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_109969948.1 DK846_RS15740 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q52815 (257 letters) >NCBI__GCF_003173355.1:WP_109969948.1 Length = 250 Score = 233 bits (594), Expect = 3e-66 Identities = 116/244 (47%), Positives = 170/244 (69%) Query: 11 VSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQ 70 +S +E +++ ++ K +G VL+ ++ V +GE I GPSG+GKST++RCIN+L Sbjct: 1 MSESEFILKVEDIRKSFGSSEVLKGVSFNVKKGETICFIGPSGTGKSTLLRCINQLTIPD 60 Query: 71 KGKIVVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAE 130 GK++++G E+T+ +I+ R+++GMVFQ+F LF HLT + N +A + V+ M K A Sbjct: 61 SGKVLLNGEEVTHSGSQINHFRQKIGMVFQNFFLFDHLTAVRNVEIALLKVKGMNAKDAR 120 Query: 131 EVAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKE 190 AM L++V + E A+ +P +LSGGQ QRV+IAR+L M+P +MLFDEPTSALDPE+ +E Sbjct: 121 AKAMKELQQVGMAEWADHFPAELSGGQAQRVSIARALAMDPDVMLFDEPTSALDPELTRE 180 Query: 191 VLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKL 250 VL+ M LA +GMTML VTHEMGFA VAN+++FM+ G I EQ P ++P+ ER K Sbjct: 181 VLEVMKKLALDGMTMLVVTHEMGFACSVANQILFMEHGVIKEQGSPQVLLNDPKFERCKA 240 Query: 251 FLSQ 254 F+ Q Sbjct: 241 FIGQ 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: 198 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: 250 Length adjustment: 24 Effective length of query: 233 Effective length of database: 226 Effective search space: 52658 Effective search space used: 52658 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 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