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_012048835.1 SWIT_RS13330 ABC transporter permease subunit
Query= TCDB::Q52814 (384 letters) >NCBI__GCF_000016765.1:WP_012048835.1 Length = 374 Score = 75.1 bits (183), Expect = 3e-18 Identities = 33/85 (38%), Positives = 58/85 (68%) Query: 246 KLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVI 305 + + L G I+ SA+ AE++RGGL +P+GQ+E + +LGL Q RL+I+PQA+++++ Sbjct: 242 EFVAVLWGSVIYASAFAAEIVRGGLDGVPRGQWEASRALGLSKRQSLRLVIVPQALRMIV 301 Query: 306 PSIVNTFIGTFKDTSLVTIIGMFDL 330 P + + FI K+++L ++G DL Sbjct: 302 PPMNSQFITILKNSTLALVVGYPDL 326 Score = 38.1 bits (87), Expect = 4e-07 Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 1/67 (1%) Query: 174 GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLIT-VLFMASV 232 GL ++ L+ + I +S G+ +AL R S + R L F++++R VPL+ +LF V Sbjct: 78 GLGNSIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRNVPLVVQLLFWYGV 137 Query: 233 MLPLFLP 239 +L F P Sbjct: 138 ILMAFPP 144 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: 388 Number of extensions: 17 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 384 Length of database: 374 Length adjustment: 30 Effective length of query: 354 Effective length of database: 344 Effective search space: 121776 Effective search space used: 121776 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: 50 (23.9 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