Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_011650503.1 RL_RS03925 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_000009265.1:WP_011650503.1 Length = 362 Score = 450 bits (1158), Expect = e-131 Identities = 235/354 (66%), Positives = 277/354 (78%), Gaps = 1/354 (0%) Query: 1 MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60 M L L + K+YG V VL I+LDI+QGE IVFVGPSGCGKSTLLRMIAGLE ITGG + Sbjct: 1 MTGLTLKDIRKSYGSVDVLHGIDLDIKQGEFIVFVGPSGCGKSTLLRMIAGLEAITGGEM 60 Query: 61 EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120 IDG +VNDVPP++RGIAMVFQSYALYPHMTV +NM+F +KIA +S+ EID V+AAAE Sbjct: 61 YIDGHLVNDVPPSKRGIAMVFQSYALYPHMTVFDNMAFGMKIAGESKQEIDRRVKAAAES 120 Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180 LQL QYL RLPKALSGGQRQRVAIGR+I RDPKV+LFDEPLSNLDAALRVATR+EIA+L Sbjct: 121 LQLTQYLGRLPKALSGGQRQRVAIGRAICRDPKVFLFDEPLSNLDAALRVATRIEIARLN 180 Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240 E M ++TM+YVTHDQVEAMTLA RIVVL+ G I QVG+PL+LYE+P N FVA+FIGSP M Sbjct: 181 EQMADTTMIYVTHDQVEAMTLADRIVVLSAGNIEQVGAPLDLYERPANLFVAKFIGSPAM 240 Query: 241 NLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVFE 300 N++P I GTG+QTTV +T G D +D S MG + GVRPED+ A G DY+FE Sbjct: 241 NIIPATISGTGSQTTVTLTGGMSVTLDVATDASEMGKQASFGVRPEDL-RVADGADYLFE 299 Query: 301 GKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354 G+V+I EALGEVTLLY E +P + KL GI+ KGQ R A+ K+H+F Sbjct: 300 GEVSIVEALGEVTLLYIEGLVPGEPIVVKLPGIYDVKKGQRMRFAADRQKLHLF 353 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: 468 Number of extensions: 22 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: 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