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_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= TCDB::Q52815 (257 letters) >NCBI__GCF_900142125.1:WP_072908814.1 Length = 415 Score = 147 bits (372), Expect = 3e-40 Identities = 79/222 (35%), Positives = 135/222 (60%), Gaps = 4/222 (1%) Query: 33 LRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVDGTELT--NDLKKIDE 90 ++D + ++ +GE VI G SGSGKSTM+R +NRL E G++++DG ++ ND + + Sbjct: 46 VQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKV 105 Query: 91 VRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFLKRVKIPEQANKYP 150 R ++ MVFQ F L PH+T+L+N + + + K+ E+ A+ L++V + A P Sbjct: 106 RRAKLSMVFQSFALMPHMTVLQNAAFG-LEMDGVDKQTREQRALQALEQVGLEAWAESMP 164 Query: 151 GQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVGL-AEEGMTMLCVT 209 +LSGG QQRV +AR L ++P I+L DE SALDP + E+ D ++ L A+ T++ ++ Sbjct: 165 DELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFIS 224 Query: 210 HEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLF 251 H++ A ++ +R+ M+ G++V+ P NP + + F Sbjct: 225 HDLDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAF 266 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: 231 Number of extensions: 14 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: 415 Length adjustment: 28 Effective length of query: 229 Effective length of database: 387 Effective search space: 88623 Effective search space used: 88623 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 Apr 09 2024. 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