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 8502446 DvMF_3152 extracellular solute-binding protein family 3 (RefSeq)
Query= TCDB::Q52812 (341 letters) >FitnessBrowser__Miya:8502446 Length = 271 Score = 117 bits (292), Expect = 4e-31 Identities = 79/253 (31%), Positives = 126/253 (49%), Gaps = 13/253 (5%) Query: 4 KLLSAAIGAAVLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDA-SGNWAGFDVD 62 +L+ A+ V+ G + A A + D+KA+G + CGV F D S GFD+D Sbjct: 3 RLVLLAVALCVVLTG-TMAHAGKIEDIKARGALVCGVKDSTVPFGYIDEQSKQIVGFDID 61 Query: 63 FCKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRPVT 122 CKAVA + K++ + R L G +D+++ T RD + F+ +T Sbjct: 62 ICKAVADKL---GVKLELKTVTSATRIPMLTQGSVDMVAATMTHKFERDDVIDFS---IT 115 Query: 123 YY-DGQGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENLPE 181 Y+ DGQ +V+KG VKSA +L G + G+T+E N+ K + V F+ P+ Sbjct: 116 YFMDGQKLLVKKGGGVKSAADLKGKKVATAKGSTSEKNI----KAAQPEATVVSFDEYPQ 171 Query: 182 VNAAYDAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFDIV 241 A G+ + TTD + L LR + PD+ I+ + IS EP G + + D ++ D+V Sbjct: 172 AFLALKQGKAEAVTTDSTILLGLRNSDPEPDKWEIVGDYISPEPYGLGLAENDSKFRDLV 231 Query: 242 SWTAYALINAEEF 254 + T L N+ E+ Sbjct: 232 NRTLVDLWNSGEY 244 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: 198 Number of extensions: 13 Number of successful extensions: 4 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: 271 Length adjustment: 27 Effective length of query: 314 Effective length of database: 244 Effective search space: 76616 Effective search space used: 76616 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