Align Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate Dsui_0637 Dsui_0637 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= TCDB::Q9HU30 (231 letters) >FitnessBrowser__PS:Dsui_0637 Length = 224 Score = 94.7 bits (234), Expect = 1e-24 Identities = 65/207 (31%), Positives = 101/207 (48%), Gaps = 4/207 (1%) Query: 15 GTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETLWVLMIYFG 74 G +TL+++L A+ VG+ G L A+A+ S L FL Y + R VP + +L Y Sbjct: 19 GLLVTLEVTLTAIVVGIGWGTLLAVARLSSNRLLSFLAAGYVNLFRSVPLVMVILWFYLI 78 Query: 75 TVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIPRGHREAGQALG 134 AL LFG+ D+ + +A L AY +E+ R + S+P+G AG ALG Sbjct: 79 VPQ---ALKGLFGQ-DIGDIRLVSALVAFALFEAAYYSEIIRAGIQSVPKGQVAAGLALG 134 Query: 135 LSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQVASNATKEPF 194 L+PG+ +VLPQ +R +P L +IL +DT+LV +I L + A + Sbjct: 135 LTPGQTMRLVVLPQAFRNMIPLLLTQAIILFQDTSLVYVIGLSDFFGTAYKVGDRDGRLV 194 Query: 195 TFYMTAAAIYLSLTVVIMVALHFLERR 221 + A A Y + + + L+ R Sbjct: 195 ELLLFAGAAYFVICFTVSRLVKHLQAR 221 Lambda K H 0.327 0.143 0.431 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: 124 Number of extensions: 4 Number of successful extensions: 1 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: 231 Length of database: 224 Length adjustment: 22 Effective length of query: 209 Effective length of database: 202 Effective search space: 42218 Effective search space used: 42218 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 46 (22.3 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