Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding 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 SM_b20706 SM_b20706 amino acid uptake ABC transporter substrate-binding protein precursor
Query= TCDB::Q9HU31 (250 letters) >FitnessBrowser__Smeli:SM_b20706 Length = 258 Score = 237 bits (604), Expect = 2e-67 Identities = 135/254 (53%), Positives = 166/254 (65%), Gaps = 9/254 (3%) Query: 5 KKILLAAAATLAFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCAKMKT 64 K IL A A A + A AA+KL+IGTEGAYPPFN +D+SG+ GFD++IG ALC +MK Sbjct: 3 KLILALALAGTALSSSAVAAEKLKIGTEGAYPPFNFVDSSGKIGGFDVEIGLALCERMKV 62 Query: 65 ECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKSVDFK 124 ECEVV DWDGIIP L AKK+D I+ASM IT+ERK+ V FT+PYY + APK Sbjct: 63 ECEVVAQDWDGIIPGLLAKKYDMIIASMFITEERKKQVAFTNPYYLAAMTHAAPKGAGIS 122 Query: 125 T-DKDSLKGKVIGAQRATIAGTWLEDNMADVVTIKLYDTQENAYLDLSSGRLDGVLADKF 183 ++L+GKVIGAQ T ++ D IKLY TQ+ A LD+ +GRLD + D Sbjct: 123 AFSNEALQGKVIGAQSGTTQADYIAAVYPD-AEIKLYPTQDEANLDMVNGRLDLQVGDML 181 Query: 184 VQYDWL-KSDAGKE-FEFKGEPVFD----NDKIGIAVRKGD-PLREKLNAALKEIVADGT 236 DW+ K+D GK E GEP+ D D +GIAVR+ D +REKLN AL EI ADGT Sbjct: 182 PLLDWVTKNDDGKGCCELVGEPITDKKFVGDGVGIAVRQEDNEMREKLNKALDEIRADGT 241 Query: 237 YKKINDKYFPFSIY 250 YKKINDKYF +Y Sbjct: 242 YKKINDKYFTIDVY 255 Lambda K H 0.317 0.135 0.392 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: 225 Number of extensions: 15 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: 250 Length of database: 258 Length adjustment: 24 Effective length of query: 226 Effective length of database: 234 Effective search space: 52884 Effective search space used: 52884 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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