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 352022 BT2494 ABC transporter, ATP-binding protein (NCBI ptt file)
Query= TCDB::Q52815 (257 letters) >FitnessBrowser__Btheta:352022 Length = 238 Score = 142 bits (359), Expect = 5e-39 Identities = 82/224 (36%), Positives = 134/224 (59%), Gaps = 9/224 (4%) Query: 18 VEIVNMNKWYGD---FHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKI 74 +++ ++NK Y + HVL+ INL + RGE + I G SGSGKST++ + L+ + G Sbjct: 2 IKLTDINKTYNNGAPLHVLKGINLDIQRGEFVSIMGASGSGKSTLLNILGILDNYDTGDY 61 Query: 75 VVDGTELTN--DLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEV 132 ++ + + + K + R +G +FQ FNL +EN L P++ + + +K+ + Sbjct: 62 YLNNVLIKDLSETKAAEYRNRMIGFIFQSFNLISFKDAVENVAL-PLFYQGVSRKKRNAL 120 Query: 133 AMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVL 192 A+ +L R+ + E A+ P ++SGGQ+QRVAIAR+L P+I+L DEPT ALD + EV+ Sbjct: 121 ALEYLDRLGLKEWAHHMPNEMSGGQKQRVAIARALITQPQIILADEPTGALDSKTSVEVM 180 Query: 193 DTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQI--VEQN 234 + L GMT++ VTHE G A Q +++I + G I +E+N Sbjct: 181 QILKDLHRMGMTIVVVTHESGVANQ-TDKIIHIKDGIIERIEEN 223 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: 129 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: 238 Length adjustment: 24 Effective length of query: 233 Effective length of database: 214 Effective search space: 49862 Effective search space used: 49862 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: 46 (22.3 bits)
This GapMind analysis is from Sep 17 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