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_011613447.1 TERY_RS19750 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= TCDB::Q52815 (257 letters) >NCBI__GCF_000014265.1:WP_011613447.1 Length = 407 Score = 145 bits (366), Expect = 1e-39 Identities = 84/226 (37%), Positives = 132/226 (58%), Gaps = 4/226 (1%) Query: 33 LRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVDGTELTN-DLKKIDEV 91 L D+++ + GE V+ G SGSGKST++RCINRL + G I +DG ++ + D K++ ++ Sbjct: 54 LADVSIDIGTGELFVVMGLSGSGKSTLVRCINRLVDPTSGHIYIDGEDIAHADEKRMRDI 113 Query: 92 R-REVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFLKRVKIPEQANKYP 150 R +V MVFQ F LFPH T+ EN + VR + + A+ L+ V + + AN P Sbjct: 114 RLNKVSMVFQRFGLFPHKTVAENVEYG-LKVRGVSTTHRRQKALETLEVVGLEKWANYQP 172 Query: 151 GQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVGLAEE-GMTMLCVT 209 LSGG QQRV +AR+L + I+L DE SALDP E+ D ++ L +E T++ ++ Sbjct: 173 TSLSGGMQQRVGLARALATDADILLMDEAFSALDPLTRGEMQDELLRLQKELHKTIVFIS 232 Query: 210 HEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQI 255 H+M ++ +R+ M G IV+ P NP+++ K F ++ Sbjct: 233 HDMQEGLKLGDRIAVMKDGAIVQLGTPEELVTNPKNDYIKAFTEEV 278 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: 200 Number of extensions: 10 Number of successful extensions: 4 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: 407 Length adjustment: 28 Effective length of query: 229 Effective length of database: 379 Effective search space: 86791 Effective search space used: 86791 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: 48 (23.1 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