Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_000744815.1:WP_037572389.1 Length = 386 Score = 235 bits (599), Expect = 2e-66 Identities = 128/290 (44%), Positives = 180/290 (62%), Gaps = 10/290 (3%) Query: 2 GQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIY 61 G ++LT LTK+FG AVD + L I F L+G SGCGK+TTLRM++GLE PT+G I+ Sbjct: 17 GDLRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIH 76 Query: 62 IGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAET 121 +G + R P R + VFQ+YAL+PH+ + +N+ FGL G S ++ V ++ + Sbjct: 77 LGDQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRR-GIRSVKKP--VEDMLDL 133 Query: 122 LGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQ 181 + + L RKP +LSGGQQQR+AL RA++ P+V L+DEPL LD KLR +M+ EL+ +Q Sbjct: 134 VELGHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQ 193 Query: 182 DQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMIN 241 ++ +T V+VTH+Q EAMTMAD IAVM+ G ++Q+ SP E Y PN FVA F+G+ N Sbjct: 194 LEVGLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQS--N 251 Query: 242 LVRGT----RSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVA 287 L+ GT + V H L +LGVRPE + +A Sbjct: 252 LIAGTVESVSGDVVQVAAH-GRSLALPAARCRTTSGPVILGVRPEKVRIA 300 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: 369 Number of extensions: 13 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: 386 Length adjustment: 30 Effective length of query: 353 Effective length of database: 356 Effective search space: 125668 Effective search space used: 125668 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: 50 (23.9 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