Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_085638891.1 MGEO_RS13900 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_002115805.1:WP_085638891.1 Length = 362 Score = 548 bits (1412), Expect = e-161 Identities = 286/363 (78%), Positives = 313/363 (86%), Gaps = 3/363 (0%) Query: 1 MADLKLTGVEKAY-GDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 59 MA+LKLT VEK Y G V VL+NINLDI++GELIVFVGPSGCGKSTLLRMIAGLEKITGGT Sbjct: 1 MANLKLTNVEKTYAGAVNVLNNINLDIEKGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 60 Query: 60 LEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAE 119 LEIDG VVND+PPA RGIAMVFQSYALYPHMTVRENMSFALKIAKK Q+EIDAAVE AA+ Sbjct: 61 LEIDGQVVNDMPPAMRGIAMVFQSYALYPHMTVRENMSFALKIAKKPQSEIDAAVERAAK 120 Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179 LQL YLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATR+EIAQL Sbjct: 121 MLQLDPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRIEIAQL 180 Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPK 239 KE MPESTM+YVTHDQVEAMTLA+RIVVLA GIAQVG+PLELYE+P +EFVAQFIGSP Sbjct: 181 KEQMPESTMIYVTHDQVEAMTLASRIVVLANKGIAQVGAPLELYERPNSEFVAQFIGSPS 240 Query: 240 MNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVF 299 MNLLPG+I+GTG QTTV+M GG AVSDYP+ D+ MG VNVGVRPED V GD++F Sbjct: 241 MNLLPGEIVGTGQQTTVKMDGGGVAVSDYPTTDADMGLKVNVGVRPEDFV--GTSGDHIF 298 Query: 300 EGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVFKDGVS 359 EG+V ITEALGEVTLLYFE IGKL GIH +L+G+ +L A P KVH+F +G S Sbjct: 299 EGRVEITEALGEVTLLYFEKQGDGHAVIGKLPGIHAELRGKTVKLGASPDKVHIFHNGTS 358 Query: 360 LHY 362 L Y Sbjct: 359 LLY 361 Lambda K H 0.316 0.135 0.379 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: 548 Number of extensions: 27 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: 373 Length of database: 362 Length adjustment: 30 Effective length of query: 343 Effective length of database: 332 Effective search space: 113876 Effective search space used: 113876 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