Align AapJ, 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 GFF4561 PS417_23345 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52812 (341 letters) >FitnessBrowser__WCS417:GFF4561 Length = 342 Score = 424 bits (1089), Expect = e-123 Identities = 203/340 (59%), Positives = 254/340 (74%), Gaps = 4/340 (1%) Query: 4 KLLSAAIGA-AVLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFDVD 62 K AAIGA AVL + ++A + TTL ++ KGF+QCGV+ GL GF PD+ G G DVD Sbjct: 5 KTTLAAIGATAVLGLASTAEAGTTLDAIQKKGFIQCGVSDGLPGFGVPDSKGKMTGIDVD 64 Query: 63 FCKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRPVT 122 C AVA+AVFGD +KVK+T AKERFTALQSGEID++SRNTTWT +RD+ +G F VT Sbjct: 65 VCHAVAAAVFGDASKVKFTQLTAKERFTALQSGEIDLISRNTTWTSSRDSGMGLVFTGVT 124 Query: 123 YYDGQGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENLPEV 182 YYDG GF+V L V +A +L GA +C+Q+GTTTELN++DYF+T+ ++Y P+ F+ E Sbjct: 125 YYDGIGFLVNNKLGVTAAKQLDGATVCIQAGTTTELNVSDYFRTHGMKYTPITFDTADES 184 Query: 183 NAAYDAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFDIVS 242 +AGRCDV TTDQSGLY+ R+ + PDE ++LPE+ISKEPLGP VR+GDD+WF IV Sbjct: 185 AKGLEAGRCDVLTTDQSGLYAQRIKMAQPDEFVVLPEVISKEPLGPLVRKGDDEWFSIVK 244 Query: 243 WTAYALINAEEFGITQANVDEM-KNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVIKG 301 WT +A++NAEE GIT NV+E K + NPD+ R LG+ D + G DL L DW ++K Sbjct: 245 WTLFAMLNAEEMGITSQNVEEQAKTTKNPDVARLLGA--DGEYGKDLKLRKDWVVQIVKQ 302 Query: 302 VGNYGEIFERNIGQGSPLKIARGLNALWNKGGIQYAPPVR 341 VGNYGE+FERNIGQGS LKI RGLNALWN GGIQYAPPVR Sbjct: 303 VGNYGEVFERNIGQGSVLKIKRGLNALWNNGGIQYAPPVR 342 Lambda K H 0.316 0.134 0.398 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: 385 Number of extensions: 15 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: 341 Length of database: 342 Length adjustment: 29 Effective length of query: 312 Effective length of database: 313 Effective search space: 97656 Effective search space used: 97656 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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