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 RR42_RS05960 RR42_RS05960 multidrug DMT transporter permease
Query= TCDB::Q31PG5 (330 letters) >FitnessBrowser__Cup4G11:RR42_RS05960 Length = 300 Score = 92.4 bits (228), Expect = 1e-23 Identities = 83/283 (29%), Positives = 133/283 (46%), Gaps = 18/283 (6%) Query: 22 LQLAIATALWGGTFTAGRIAVQQLSPL-AVACGRYLLATTVLLLILWQR----EGWPPLN 76 L +A++ + +G R A + + + R++LA L L + R GW Sbjct: 12 LLIALSASAFGAMAIFARFAYDAGTDVYGLLAVRFVLAAGALALAMRLRGVSLPGW---- 67 Query: 77 RRQQLLLFGLGVSGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRLRSW 136 R+ L L +G G ++ FF L+ AS AL++ L P + + AA++ +RL + Sbjct: 68 -RKVLALAAMGGIGYVGQSFCFFTALNHAQASLVALLLYLYPLFVTILAAVFLKERLGTA 126 Query: 137 QWAGVGLSLIGAILLLGSRQAGALTLPGWGDLALVGCVLCWTVYSLLARQALRSLSPLTV 196 + L +GA L +G Q AL + L L + ++VY ++ + ++PL Sbjct: 127 SVIALVLCSVGAGLTVGGGQGSALGI----GLGLASAAI-YSVYIIVGARVTAGVNPLAT 181 Query: 197 TTGACCWGSVLLIGLW-LGQGAQLPVNVSFSTGSAIAFLGLG--GTALAFCLYANGIERL 253 TT C +V+ + + L GA +P S +A L + T LA + G++RL Sbjct: 182 TTVVCGAAAVVYVVVGVLRAGAGVPPQFPQSAAGWLALLAIALLSTVLAILAFFAGLQRL 241 Query: 254 GAARAGLFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGV 296 GAARA + L PV + ALLL E + LGG L+LAGV Sbjct: 242 GAARASMLSTLEPVVTVVLAALLLGEHVGMTQALGGGLILAGV 284 Score = 42.7 bits (99), Expect = 1e-08 Identities = 40/131 (30%), Positives = 60/131 (45%), Gaps = 8/131 (6%) Query: 32 GGTFTAGRIAVQQLSPLAVACGRYLLATTVLLLILWQREGWPPLNRRQQ---LLLFGLGV 88 G TAG V L+ V CG + V++ +L G PP + L L + + Sbjct: 169 GARVTAG---VNPLATTTVVCGAAAVVY-VVVGVLRAGAGVPPQFPQSAAGWLALLAIAL 224 Query: 89 SGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRLRSWQWAGVGLSLIGA 148 L FF GL + A+RA+++ L P + AA+ G+ + Q G GL L G Sbjct: 225 LSTVLAILAFFAGLQRLGAARASMLSTLEPVVTVVLAALLLGEHVGMTQALGGGLILAG- 283 Query: 149 ILLLGSRQAGA 159 +L L S+ +GA Sbjct: 284 VLWLTSKGSGA 294 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: 281 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: 300 Length adjustment: 27 Effective length of query: 303 Effective length of database: 273 Effective search space: 82719 Effective search space used: 82719 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