Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_018371126.1 BN415_RS08120 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_000341525.1:WP_018371126.1 Length = 377 Score = 199 bits (505), Expect = 1e-55 Identities = 117/309 (37%), Positives = 180/309 (58%), Gaps = 29/309 (9%) Query: 1 MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60 MV++ + V K + + ++++ N++I++ E +GPSG GK+T +R+IAGL+ + G Sbjct: 1 MVQVKLDKVYKRYPNSEHYSVEDFNLDIQDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 Query: 61 ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 E D +++ V P+DR I MVFQ +ALYP++T +EN+AF L K +K+EI +R Sbjct: 61 EFLIDGQVMND-----VAPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYAKDEIDRR 115 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 V E A+IL + L+ P +LSGGQ+QRVA+ RA+V+D + L+DEP SNLDA++R S R Sbjct: 116 VREAAEILGLIEFLDRKPADLSGGQRQRVAMGRAIVRDSKIFLMDEPLSNLDAKLRVSMR 175 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRV----------GVLVKGKLVQVGKPEDLYD 230 A + ++ R+G T + V+HD + +ADR+ G G++ Q+G P++LY+ Sbjct: 176 AEIAKLHRRIGATTIYVTHDQTEAMTLADRIVIMSATKNPSGTGTIGRIEQIGSPQELYN 235 Query: 231 NPVSIQVASLIGEINELEGKVTNEGVVIG-----SLRFP---------VSVSSDRAIIGI 276 P + VA IG KV + VI SLR P + I GI Sbjct: 236 TPANKFVAGFIGSPAMNFFKVALKDGVISSEQGLSLRLPEGKRKLLEDKGYNGKELIFGI 295 Query: 277 RPEDVKLSK 285 RPED+K S+ Sbjct: 296 RPEDIKASQ 304 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: 313 Number of extensions: 16 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: 353 Length of database: 377 Length adjustment: 30 Effective length of query: 323 Effective length of database: 347 Effective search space: 112081 Effective search space used: 112081 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 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