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 Dsui_0637 Dsui_0637 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__PS:Dsui_0637 Length = 224 Score = 117 bits (294), Expect = 2e-31 Identities = 72/206 (34%), Positives = 116/206 (56%), Gaps = 12/206 (5%) Query: 170 PLWG-GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLF 228 PL G GL+VTL ++ I V + G LLA+ R S ++ L ++ + R VPL+ V+ Sbjct: 14 PLLGKGLLVTLEVTLTAIVVGIGWGTLLAVARLSSNRLLSFLAAGYVNLFRSVPLVMVIL 73 Query: 229 MASVMLPLFLPTGWNVD----KLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSL 284 +++P L + D +L+ AL+ ++F +AY +E+IR G+Q++PKGQ +L Sbjct: 74 WFYLIVPQALKGLFGQDIGDIRLVSALVAFALFEAAYYSEIIRAGIQSVPKGQVAAGLAL 133 Query: 285 GLGYWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIV-KLNFSDANW 343 GL Q RL+++PQA + +IP ++ I F+DTSLV +IG+ D G K+ D Sbjct: 134 GLTPGQTMRLVVLPQAFRNMIPLLLTQAIILFQDTSLVYVIGLSDFFGTAYKVGDRDGRL 193 Query: 344 ASAVTPITGLIFAGFIFWLFCFGMSR 369 L+FAG +++ CF +SR Sbjct: 194 VEL------LLFAGAAYFVICFTVSR 213 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: 263 Number of extensions: 17 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: 224 Length adjustment: 26 Effective length of query: 358 Effective length of database: 198 Effective search space: 70884 Effective search space used: 70884 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