Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_000016745.1:WP_011938227.1 Length = 353 Score = 204 bits (518), Expect = 4e-57 Identities = 116/282 (41%), Positives = 177/282 (62%), Gaps = 13/282 (4%) Query: 16 GKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKL 75 GK L V++++ GE +LGPSG+GKTT +R IAGL++PS G + +++V + K Sbjct: 16 GKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIRIGEQMVFESAKK 75 Query: 76 I-VPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHHVL 134 I V E R +G VFQ++AL+P+ T +EN+A+ L K+ EIR+RV+EV L + + Sbjct: 76 IEVSVEKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQRVQEVLANLGLGDLS 135 Query: 135 NHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTL 194 P +LSGGQQQRVALAR+LV +P ++LLDEP SNLDA++R+ AR ++++ L ++ Sbjct: 136 ERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEARIWLRQLIIDLNLSA 195 Query: 195 LVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELEGKVT-- 252 + V+HD A+ A+AD+V +L G + Q G P+++Y P S+ VA +G N + G VT Sbjct: 196 VCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAEFMGANNTISGLVTDV 255 Query: 253 ---------NEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSK 285 N + G LR P+ + DRA +R E +KL++ Sbjct: 256 DGDSARIEGNGWALRGRLRTPLK-AGDRATAVVRLEKIKLAQ 296 Lambda K H 0.319 0.139 0.390 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: 270 Number of extensions: 9 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: 353 Length of database: 353 Length adjustment: 29 Effective length of query: 324 Effective length of database: 324 Effective search space: 104976 Effective search space used: 104976 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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