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 GFF355 PS417_01810 ABC transporter permease
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__WCS417:GFF355 Length = 319 Score = 118 bits (295), Expect = 3e-31 Identities = 73/213 (34%), Positives = 114/213 (53%), Gaps = 17/213 (7%) Query: 170 PLWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFM 229 PL GL TL LS V + L +G+ L R S P +R L ++E++RG PL+ +F+ Sbjct: 116 PLMWGLWTTLWLSVVSGILGLIIGLATGLCRLSSNPTLRDLSTIYVELVRGTPLLVQIFI 175 Query: 230 ASVMLPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYW 289 F+ T N+ + + +S+FT AY+AE++R G+Q+I +GQ E A SLGL Sbjct: 176 ----FYFFIGTVLNLSREFAGIAALSLFTGAYVAEIVRAGVQSITRGQNEAARSLGLSAS 231 Query: 290 QKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLL----GIVKLNFSDANWAS 345 Q R +++PQA K V+P + FI KDTSLV++I + +LL ++ +FS Sbjct: 232 QSMRHVVLPQAFKRVLPPLAGQFISLVKDTSLVSVIAITELLKSGREVITTSFS------ 285 Query: 346 AVTPITGLIFAGFIFWLFCFGMSRYSGFMERHL 378 P L ++ L +S+ + +ER L Sbjct: 286 ---PFEILFCVAGLYLLINLPLSKMASRLERRL 315 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: 277 Number of extensions: 16 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: 319 Length adjustment: 29 Effective length of query: 355 Effective length of database: 290 Effective search space: 102950 Effective search space used: 102950 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 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