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 WP_083710231.1 BW971_RS16650 ABC transporter permease subunit
Query= TCDB::Q9HU29 (230 letters) >NCBI__GCF_900156495.1:WP_083710231.1 Length = 589 Score = 114 bits (284), Expect = 5e-30 Identities = 75/225 (33%), Positives = 121/225 (53%), Gaps = 12/225 (5%) Query: 4 WELILKWMPKMLQ-GAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFR 62 W+L K +P +L+ G TL L ++ V G L + L +A SR ++R Y FR Sbjct: 348 WDLYAKALPDLLKTGLPNTLILSVVSGVLGTILGMVLAVAGISRSRWLRWPARIYTDIFR 407 Query: 63 GTPLLLQLFIVYYGLAQFEEVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHSV 122 G P ++ + +V G+ + +PYW + + L AAYI EI R I SV Sbjct: 408 GLPAVVVILVVGLGIGPVVKNLTG------NNPYWLGAVALALLAAAYIGEIFRSGIQSV 461 Query: 123 PVGEVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLF----D 178 G++EA+RA+G S RQ++ +++P+ VR LPA N+ I ++K S++VY + L + Sbjct: 462 DDGQLEASRAIGFSYRQSMRLVVVPQGVRRVLPALMNQFISLIKDSSLVYFLGLLASQRE 521 Query: 179 IMGMARTIIARTYESMLFFCLAGALYLVITIVLTRIFRLIERWLR 223 + + R + A+T ++ AG +YLV+TI LT + I+ LR Sbjct: 522 LFAVGRDLNAQT-GNLSPLVAAGLIYLVLTIPLTHLVNYIDHRLR 565 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: 237 Number of extensions: 12 Number of successful extensions: 3 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: 589 Length adjustment: 29 Effective length of query: 201 Effective length of database: 560 Effective search space: 112560 Effective search space used: 112560 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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