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 SMc00140 SMc00140 amino-acid binding periplasmic protein
Query= TCDB::Q9HU31 (250 letters) >FitnessBrowser__Smeli:SMc00140 Length = 260 Score = 226 bits (577), Expect = 3e-64 Identities = 126/253 (49%), Positives = 163/253 (64%), Gaps = 11/253 (4%) Query: 8 LLAAAATLAFALDASAA----DKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCAKMK 63 L A A+ F L A A +K+ IGTEGAYPPFN +++ G GFD+DI KALC +MK Sbjct: 7 LAATASAAVFVLMAGVAMAEGEKVVIGTEGAYPPFNNLESDGTLTGFDIDIAKALCEEMK 66 Query: 64 TECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPK-SVD 122 EC VT DWDGIIPAL AKKFD IVASMSIT+ERKQ VDFT+ YY V PK S Sbjct: 67 AECTFVTQDWDGIIPALIAKKFDAIVASMSITEERKQQVDFTNKYYNTPPAIVVPKDSPI 126 Query: 123 FKTDKDSLKGKVIGAQRATIAGTWLEDNMADVVTIKLYDTQENAYLDLSSGRLDGVLADK 182 + +L GK +GAQ +T + E +M + +KLY T + LDL++GR+D + D Sbjct: 127 TEATAAALSGKALGAQGSTTHSNYAEAHMKE-SEVKLYPTADEYKLDLANGRIDAAIDDV 185 Query: 183 FVQYDWLKSDAGKEFEFKG----EPVFDNDKIGIAVRKG-DPLREKLNAALKEIVADGTY 237 V +WLK++ G + G +PV + + GIA+RKG D LREKLN A++ I A+G Y Sbjct: 186 VVLSEWLKTEDGACCKLLGTLPIDPVINGEGAGIAIRKGDDALREKLNKAIEAIRANGKY 245 Query: 238 KKINDKYFPFSIY 250 K+IN+KYFPF +Y Sbjct: 246 KQINEKYFPFDVY 258 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: 229 Number of extensions: 10 Number of successful extensions: 5 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: 260 Length adjustment: 24 Effective length of query: 226 Effective length of database: 236 Effective search space: 53336 Effective search space used: 53336 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