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_109939172.1 DLD82_RS00420 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= TCDB::Q52815 (257 letters) >NCBI__GCF_003173335.1:WP_109939172.1 Length = 376 Score = 133 bits (334), Expect = 6e-36 Identities = 75/231 (32%), Positives = 132/231 (57%), Gaps = 4/231 (1%) Query: 28 GDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVDGTELTN-DLK 86 G L++I+ V +GE V+ G SG GKST++RC+NRL G I++DG ++ + + Sbjct: 19 GHVVALKNISFSVKKGEIFVLMGLSGCGKSTLLRCLNRLISPTAGSILLDGEDIASVSTE 78 Query: 87 KIDEVRRE-VGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFLKRVKIPEQ 145 ++ +RR +GMVFQ F L PH I +N + ++ + ++ +A L V + Sbjct: 79 RMRTIRRSRMGMVFQSFALLPHKNIQDNVAFG-LEIQGISAEERAGIAKETLDLVGLSGY 137 Query: 146 ANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVGLAEE-GMT 204 N YP QLSGG +QRV +AR++ +P I+L DE SALDP + +++ + ++ + + T Sbjct: 138 ENSYPDQLSGGMKQRVGLARAIASSPDILLMDEAFSALDPMIRRDMQNELLDIQDRLEKT 197 Query: 205 MLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQI 255 ++ V+H++ A ++ R+ M G+IV+ P P++E + F+ + Sbjct: 198 IIFVSHDLDEALKLGTRIGLMKAGEIVQIGTPEEILTQPKNEFVERFVEDV 248 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: 190 Number of extensions: 11 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: 376 Length adjustment: 27 Effective length of query: 230 Effective length of database: 349 Effective search space: 80270 Effective search space used: 80270 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