Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_008411393.1 DESHY_RS06575 ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_000315365.1:WP_008411393.1 Length = 227 Score = 178 bits (452), Expect = 1e-49 Identities = 92/215 (42%), Positives = 145/215 (67%), Gaps = 3/215 (1%) Query: 13 FKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASN 72 +K ++ ++ VN++I GE ILG SG+GK+T +R++AGL+ P +G + D++++ N Sbjct: 12 YKNSQLSTINKVNLSISRGEIIAILGQSGSGKSTILRLLAGLEKPCSGTIVIDNKVMFDN 71 Query: 73 GKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHH 132 V PE+R +GMVFQ +AL+P++T +NI + L K+ ++E KR++EV ++++ Sbjct: 72 NTY-VNPENRGVGMVFQDYALFPHMTVEKNIIYGLA--KLDRKERTKRLKEVLTLVNLEE 128 Query: 133 VLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGV 192 + +P ELSGGQQQRVALARAL P++LLLDEPFSNLDA +R R +K + +G+ Sbjct: 129 FRDRYPYELSGGQQQRVALARALAPKPAVLLLDEPFSNLDADLRCKIRDELKRIIKDVGI 188 Query: 193 TLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPED 227 T + V+HD D ++ADRV L KG +++V E+ Sbjct: 189 TSIFVTHDQEDAISLADRVVYLHKGTVLKVKTKEE 223 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: 195 Number of extensions: 11 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: 227 Length adjustment: 26 Effective length of query: 327 Effective length of database: 201 Effective search space: 65727 Effective search space used: 65727 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: 47 (22.7 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