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 7023653 Shewana3_0882 extracellular solute-binding protein (RefSeq)
Query= TCDB::Q9HU31 (250 letters) >FitnessBrowser__ANA3:7023653 Length = 244 Score = 92.8 bits (229), Expect = 6e-24 Identities = 73/238 (30%), Positives = 113/238 (47%), Gaps = 15/238 (6%) Query: 9 LAAAATLAFALDASAADKLRIGTEGAYPPFN--GIDASGQAVGFDLDIGKALCAKMKTEC 66 LA ATL A + D L +GT A+PPF G + + GFD+++ K + Sbjct: 10 LALTATLLLAGCGKSNDILVVGTNAAFPPFEYVGGQSGDEIKGFDIELAKRIAKDAGKTL 69 Query: 67 EVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKSVDFKTD 126 +V +D +I ALN+ K DFI + M+IT ER+ +V+F++PYY + K D Sbjct: 70 KVENMKFDSLIVALNSGKIDFIASGMTITPERQASVNFSEPYYEATQVLLVNKDNDTIHT 129 Query: 127 KDSLKGKVIGAQRATIAGTWLEDNMADVVT--IKLYDTQENAYLDLSSGRLDGVLADKFV 184 D +K K Q + A D M+ T + ++T A ++L +G++D VL D Sbjct: 130 LDDIKDKHFAVQLGSTA-----DMMSKKYTQNVTAFNTGFEAIMELKNGKVDLVLFDSEP 184 Query: 185 QYDWL-KSDAGKEFEFKGEPVFDNDKIGIAVRKGDP-LREKLNAALKEIVADGTYKKI 240 ++L K+ K + P F G AV K P L +N LK + G Y+ + Sbjct: 185 AANYLAKNPDLKLIKLDFPPEF----YGFAVSKQQPELLNSINNTLKNLKESGQYQTL 238 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: 150 Number of extensions: 6 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: 250 Length of database: 244 Length adjustment: 24 Effective length of query: 226 Effective length of database: 220 Effective search space: 49720 Effective search space used: 49720 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