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 PP_0282 PP_0282 L-arginine ABC transporter - periplasmic binding subunit
Query= TCDB::Q9HU31 (250 letters) >FitnessBrowser__Putida:PP_0282 Length = 250 Score = 391 bits (1004), Expect = e-114 Identities = 196/250 (78%), Positives = 216/250 (86%), Gaps = 2/250 (0%) Query: 1 MKNYKKILLAAAATLAFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCA 60 M YKK LLAAAATL + +A AA+KLR+G E AYPPFN DASG VGFD DIG ALCA Sbjct: 1 MHTYKKFLLAAAATLVMSANAMAAEKLRMGIEAAYPPFNNKDASGNVVGFDKDIGDALCA 60 Query: 61 KMKTECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKS 120 KMK EC VVTSDWDGIIPALNAKKFDF+V+S+SITDERKQAVDFT+PYY+NKLQF+APK+ Sbjct: 61 KMKVECSVVTSDWDGIIPALNAKKFDFLVSSLSITDERKQAVDFTNPYYSNKLQFIAPKN 120 Query: 121 VDFKTDKDSLKGKVIGAQRATIAGTWLEDNMADVVTIKLYDTQENAYLDLSSGRLDGVLA 180 VDFKTDK+SLKGKVIG QRAT+AGT+LEDN D V IKLYDTQENAYLDL SGR+DG+LA Sbjct: 121 VDFKTDKESLKGKVIGTQRATLAGTYLEDNYPD-VEIKLYDTQENAYLDLVSGRIDGILA 179 Query: 181 DKFVQYDWLKSDAGKEFEFKGEPVFDNDKIGIAVRKGD-PLREKLNAALKEIVADGTYKK 239 DK+VQY+WLKS G FEFKGEPV D+DKIGIAVRKGD LR+ LN AL EI ADGTYKK Sbjct: 180 DKYVQYEWLKSKDGSNFEFKGEPVMDSDKIGIAVRKGDTKLRDDLNKALAEIKADGTYKK 239 Query: 240 INDKYFPFSI 249 INDKYFPFSI Sbjct: 240 INDKYFPFSI 249 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: 311 Number of extensions: 10 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: 250 Length of database: 250 Length adjustment: 24 Effective length of query: 226 Effective length of database: 226 Effective search space: 51076 Effective search space used: 51076 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: 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