Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease
Query= TCDB::Q52814 (384 letters) >NCBI__GCF_900115975.1:WP_092487756.1 Length = 234 Score = 122 bits (307), Expect = 8e-33 Identities = 75/239 (31%), Positives = 123/239 (51%), Gaps = 31/239 (12%) Query: 164 LEVVETPLWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPL 223 +E + ++ G +TL ++ + +A+ +G++ L R SR V+R L +++ RG PL Sbjct: 5 IENLPVLIFQGAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPL 64 Query: 224 ITVLFMASVMLPLFL----------------PTGWNVDKLLRALIGVSIFTSAYMAEVIR 267 + +F+ +P L + + + L A+I S+ + AY+AE+ R Sbjct: 65 LVQIFIVYFGIPKLLMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFR 124 Query: 268 GGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGM 327 G+Q+I +GQ E A SLG+ + Q R +I+PQA K VIP + N FI KDTSL+++IG Sbjct: 125 AGVQSIERGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGF 184 Query: 328 FDL-----LGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMSRYSGFMERHLDTG 381 +L L I + S A W + GFI+ + F +SR ++ER TG Sbjct: 185 AELTRNGQLIIARTYESFAIW----------LTVGFIYLIMTFTLSRIVDYLERRYKTG 233 Lambda K H 0.330 0.145 0.469 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: 202 Number of extensions: 9 Number of successful extensions: 3 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: 384 Length of database: 234 Length adjustment: 27 Effective length of query: 357 Effective length of database: 207 Effective search space: 73899 Effective search space used: 73899 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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