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_089301524.1 CHB84_RS11340 ectoine/hydroxyectoine ABC transporter permease subunit EhuD
Query= TCDB::Q52814 (384 letters) >NCBI__GCF_900188115.1:WP_089301524.1 Length = 218 Score = 102 bits (254), Expect = 1e-26 Identities = 58/186 (31%), Positives = 111/186 (59%), Gaps = 5/186 (2%) Query: 171 LWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMA 230 L GGL VT+ + I ++L +G+++A+ R R+PV+ + +++ +RG PL+ F A Sbjct: 15 LLGGLWVTIQATMAAIVIALALGLVVAVIRYLRIPVLSAVFGFYVQFVRGTPLLVQAFAA 74 Query: 231 SVMLPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQ 290 +LP + G + L+ +I + + S+Y AEV R G++ + KGQ+E A +L L Sbjct: 75 FYILPDY---GIVLSPLITGIIVLGVNYSSYTAEVYRSGIEDVGKGQWEAATALSLPVRP 131 Query: 291 KTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVK-LNFSDANWASAVTP 349 I++PQA++ ++P + N +I FKD++++++I M +LL + + + S+ + +T Sbjct: 132 TWTRIVLPQAVRSIVPMLGNYWIQMFKDSAILSLITMNELLNVAQTIGSSEFRYLEPLT- 190 Query: 350 ITGLIF 355 I G++F Sbjct: 191 IVGILF 196 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: 243 Number of extensions: 15 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: 384 Length of database: 218 Length adjustment: 26 Effective length of query: 358 Effective length of database: 192 Effective search space: 68736 Effective search space used: 68736 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 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