLGPVLTIFFSWWLLQEPVSAAQLAGAGLVLAGVLLVS 296 Query: 301 LQRLQP 306 + +P Sbjct: 297 RSKRKP 302 Score = 30.0 bits (66), Expect = 8e-05 Identities = 24/95 (25%), Positives = 39/95 (41%) Query: 211 LWLGQGAQLPVNVSFSTGSAIAFLGLGGTALAFCLYANGIERLGAARAGLFINLVPVFGS 270 LW+G A + ++ + LG+ G + L G++ + A L + P Sbjct: 57 LWIGFTAGNAIPLTRRDWGTLVVLGVLGYYASSMLDFLGLQYISAGLERLILFTYPTLTV 116 Query: 271 AIGALLLQEPLSGLTLLGGLLVLAGVGLGTLQRLQ 305 IG L + + L + LL AG+GL LQ Sbjct: 117 LIGVLFMGQSLEKRQVGALLLSYAGIGLAFAHDLQ 151 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: 285 Number of extensions: 21 Number of successful extensions: 3 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: 303 Length adjustment: 27 Effective length of query: 303 Effective length of database: 276 Effective search space: 83628 Effective search space used: 83628 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