Align Probable permease of ABC transporter, 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 WP_061533332.1 CAter10_RS10280 amino acid ABC transporter permease
Query= TCDB::Q9HU30 (231 letters) >NCBI__GCF_001584165.1:WP_061533332.1 Length = 250 Score = 116 bits (290), Expect = 5e-31 Identities = 78/233 (33%), Positives = 122/233 (52%), Gaps = 17/233 (7%) Query: 13 LAGTWMTLKLSLAAVCVGLLLGLL---GAIAKTSKYAALRFLGGT-------YTTIVRGV 62 + GT MTLK+++ V G LGLL G +A+ A FL Y + RG Sbjct: 18 IEGTLMTLKVAVICVVTGTFLGLLLGVGRVAEARHGAMKYFLRYAVQWPVRFYVSFFRGT 77 Query: 63 PETLWVLMIYFGTV-------SGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVF 115 P + +L+I+F + GL GD+ + F + LA+ L GAY +E+F Sbjct: 78 PLFVQILLIHFALMPLLINPNGGLLLSGDIAREVRSQYGAFLSAVLAITLNSGAYVSEIF 137 Query: 116 RGALLSIPRGHREAGQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLIT 175 R + SI RG EA ++LG++ + ++VLPQ +R LP LGN + ++KD++L S I Sbjct: 138 RAGIQSIDRGQSEASRSLGMTYLQTLRKVVLPQAFRRMLPPLGNNAIAIVKDSSLASAIG 197 Query: 176 LDEIMRKAQVASNATKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRGFVR 228 L E+ A+ S A + Y+T + IY +T+++ V + LE+R G+G R Sbjct: 198 LAELAYAARTVSGAYARYWEPYLTISLIYWGITLLLSVFVQHLEKRYGKGDTR 250 Lambda K H 0.327 0.143 0.431 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: 146 Number of extensions: 8 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: 231 Length of database: 250 Length adjustment: 23 Effective length of query: 208 Effective length of database: 227 Effective search space: 47216 Effective search space used: 47216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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