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_011842387.1 RSPH17029_RS17510 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q52815 (257 letters) >NCBI__GCF_000015985.1:WP_011842387.1 Length = 266 Score = 222 bits (565), Expect = 7e-63 Identities = 118/245 (48%), Positives = 162/245 (66%), Gaps = 12/245 (4%) Query: 23 MNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVDGTELT 82 + K +G F VL+ ++L V +GE + I G SGSGKST +R IN +E Q G +D + Sbjct: 13 IRKSFGTFEVLKGVSLDVAQGEVVSIIGASGSGKSTFLRSINVMEMPQAG--TMDFGDFH 70 Query: 83 NDLKK----------IDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEV 132 D +K + ++R E+GMVFQ +NL+PH+T+L+N AP+ +R+ P+ QA E Sbjct: 71 FDFRKGAASHPTKVQLQKLRAEIGMVFQSYNLWPHMTVLQNVIHAPMTLRRTPRAQAVEE 130 Query: 133 AMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVL 192 A L R+ + E+ + YP +LSGGQQQRVAIAR+L M P++MLFDE TSALDPE++ EVL Sbjct: 131 AEALLARIGLYEKRDSYPARLSGGQQQRVAIARALAMKPRLMLFDEVTSALDPELVHEVL 190 Query: 193 DTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFL 252 M LA +GMTML VTHE+ FAR V++RV+F DQG + EQ P NP+ R + FL Sbjct: 191 VLMASLAADGMTMLLVTHEIAFARDVSSRVLFFDQGVMAEQGPPDRVLRNPESPRLRQFL 250 Query: 253 SQILH 257 +ILH Sbjct: 251 HRILH 255 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: 184 Number of extensions: 5 Number of successful extensions: 2 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: 266 Length adjustment: 25 Effective length of query: 232 Effective length of database: 241 Effective search space: 55912 Effective search space used: 55912 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 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