Align AapP, 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 WP_053938863.1 WG78_RS16125 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q52815 (257 letters) >NCBI__GCF_001294205.1:WP_053938863.1 Length = 246 Score = 288 bits (738), Expect = 6e-83 Identities = 142/235 (60%), Positives = 182/235 (77%), Gaps = 1/235 (0%) Query: 23 MNKWYG-DFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVDGTEL 81 +NKWYG D HVL++I+L+V +GE +V+ GPSGSGKST+IR IN+LE G+I VDG ++ Sbjct: 7 VNKWYGRDHHVLKNISLEVKQGEVVVVCGPSGSGKSTLIRTINQLEPVNDGEIWVDGVQV 66 Query: 82 TNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFLKRVK 141 + I+ +R EVG VFQHFNL+PHL++L+N TLAP+ VRKM + A++ M L+RV Sbjct: 67 NHPRTNINRLREEVGFVFQHFNLYPHLSVLQNITLAPVKVRKMSQADADQRGMELLERVG 126 Query: 142 IPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVGLAEE 201 + + + YP QLSGGQQQRVAIAR L M PK+MLFDEPTSALDPEMI EVL M LAE Sbjct: 127 LSNKRDAYPSQLSGGQQQRVAIARGLAMQPKVMLFDEPTSALDPEMIGEVLKVMQNLAES 186 Query: 202 GMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQIL 256 GMTM+ VTHEMGFAR+VA+RV+F+D G+I+EQ PA FF+NPQ +R + FL Q+L Sbjct: 187 GMTMMVVTHEMGFAREVADRVVFLDHGEILEQAAPAQFFNNPQCDRAQQFLRQVL 241 Lambda K H 0.321 0.135 0.394 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: 229 Number of extensions: 9 Number of successful extensions: 1 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: 257 Length of database: 246 Length adjustment: 24 Effective length of query: 233 Effective length of database: 222 Effective search space: 51726 Effective search space used: 51726 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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