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_090443962.1 BLS63_RS11280 amino acid ABC transporter permease
Query= TCDB::Q9HU29 (230 letters) >NCBI__GCF_900100495.1:WP_090443962.1 Length = 215 Score = 105 bits (261), Expect = 9e-28 Identities = 72/225 (32%), Positives = 118/225 (52%), Gaps = 13/225 (5%) Query: 2 SEWELILKWMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFF 61 S W+++ +L G TL L +A V G L L +AR + RA+ YI F Sbjct: 4 SFWDILRN----LLVGLQWTLLLSLVAFVCGGIAGLLLLLARIAPLPAARALARGYIELF 59 Query: 62 RGTPLLLQLFIVYYGLAQFEEVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHS 121 +GTPLL+QLF+V++G+A V S P+ A +TL T+A++AEI RG + + Sbjct: 60 QGTPLLMQLFLVFFGIALLG-VDVS--------PWLAAASALTLFTSAFLAEIWRGCVEA 110 Query: 122 VPVGEVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMG 181 +P G+ EAA++L MSR + L H++LP+A+RI + + ++K +AV + ++ Sbjct: 111 IPRGQWEAAQSLAMSRLELLRHVVLPQALRIAVAPTVGFSVQVVKGTAVTSIIGFSELTK 170 Query: 182 MARTIIARTYESMLFFCLAGALYLVITIVLTRIFRLIERWLRVDA 226 + T+E + + L Y ++ L+ +ER L V A Sbjct: 171 TGGMLANATFEPFMVYGLVALGYFLLCYPLSLAAHRLERRLNVTA 215 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: 125 Number of extensions: 7 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: 215 Length adjustment: 22 Effective length of query: 208 Effective length of database: 193 Effective search space: 40144 Effective search space used: 40144 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: 45 (21.9 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