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_092344926.1 BLU87_RS03900 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52812 (341 letters) >NCBI__GCF_900107645.1:WP_092344926.1 Length = 339 Score = 364 bits (934), Expect = e-105 Identities = 186/338 (55%), Positives = 233/338 (68%), Gaps = 3/338 (0%) Query: 4 KLLSAAIGAAVLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFDVDF 63 K+L + ++ V A + L V+ KGF+Q GVN + GF PDA G W G DVD Sbjct: 5 KILVLVLSLCLMLV-TFAHAGKDLDAVRNKGFIQTGVNGAVFGFGMPDAKGVWEGLDVDT 63 Query: 64 CKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRPVTY 123 +AVA+A+FGD +KVK+TP +A++RFTALQSGEID+L+RN T T++R+T LG NF V Y Sbjct: 64 ARAVAAAIFGDASKVKFTPLSAQQRFTALQSGEIDILTRNATRTLSRETQLGLNFVTVNY 123 Query: 124 YDGQGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENLPEVN 183 YDGQGF+V K L VKSA EL GA +CV GTTTE N AD+F+T+ + + PVV E+ E+ Sbjct: 124 YDGQGFLVSKELGVKSAKELDGATVCVLPGTTTEQNAADFFRTHKMAWKPVVIESTAELA 183 Query: 184 AAYDAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFDIVSW 243 + AGRCDV T+D S L R +P ++ILPEIISKEPL PAVR GDDQ+ DIV + Sbjct: 184 KTFFAGRCDVLTSDASQLAGARAISADPKGYVILPEIISKEPLAPAVRHGDDQFRDIVDF 243 Query: 244 TAYALINAEEFGITQANVDEMKNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVIKGVG 303 + A+INAEE GIT NVDEM NS NP I+RFLG G LGL WA N+IK VG Sbjct: 244 SVLAMINAEELGITSKNVDEMLNSKNPVIQRFLGVSPGN--GKALGLDEKWAYNIIKQVG 301 Query: 304 NYGEIFERNIGQGSPLKIARGLNALWNKGGIQYAPPVR 341 NYGE+FERN+G + L I RGLNALW GG+ Y+PP + Sbjct: 302 NYGEVFERNVGINTTLGIERGLNALWTNGGLMYSPPFK 339 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: 357 Number of extensions: 16 Number of successful extensions: 2 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: 339 Length adjustment: 28 Effective length of query: 313 Effective length of database: 311 Effective search space: 97343 Effective search space used: 97343 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 24 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