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 7023652 Shewana3_0881 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__ANA3:7023652 Length = 226 Score = 107 bits (268), Expect = 2e-28 Identities = 64/197 (32%), Positives = 111/197 (56%), Gaps = 5/197 (2%) Query: 174 GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVM 233 GL VTL+++F + + +G+ L + S IR ++ VIRG P++ L V+ Sbjct: 27 GLKVTLIVTFFAMLLGAVLGVGTTLMKMSSKWYIRFPAELYVGVIRGTPVVVQL----VI 82 Query: 234 LPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTR 293 L + ++VDK+ A+I + + AY++E+IR G+QA+ KGQ E A SLGL + Sbjct: 83 LYFIVLAAFDVDKVTAAIIAFGLNSGAYISEIIRAGIQAVDKGQTEAARSLGLSQAMTMK 142 Query: 294 LIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGL 353 LII+PQAIK ++P++ N FI K+T+++ IG DL+ ++ + ++ T Sbjct: 143 LIILPQAIKNILPALGNEFIVLLKETAVIGFIGGVDLMRAGEI-IRSRTFEDSIPLFTCA 201 Query: 354 IFAGFIFWLFCFGMSRY 370 + F+ + F F +S++ Sbjct: 202 LIYLFLTYSFTFMLSKF 218 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: 14 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: 226 Length adjustment: 26 Effective length of query: 358 Effective length of database: 200 Effective search space: 71600 Effective search space used: 71600 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