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 207829 DVU2342 amino acid ABC transporter, periplasmic amino acid-binding protein
Query= TCDB::Q52812 (341 letters) >MicrobesOnline__882:207829 Length = 270 Score = 102 bits (254), Expect = 1e-26 Identities = 73/244 (29%), Positives = 116/244 (47%), Gaps = 14/244 (5%) Query: 1 MKNKLLSAAIGAAVLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPD-ASGNWAGF 59 MK LL A VL A+ A A L ++K +G + CGV + F D S GF Sbjct: 1 MKRLLLLALTLGLVLT--AAVAHAGKLDEIKQRGTLVCGVKDSVVPFGFIDETSKQLVGF 58 Query: 60 DVDFCKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFR 119 DVD C+ +A K++ + R L G +D+++ T RD + F+ Sbjct: 59 DVDICQFIADRA---GVKLEVKTVTSATRIPMLTQGSVDLVAATMTHKFERDDVIDFS-- 113 Query: 120 PVTYYD-GQGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFEN 178 +TY+D GQ +V+KG +KSA +L G + G+T+E N+ K V F+ Sbjct: 114 -ITYFDAGQRLLVKKGGGIKSAADLKGKKVATVKGSTSEKNM----KAAQPDCVVVSFDE 168 Query: 179 LPEVNAAYDAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWF 238 P+ A G+ + TTD+ L L+ + PD+ I+ + I+ EP G + + D ++ Sbjct: 169 YPQAFLALKQGKAEAVTTDEPILVGLKNSDPEPDKWDIVGDFIASEPYGLGLVENDSKFR 228 Query: 239 DIVS 242 D V+ Sbjct: 229 DFVN 232 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: 195 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: 270 Length adjustment: 27 Effective length of query: 314 Effective length of database: 243 Effective search space: 76302 Effective search space used: 76302 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: 48 (23.1 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