Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 145 bits (367), Expect = 9e-40 Identities = 84/220 (38%), Positives = 125/220 (56%), Gaps = 11/220 (5%) Query: 19 GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEG-------ELRLEDRV 71 G A+ +SLD+ GE +V+ GPSG GKST +R + GLET EG E+R + RV Sbjct: 12 GGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEVRPDRRV 71 Query: 72 LNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISD 131 L + A+ + MVFQ + L+PH ++ N + + GL D E + + I+D Sbjct: 72 LQRIRAR---VGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVRIAD 128 Query: 132 LLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGV 191 D+ P QLSGGQQQR A+ RA+ PE+ L DEP S LDA++ E+ ++ L E G+ Sbjct: 129 QADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKALATE-GI 187 Query: 192 TTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRP 231 T + VTH+ A + DR+ +D G++ + G+P D + P Sbjct: 188 TMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAP 227 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: 229 Number of extensions: 17 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: 383 Length of database: 241 Length adjustment: 27 Effective length of query: 356 Effective length of database: 214 Effective search space: 76184 Effective search space used: 76184 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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