Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 199 bits (505), Expect = 1e-55 Identities = 118/297 (39%), Positives = 171/297 (57%), Gaps = 13/297 (4%) Query: 4 LTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEG 63 L++ +T+ Y G A+++ SLDI +GEF+ L+GPSG GKS+ LR++AGL+ G Sbjct: 3 LSIRQLTRRY-----GAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRG 57 Query: 64 ELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLE---ESTGLPDDEIRQRV 120 ++ + L + AQ RDI +VFQ YAL+PH +V N++FGL + +I RV Sbjct: 58 DVLRDGTDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARV 117 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 E+ + + +L R P QLSGGQ+QRVAL RA+ +P + L+DEP LDA++R +R Sbjct: 118 EDLLRRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRV 177 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 L+ LQ LG+TTV VTHDQ EA+ + DRV V++ G ++QVG P + Y P FV GF+ Sbjct: 178 WLRDLQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFV 237 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSG 297 G N G + D G + G L G + +RPE + + R G Sbjct: 238 GR--ANRIRGHVERDRLHLGGHSF--QGELPGDLAGRE-IEAWLRPEHLALASRGLG 289 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: 425 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: 384 Length adjustment: 30 Effective length of query: 353 Effective length of database: 354 Effective search space: 124962 Effective search space used: 124962 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: 50 (23.9 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