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 GFF18 Psest_0018 ectoine/hydroxyectoine ABC transporter, permease protein EhuC
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__psRCH2:GFF18 Length = 219 Score = 94.4 bits (233), Expect = 3e-24 Identities = 54/157 (34%), Positives = 89/157 (56%), Gaps = 1/157 (0%) Query: 174 GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVM 233 G VT+ ++F G +++ ++ AL R S + +R L +T+IEV RG L+ LF + Sbjct: 11 GAWVTVKVTFFGSLLAIACALIAALARLSPVAPLRWLAITYIEVFRGSSLLVQLFWLYFV 70 Query: 234 LPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTR 293 LP+ P + A++G+ + AY AEV+RG ++++ +GQ E +L + + R Sbjct: 71 LPM-PPFNIEMSAFAVAVVGLGLNIGAYGAEVLRGAIRSVHRGQHEACQALNMTPLTRMR 129 Query: 294 LIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDL 330 II+PQA+ IP N I K+TSLV++I + DL Sbjct: 130 RIILPQALLAAIPPGTNLLIELLKNTSLVSLITLSDL 166 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: 203 Number of extensions: 9 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: 219 Length adjustment: 26 Effective length of query: 358 Effective length of database: 193 Effective search space: 69094 Effective search space used: 69094 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 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