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_011384493.1 AMB_RS10565 ABC transporter ATP-binding protein
Query= TCDB::Q52815 (257 letters) >NCBI__GCF_000009985.1:WP_011384493.1 Length = 257 Score = 146 bits (369), Expect = 4e-40 Identities = 85/243 (34%), Positives = 143/243 (58%), Gaps = 8/243 (3%) Query: 18 VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77 +E+ ++K +G VL I+L V RGE +V+ G SG+GKS M++CI L + G I +D Sbjct: 7 IELTGVHKAFGPKVVLDGIDLSVARGESVVVIGGSGTGKSVMLKCILGLLRPESGSIRID 66 Query: 78 GTELTN-DLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHF 136 G ++ K D + ++ GM+FQ LF L + EN I +KM + +A ++A+ Sbjct: 67 GEDVVGMGPKDRDRIMKKFGMLFQGGALFDSLKVWENVAFGLIQGQKMERAKARDIAIEK 126 Query: 137 LKRVKIPEQANKY-PGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTM 195 L +V + + P +LSGG Q+RV++AR++ NP+I+ FDEPT+ LDP M + D + Sbjct: 127 LAQVGLAASTGELSPSELSGGMQKRVSLARAIATNPEIIFFDEPTTGLDPIMADVINDLI 186 Query: 196 VGLAEE-GMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQ 254 V +E G T L +TH+M AR++++R+ + +G+++ PA D+ +E ++ Q Sbjct: 187 VKCCKEVGATALSITHDMASARKISDRIAMLYKGRLIWVG-PAKDIDHSGNE----YVDQ 241 Query: 255 ILH 257 +H Sbjct: 242 FIH 244 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: 162 Number of extensions: 7 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: 257 Length of database: 257 Length adjustment: 24 Effective length of query: 233 Effective length of database: 233 Effective search space: 54289 Effective search space used: 54289 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: 47 (22.7 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