Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 5210215 Shew_2658 ABC transporter-related protein (RefSeq)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__PV4:5210215 Length = 227 Score = 140 bits (354), Expect = 3e-38 Identities = 77/202 (38%), Positives = 123/202 (60%), Gaps = 8/202 (3%) Query: 18 AVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMNYRVPQ---- 73 AV L L I EF+ ++GPSG GK+T L M+ G+++P+SG ++I G+ + + Q Sbjct: 22 AVKSLDLTIAQGEFVAIMGPSGSGKTTLLNMIGGIDSPSSGAVFIDGEDITHLSEQALIA 81 Query: 74 -NRD-IAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLLDRK 131 RD + +FQDY+L P +T +N+ F ++ + G++ AE +R + + +G+A D+ Sbjct: 82 FRRDHVGFIFQDYSLLPVLTALENVEFVMQLQ-GHSEAECRDRAMALLAQVGLAAQQDKI 140 Query: 132 PDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTVYV 191 P +LSGGQQQRVA+ RA+ P + DEP +NLDAK AE+ +Q+L +Q T ++ Sbjct: 141 PAKLSGGQQQRVAVARALAPRPRFVMADEPTANLDAKSTAELLDIMQSLNEQEGTTFIFS 200 Query: 192 THNQTEAMTMADRIAVMDDGEL 213 TH+ + A R+ V +DG L Sbjct: 201 THD-PRVIARAKRVIVFEDGRL 221 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: 190 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: 227 Length adjustment: 26 Effective length of query: 357 Effective length of database: 201 Effective search space: 71757 Effective search space used: 71757 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: 48 (23.1 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