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 RR42_RS31745 RR42_RS31745 ABC transporter permease
Query= TCDB::Q9HU31 (250 letters) >FitnessBrowser__Cup4G11:RR42_RS31745 Length = 249 Score = 119 bits (297), Expect = 8e-32 Identities = 78/238 (32%), Positives = 123/238 (51%), Gaps = 9/238 (3%) Query: 9 LAAAATLAFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCAKMKTECEV 68 L+ AA LA A D + LR+ T+ +PP ++ +G+ GFD+++ +AL M E Sbjct: 15 LSLAAGLARAQDNAV---LRVATDATFPPMEFVE-NGKRTGFDVELVEALAKTMGKRVEW 70 Query: 69 VTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKSVDFKTDKD 128 D+ G+IP L +++FD V+ + IT+ER++ VDFTDPYYT L + Sbjct: 71 TDIDFKGLIPGLISRRFDMAVSGIYITEERRKVVDFTDPYYTGGLVALVKSGNTAINTPA 130 Query: 129 SLKGKVIGAQRATIAGTWLEDNMADVVTIKLYDTQENAYLDLSSGRLDGVLADKFVQYDW 188 L GK + Q T + +L +N V +++ QE L + GR D + K + Sbjct: 131 DLNGKKVSVQVGTKSVNFLRENYPQVQRVEVEKNQEMFNL-VEIGRADAAVTGKPAAMQY 189 Query: 189 LKSDAGKEFEFKGEPVFDNDKIGIAVRKGDP-LREKLNAALKEIVADGTYKKINDKYF 245 +K+ G E ++ G+AVRK P L +NAAL ++ ADGTY ++ K+F Sbjct: 190 VKARGGMRVV---EKALTTEEYGMAVRKDTPELTRAVNAALTKLKADGTYAQLVQKWF 244 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: 249 Length adjustment: 24 Effective length of query: 226 Effective length of database: 225 Effective search space: 50850 Effective search space used: 50850 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