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 WP_011840329.1 RSPH17029_RS02000 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52812 (341 letters) >NCBI__GCF_000015985.1:WP_011840329.1 Length = 338 Score = 405 bits (1041), Expect = e-118 Identities = 199/329 (60%), Positives = 240/329 (72%), Gaps = 3/329 (0%) Query: 14 VLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFDVDFCKAVASAVFG 73 V + A ASA TL DVKA+G + CGV+TGLTGF+ PDA+GNW GFDV C+AVA+AV G Sbjct: 12 VAGLAAGLASAATLDDVKARGELNCGVSTGLTGFSLPDANGNWTGFDVSLCRAVAAAVLG 71 Query: 74 DPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRPVTYYDGQGFMVRK 133 D TKVK+ PT + RFTAL SGE+D+L+RN+TWT +RDT L +F V YYDGQGFMVRK Sbjct: 72 DGTKVKFVPTTGQTRFTALASGEVDMLARNSTWTFSRDTDLKLDFVGVNYYDGQGFMVRK 131 Query: 134 GLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENLPEVNAAYDAGRCDV 193 L V SA EL GA +C+Q+GTTTELNLAD+FK NNL Y PV E E Y AG CD Sbjct: 132 DLGVTSAKELDGATVCIQTGTTTELNLADWFKVNNLSYTPVAVETNAEGEQQYAAGACDA 191 Query: 194 YTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFDIVSWTAYALINAEE 253 YTTD SGL + R +P+ HIILPEIISKEPLGPAVR GD++W DIV WT ALI AEE Sbjct: 192 YTTDASGLAATRAAFADPENHIILPEIISKEPLGPAVRHGDNEWADIVRWTLNALIAAEE 251 Query: 254 FGITQANVDEM-KNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVIKGVGNYGEIFERN 312 +G+T AN++E+ NSPNP+I+R LG + D +G + L NDWA I GNYGEIF Sbjct: 252 YGVTSANMEELAANSPNPEIQRVLGVQGD--LGKMIRLDNDWAKRAIAVGGNYGEIFAAT 309 Query: 313 IGQGSPLKIARGLNALWNKGGIQYAPPVR 341 IG+ +P+ +ARGLNA W +GG+ YAPP R Sbjct: 310 IGEATPIGLARGLNAQWTQGGLLYAPPFR 338 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: 413 Number of extensions: 11 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: 338 Length adjustment: 28 Effective length of query: 313 Effective length of database: 310 Effective search space: 97030 Effective search space used: 97030 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 Apr 10 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