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_010932579.1 AYT24_RS04145 phosphate ABC transporter ATP-binding protein PstB
Query= TCDB::Q52815 (257 letters) >NCBI__GCF_000006985.1:WP_010932579.1 Length = 286 Score = 132 bits (332), Expect = 8e-36 Identities = 84/260 (32%), Positives = 140/260 (53%), Gaps = 15/260 (5%) Query: 5 PAKKLTVSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCIN 64 P +K + V + + +YG+F ++ +N +++ I GPSG GKST +R IN Sbjct: 27 PERKAIAGGGKPHVVARDFSIYYGEFEAVKKVNAEILSKYVTAIIGPSGCGKSTFLRAIN 86 Query: 65 RLEE-----HQKGKIVVDGTELTNDLKKIDEV--RREVGMVFQHFNLFPHLTILENCTLA 117 R+ + H G ++ DG ++ K DEV R+++GMVFQ N FP +I +N Sbjct: 87 RMNDLIPNCHTTGALMFDGEDIYG--KFTDEVLLRKKIGMVFQKPNPFPK-SIFDNIAYG 143 Query: 118 PIWVRKMPKKQAEEVAMHFLKRV----KIPEQANKYPGQLSGGQQQRVAIARSLCMNPKI 173 P KK+ E+ L++ ++ ++ +K LSGGQQQR+ +AR+L + P+I Sbjct: 144 PKLHGIKDKKKLSEIVEKSLRKAALWDEVSDRLDKNALGLSGGQQQRLCVARALAVEPEI 203 Query: 174 MLFDEPTSALDPEMIKEVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQ 233 +L DEPTSALDP+ ++ D + L T++ VTH M A +V++ +F +G +VE Sbjct: 204 LLLDEPTSALDPKATAKIEDLIQEL-RGSYTIMIVTHNMQQASRVSDYTMFFYEGVLVEH 262 Query: 234 NEPAAFFDNPQHERTKLFLS 253 F P+ T+ +++ Sbjct: 263 APTTQLFTRPKDSMTEDYIT 282 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: 183 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: 286 Length adjustment: 25 Effective length of query: 232 Effective length of database: 261 Effective search space: 60552 Effective search space used: 60552 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