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 HSERO_RS07530 HSERO_RS07530 amino acid ABC transporter permease
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__HerbieS:HSERO_RS07530 Length = 216 Score = 115 bits (288), Expect = 1e-30 Identities = 67/211 (31%), Positives = 124/211 (58%), Gaps = 13/211 (6%) Query: 166 VVETPLWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLIT 225 ++E W L+ L GIA G ++AL R S + +R+L +I++I+G P++ Sbjct: 13 LLEAARWTLLLSALAFLGGGIA-----GFIVALMRTSHLAPLRLLSAVYIQIIQGTPVLI 67 Query: 226 VLFMASVMLPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLG 285 +LF++ L +F G+ + ++ A I ++I++SAY+ E+ RG ++A+P Q+E + +L Sbjct: 68 LLFLSFYGLAIF---GYKLPPMVAATIAMTIYSSAYLGEIWRGCIEAVPVPQWEASTALA 124 Query: 286 LGYWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWAS 345 + WQ+ R +I+PQA+++ +P V + K+TS+ +IIG+ +L KL + Sbjct: 125 MTRWQQLRYVILPQAVRISLPPTVGFLVQIVKNTSIASIIGLVELAQAGKLVSNATFQPF 184 Query: 346 AVTPITGLIFAGFIFWLFCFGMSRYSGFMER 376 V PI AG I+++FC+ +SR++ +ER Sbjct: 185 LVFPIV----AG-IYFVFCYPLSRFAFALER 210 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: 223 Number of extensions: 12 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: 216 Length adjustment: 26 Effective length of query: 358 Effective length of database: 190 Effective search space: 68020 Effective search space used: 68020 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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