Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Pedo557:CA265_RS15880 Length = 330 Score = 146 bits (369), Expect = 7e-40 Identities = 81/245 (33%), Positives = 144/245 (58%), Gaps = 16/245 (6%) Query: 4 LTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEG 63 +++ ++TK Y E G I + +S +I G+ + ++G SG GKST L+ + GL EG Sbjct: 6 ISVKNLTKQYQAEQAGGI---KNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDEG 62 Query: 64 ELRLEDRVLNGVSAQ----DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQR 119 E+ ED+ + G Q + + MV Q ++L + V N++ + L + +++ + Sbjct: 63 EIFFEDKRVKGPDEQLIPGHKQMKMVTQDFSLNIYAKVYDNIA------SQLSNTDLKTK 116 Query: 120 VEETTDM---LGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRA 176 E+T + L I L ++K +LSGG+QQRVA+ +A+V D +V L+DEP S +DA L+ Sbjct: 117 AEKTLQIMEHLRILPLQNKKIIELSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKN 176 Query: 177 EMRTELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFV 236 ++R +++R+ E GVT + V+HD + + + D++ +L +GEL Q G P + Y P +++ Sbjct: 177 QLRADIKRVASETGVTVILVSHDPADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIYT 236 Query: 237 AGFIG 241 A +G Sbjct: 237 AQILG 241 Lambda K H 0.316 0.136 0.384 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: 275 Number of extensions: 19 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: 383 Length of database: 330 Length adjustment: 29 Effective length of query: 354 Effective length of database: 301 Effective search space: 106554 Effective search space used: 106554 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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