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 GFF2246 HP15_2196 glutamate/glutamine/aspartate/asparagine ABC transporter, periplasmic substrate-binding protein
Query= TCDB::Q52812 (341 letters) >FitnessBrowser__Marino:GFF2246 Length = 347 Score = 404 bits (1038), Expect = e-117 Identities = 196/342 (57%), Positives = 248/342 (72%), Gaps = 7/342 (2%) Query: 4 KLLSAAIGAAVLAVGASAAS----ATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGF 59 K S A+G A LAVG +A+ ATTL +VK KG +QCGV +GL GF+ PD GNW G Sbjct: 9 KTKSIALGIA-LAVGTFSATGAMAATTLENVKEKGHLQCGVTSGLPGFSQPDEKGNWTGI 67 Query: 60 DVDFCKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFR 119 DVD C+AVA+A+FGD V++TP AKERFTALQSGEID+LSRNTTWT+ RD +LG NF Sbjct: 68 DVDTCRAVAAAIFGDANAVEFTPLTAKERFTALQSGEIDMLSRNTTWTLTRDASLGLNFA 127 Query: 120 PVTYYDGQGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENL 179 V YYDGQGF++ KG+ V A +L GA IC+Q+GTTTELNL+DYF+ +++ P+VF+ Sbjct: 128 GVNYYDGQGFLINKGIGVDDATQLDGATICIQAGTTTELNLSDYFRAKGMEFKPIVFDTS 187 Query: 180 PEVNAAYDAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFD 239 + + AGRCDV T+D+S L +LR L +P ILP ISKEPLGP VRQGDDQWF+ Sbjct: 188 EQTVQGFAAGRCDVLTSDRSQLAALRSKLSDPSSAKILPNTISKEPLGPVVRQGDDQWFN 247 Query: 240 IVSWTAYALINAEEFGITQANVDEMKNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVI 299 IV W +A INAEE G+T AN D+M S NP+I+R LG TD +G LGL +D+ + Sbjct: 248 IVKWVLFAQINAEELGVTSANADDMLKSDNPNIQRLLG--TDGDMGAKLGLPDDFGYQAV 305 Query: 300 KGVGNYGEIFERNIGQGSPLKIARGLNALWNKGGIQYAPPVR 341 K VGNYGE+++RN+G +PL + RG+NALW +GGI YAPPVR Sbjct: 306 KLVGNYGEMYDRNVGPDTPLGLDRGINALWTEGGIMYAPPVR 347 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: 407 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: 347 Length adjustment: 29 Effective length of query: 312 Effective length of database: 318 Effective search space: 99216 Effective search space used: 99216 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