Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate BWI76_RS06035 BWI76_RS06035 ferric transporter ATP-binding subunit
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Koxy:BWI76_RS06035 Length = 348 Score = 204 bits (520), Expect = 2e-57 Identities = 111/313 (35%), Positives = 185/313 (59%), Gaps = 16/313 (5%) Query: 6 VKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFD 65 ++NV+K F G + +DN+N+ I G+ +LGPSG GKTT +R++AGL+ PS G++Y D Sbjct: 9 LRNVTKRF--GSNMVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIYID 66 Query: 66 DRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVA 125 V + R I MVFQ++AL+P+++ +N+ + L + + + +++ RV+E Sbjct: 67 GEDVTHRSI-----QQRDICMVFQSYALFPHMSLGDNVGYGLKMLGVPRGDVKARVKEAL 121 Query: 126 KILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKE 185 ++D+ + + ++SGGQQQRVALARAL+ P +LL DEP SNLDA +R S R ++E Sbjct: 122 AMVDLEGFEDRYVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIRE 181 Query: 186 VQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEIN 245 +Q + +T L V+HD ++ FA++D V V+ KG ++Q+G P++LY P S +AS +G+ N Sbjct: 182 LQKQFDITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQELYRQPASRFMASFMGDAN 241 Query: 246 ELEGKVTNEGVVIGSLRFPVS---VSSDRAIIGIRPEDVKLSKDVIKDDSWILVGKGKVK 302 + + V I R P + +G+RPE + LS D + ++ Sbjct: 242 LFPAAFSEDFVDIYGYRLPRPPHFAAHGEGSVGVRPEAITLS------DRGEESQRCTIR 295 Query: 303 VIGYQGGLFRITI 315 + Y G + +T+ Sbjct: 296 HVAYMGPQYEVTV 308 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: 276 Number of extensions: 15 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: 348 Length adjustment: 29 Effective length of query: 324 Effective length of database: 319 Effective search space: 103356 Effective search space used: 103356 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 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