Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, 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::Q9HU29 (230 letters) >FitnessBrowser__PS:Dsui_0637 Length = 224 Score = 98.6 bits (244), Expect = 9e-26 Identities = 64/218 (29%), Positives = 109/218 (50%), Gaps = 4/218 (1%) Query: 3 EWELILKWMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFR 62 +W I +P + +G +TLE+ A+V G+ L +AR S + + + Y+ FR Sbjct: 5 DWSSIPGALPLLGKGLLVTLEVTLTAIVVGIGWGTLLAVARLSSNRLLSFLAAGYVNLFR 64 Query: 63 GTPLLLQLFIVYYGLAQFEEVRKSAFWPYLRD-PYWCALLTMTLHTAAYIAEILRGAIHS 121 PL++ + Y + Q K F + D AL+ L AAY +EI+R I S Sbjct: 65 SVPLVMVILWFYLIVPQ---ALKGLFGQDIGDIRLVSALVAFALFEAAYYSEIIRAGIQS 121 Query: 122 VPVGEVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMG 181 VP G+V A ALG++ Q + ++LP+A R +P + I++ + +++VY + L D G Sbjct: 122 VPKGQVAAGLALGLTPGQTMRLVVLPQAFRNMIPLLLTQAIILFQDTSLVYVIGLSDFFG 181 Query: 182 MARTIIARTYESMLFFCLAGALYLVITIVLTRIFRLIE 219 A + R + AGA Y VI ++R+ + ++ Sbjct: 182 TAYKVGDRDGRLVELLLFAGAAYFVICFTVSRLVKHLQ 219 Lambda K H 0.332 0.142 0.443 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: 119 Number of extensions: 2 Number of successful extensions: 2 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: 230 Length of database: 224 Length adjustment: 22 Effective length of query: 208 Effective length of database: 202 Effective search space: 42016 Effective search space used: 42016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (22.0 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