Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_011384493.1 AMB_RS10565 ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_000009985.1:WP_011384493.1 Length = 257 Score = 131 bits (330), Expect = 2e-35 Identities = 82/233 (35%), Positives = 128/233 (54%), Gaps = 14/233 (6%) Query: 3 RIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGEL 62 +I + V K F G V LD +++++ GE ++G SG GK+ ++ I GL P +G + Sbjct: 6 KIELTGVHKAF--GPKVVLDGIDLSVARGESVVVIGGSGTGKSVMLKCILGLLRPESGSI 63 Query: 63 YFDDRLVASNGKLIVPPEDR-----KIGMVFQTWALYPNLTAFENIAFPLTN-MKMSKEE 116 D V G P+DR K GM+FQ AL+ +L +EN+AF L KM + + Sbjct: 64 RIDGEDVVGMG-----PKDRDRIMKKFGMLFQGGALFDSLKVWENVAFGLIQGQKMERAK 118 Query: 117 IRK-RVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARM 175 R +E++A++ P ELSGG Q+RV+LARA+ +P ++ DEP + LD M Sbjct: 119 ARDIAIEKLAQVGLAASTGELSPSELSGGMQKRVSLARAIATNPEIIFFDEPTTGLDPIM 178 Query: 176 RDSARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDL 228 D L+ + +G T L ++HD A I+DR+ +L KG+L+ VG +D+ Sbjct: 179 ADVINDLIVKCCKEVGATALSITHDMASARKISDRIAMLYKGRLIWVGPAKDI 231 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: 231 Number of extensions: 19 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: 353 Length of database: 257 Length adjustment: 27 Effective length of query: 326 Effective length of database: 230 Effective search space: 74980 Effective search space used: 74980 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: 48 (23.1 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