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_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA
Query= TCDB::Q52815 (257 letters) >NCBI__GCF_000013785.1:WP_011911265.1 Length = 279 Score = 224 bits (570), Expect = 2e-63 Identities = 126/266 (47%), Positives = 166/266 (62%), Gaps = 20/266 (7%) Query: 2 AEAPAKKLTVSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIR 61 A APA+ + V ++ K YG+ VL ++L V GE++ I GPSGSGKST++R Sbjct: 18 AAAPAQPM--------VRFASVTKRYGELTVLEGLDLDVQEGEKVAIIGPSGSGKSTLLR 69 Query: 62 CINRLEEHQKGKIVVDGTELTN-----------DLKKIDEVRREVGMVFQHFNLFPHLTI 110 + LE G I VDG LT+ + + + VR +VGMVFQ FNLFPH+ Sbjct: 70 VLMTLEGIDDGLIEVDGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQSFNLFPHMNA 129 Query: 111 LENCTLAPIWVRKMPKKQAEEVAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMN 170 L+N AP+ V + K++A E A L V + ++ +P QLSGGQQQRVAIAR+L M Sbjct: 130 LQNVMEAPVQVLGLSKREARERAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMR 189 Query: 171 PKIMLFDEPTSALDPEMIKEVLDTMVGLAE-EGMTMLCVTHEMGFARQVANRVIFMDQGQ 229 PK+MLFDE TSALDPE+ EVL + L E +TML VTH+MGFAR+ A+RV F QG+ Sbjct: 190 PKVMLFDEVTSALDPELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGR 249 Query: 230 IVEQNEPAAFFDNPQHERTKLFLSQI 255 I EQ P A F+NPQ +RT+ FLS + Sbjct: 250 IHEQGSPDALFNNPQEDRTREFLSAV 275 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: 209 Number of extensions: 8 Number of successful extensions: 3 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: 279 Length adjustment: 25 Effective length of query: 232 Effective length of database: 254 Effective search space: 58928 Effective search space used: 58928 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