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 3608830 Dshi_2222 extracellular solute-binding protein family 3 (RefSeq)
Query= TCDB::Q9HU31 (250 letters) >FitnessBrowser__Dino:3608830 Length = 242 Score = 134 bits (338), Expect = 1e-36 Identities = 86/241 (35%), Positives = 131/241 (54%), Gaps = 13/241 (5%) Query: 11 AAATL--AFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCAKMKTECEV 68 A ATL A AS +R+GTEGAYPP+N ++ +G+ GF+ ++G LCA+ + CE Sbjct: 9 ALATLMAGAAFAASDGTTVRMGTEGAYPPYNFLNDAGEVDGFERELGDELCARAELTCEW 68 Query: 69 VTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKSVDFKTDKD 128 VT+DWD IIP L + +D I+A MSITDER + +DFT Y P + ++ Sbjct: 69 VTNDWDSIIPNLVSGNYDTIIAGMSITDERDEVIDFTQNYTQPD-----PSAFMGLSEDV 123 Query: 129 SLKGKVIGAQRATIAGTWLEDNMADVVTIKLYDTQENAYLDLSSGRLDGVLADKFVQYDW 188 L+G VI AQ TI + + A ++ + + + + +G D VLADK + Sbjct: 124 DLEGGVIAAQTGTIQASHIASTGATLIE---FASPDETVAAVRNGEADAVLADKAFLEPF 180 Query: 189 LKSDAGKEFEFKGEPVFDNDKIGIAVRKGDP-LREKLNAALKEIVADGTYKKINDKYFPF 247 + +A + F GE V IG+ +R+ DP LR K +AA++ + DG+ + K+ P Sbjct: 181 VTENA--DLVFVGEDVLLGGGIGMGLRESDPELRAKFDAAIQSMKDDGSLNALIAKWLPG 238 Query: 248 S 248 S Sbjct: 239 S 239 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: 157 Number of extensions: 7 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: 242 Length adjustment: 24 Effective length of query: 226 Effective length of database: 218 Effective search space: 49268 Effective search space used: 49268 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