Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_000016745.1:WP_011938227.1 Length = 353 Score = 199 bits (507), Expect = 8e-56 Identities = 110/241 (45%), Positives = 154/241 (63%), Gaps = 9/241 (3%) Query: 3 QIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYI 62 ++ + DL G + +SLD++ E + L+GPSG GK+T LR +AGLE P+ G I I Sbjct: 5 ELSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIRI 64 Query: 63 GGDHMNYRVP-------QNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERV 115 G + M + + R + VFQ YAL+PH TV +N+ +GL+ + E +RV Sbjct: 65 G-EQMVFESAKKIEVSVEKRCLGFVFQSYALWPHRTVYENVAYGLKLRK-VPDGEIRQRV 122 Query: 116 VEVAETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 175 EV LG+ DL +R P +LSGGQQQRVAL R++V +P+V L+DEPLSNLDAKLR E R Sbjct: 123 QEVLANLGLGDLSERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEARI 182 Query: 176 ELQNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFI 235 L+ L L ++ V VTH+Q EAM MAD++ ++ DG ++Q +P E Y P +LFVAEF+ Sbjct: 183 WLRQLIIDLNLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAEFM 242 Query: 236 G 236 G Sbjct: 243 G 243 Lambda K H 0.317 0.135 0.386 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: 281 Number of extensions: 12 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: 353 Length adjustment: 30 Effective length of query: 353 Effective length of database: 323 Effective search space: 114019 Effective search space used: 114019 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: 41 (21.6 bits) S2: 49 (23.5 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