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_012755702.1 RLEG_RS26780 amino acid ABC transporter permease
Query= TCDB::Q52814 (384 letters) >NCBI__GCF_000023185.1:WP_012755702.1 Length = 309 Score = 101 bits (251), Expect = 3e-26 Identities = 73/213 (34%), Positives = 116/213 (54%), Gaps = 26/213 (12%) Query: 144 ILLFAVLPVIA--FWLL--HGGFGLEVV-----ETPLWGGLMVTLVLSFVGIAVSLPVGI 194 +L AVL + A W++ + FG VV + + GL V+L L+ V +A+ + +G+ Sbjct: 33 LLWVAVLLIAANFLWIVAHNENFGWPVVAAYFFDPTVINGLYVSLGLTVVAMAIGIVLGL 92 Query: 195 LLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFM----------ASVMLPLFLPT--GW 242 LA+ R S + R L FI RG PL+ L S+ +P F PT W Sbjct: 93 GLAIARLSNDRLARSLASLFIWFFRGTPLLVQLIFWYNLSTLFPQLSIAIP-FGPTLASW 151 Query: 243 NVDKLLR----ALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMP 298 + ++ A++G+++ +AYMAE+IRGGL ++ +GQFE A++ G+ + II+P Sbjct: 152 ETNSVITPMTAAIVGLALNEAAYMAEIIRGGLLSVDRGQFETAEAFGMTKARALWRIIIP 211 Query: 299 QAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLL 331 QA++ ++P N I K TSLV++I M DLL Sbjct: 212 QAMRSIVPPTGNQLISMIKATSLVSVIAMADLL 244 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: 328 Number of extensions: 17 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: 309 Length adjustment: 29 Effective length of query: 355 Effective length of database: 280 Effective search space: 99400 Effective search space used: 99400 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: 49 (23.5 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