Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_008411408.1 DESHY_RS06645 ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_000315365.1:WP_008411408.1 Length = 228 Score = 152 bits (385), Expect = 6e-42 Identities = 86/201 (42%), Positives = 125/201 (62%), Gaps = 6/201 (2%) Query: 4 IIVKNVSKVFKKG--KVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61 I + + K+++ G ++ LDNV+I + G+ ILGPSG+GK+T M I+ LD P+ G+ Sbjct: 9 IDARQLVKIYRNGAEQLKVLDNVSIKVNKGDFIAILGPSGSGKSTLMNILGCLDTPTAGQ 68 Query: 62 LYFD--DRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRK 119 Y D D L AS+ +L ++KIG +FQ + L P LTA +N+ PL M++E R+ Sbjct: 69 YYLDGVDVLKASDNEL-ADMRNQKIGFIFQKFNLLPRLTAEQNVMLPLLYRGMAEEAARQ 127 Query: 120 RVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSA 179 E IL + L H P ELSGGQQQRVA+ARA+V P LLL DEP NLD++ A Sbjct: 128 LAREKLTILGLGDRLQHRPNELSGGQQQRVAIARAIVGSPQLLLADEPTGNLDSKSSGDA 187 Query: 180 RALVKEVQSRLGVTLLVVSHD 200 + KE+ +R G T+++++HD Sbjct: 188 MEIFKEL-NRRGNTIVIITHD 207 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: 220 Number of extensions: 8 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: 228 Length adjustment: 26 Effective length of query: 327 Effective length of database: 202 Effective search space: 66054 Effective search space used: 66054 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