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_012384591.1 BIND_RS08120 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52812 (341 letters) >NCBI__GCF_000019845.1:WP_012384591.1 Length = 336 Score = 432 bits (1112), Expect = e-126 Identities = 206/341 (60%), Positives = 251/341 (73%), Gaps = 5/341 (1%) Query: 1 MKNKLLSAAIGAAVLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFD 60 M ++SA + + + GA A TL +VK +GF+ CG N GL GF PD G W GFD Sbjct: 1 MFKSIVSAGLFSLCVTTGALAG---TLDEVKGRGFLNCGSNPGLAGFGLPDDKGQWVGFD 57 Query: 61 VDFCKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRP 120 +DFC+AVA+A+F DPTKVK+ P + K+RFTALQSGEID+LSRNTTWT +R+ GF F Sbjct: 58 IDFCRAVAAAIFDDPTKVKFLPLSGKDRFTALQSGEIDILSRNTTWTQSREVGQGFLFTG 117 Query: 121 VTYYDGQGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENLP 180 +TYYDGQGFM + LN+ SALEL+GA+ICVQ GTTTELNLAD+F+ NNLQY PV F Sbjct: 118 ITYYDGQGFMTHRKLNLTSALELAGASICVQQGTTTELNLADFFRANNLQYEPVNFATGD 177 Query: 181 EVNAAYDAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFDI 240 E AYD GRCD TTD SGLY+ R L NPD+H++LPEIISKEPLGP VRQGDDQWF++ Sbjct: 178 EALKAYDTGRCDALTTDASGLYAQRAKLANPDDHVVLPEIISKEPLGPLVRQGDDQWFNL 237 Query: 241 VSWTAYALINAEEFGITQANVDEMKNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVIK 300 V W +A +NAEE G+T N+DE S +P+IKR LG E + G LGLT DW +IK Sbjct: 238 VKWVHFAWLNAEEDGVTSKNLDEKTKSESPEIKRLLGFEGN--FGEGLGLTRDWIYRIIK 295 Query: 301 GVGNYGEIFERNIGQGSPLKIARGLNALWNKGGIQYAPPVR 341 VGNYGE+F+RN+G+GS LKI RG+N LW KGG+ YAPPVR Sbjct: 296 HVGNYGEVFDRNLGEGSKLKIKRGINNLWTKGGLHYAPPVR 336 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: 441 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: 336 Length adjustment: 28 Effective length of query: 313 Effective length of database: 308 Effective search space: 96404 Effective search space used: 96404 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