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 Ac3H11_4360 Permease of the drug/metabolite transporter (DMT) superfamily
Query= TCDB::Q31PG5 (330 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4360 Length = 307 Score = 76.6 bits (187), Expect = 7e-19 Identities = 87/308 (28%), Positives = 135/308 (43%), Gaps = 26/308 (8%) Query: 16 LKFPVSLQLAIATALWGGTFTAGRIAVQQLSPLAVACGRYLLATT---VLLLILWQREGW 72 + P L+L + ALWGG+F R+A L L A R LL +LLL+L R + Sbjct: 1 MPLPSFLRLLLLAALWGGSFLLMRVAAPVLGALPTAFVRVLLGAAGLGLLLLVLRLRPRF 60 Query: 73 PPLNRRQQLLLFGLGVSGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDR 132 + L+ G+ SGI +F + +PA +A++ A P L A+ G+R Sbjct: 61 G--GKLGATLVLGVVNSGIPFL--MFAMAARSLPAGYSAILNATTPLMGVLIGALAFGER 116 Query: 133 LRSWQWAGVGLSLIGAILLLGSRQAGALTLPGWGDLALVGCVLCWTVYSLLARQALR--- 189 + + + G+ L + G +L QAG + L + C++ Y L R Sbjct: 117 ITAARVGGMVLGMAGVAVLA---QAGPVALTPEVLGGMAACLVATACYGLAGFLTRRWVT 173 Query: 190 ---SLSPLTVTTGACCWGSVLLIGLWLGQGAQLPVNVSFSTGS------AIAFLGLGGTA 240 L V G+ ++L+ + + + P + + A+ LGL TA Sbjct: 174 ERGGLDSRIVALGSQMGAVLVLVPVVAWELLRQPAAATAWLAAPAPVWGALLGLGLLCTA 233 Query: 241 LAFCLYANGIERLGAARAGLFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGVGLGT 300 LA+ LY I +G +A L+P+FG A G LLL EP + GG L+ A + L Sbjct: 234 LAYVLYFRLIADVGPLKALTVTFLIPLFGVAWGWLLLGEPATWAHGAGGGLIGAALWL-- 291 Query: 301 LQRLQPVP 308 L+PVP Sbjct: 292 --VLRPVP 297 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: 360 Number of extensions: 27 Number of successful extensions: 4 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: 307 Length adjustment: 27 Effective length of query: 303 Effective length of database: 280 Effective search space: 84840 Effective search space used: 84840 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