Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_078210583.1 BXU11_RS00205 ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_002017945.1:WP_078210583.1 Length = 233 Score = 125 bits (313), Expect = 2e-33 Identities = 81/218 (37%), Positives = 123/218 (56%), Gaps = 13/218 (5%) Query: 4 IQLTDLTKRFG----DTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59 I +T+L+K F +T A+ D+S+ I+ EF+ ++G SG GKST L ++ L++ TSG Sbjct: 2 IHITNLSKIFRTEELETKALSDISMTINQGEFVTIMGASGSGKSTLLNIVGLLDSATSGS 61 Query: 60 I------YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDE 113 IG + ++I +FQ++ L +TV NI L ++AER + Sbjct: 62 YELLNQQMIGLKEQEKSKVRKQNIGFIFQNFNLIDELTVFDNIELPLIYNN-VSAAERKK 120 Query: 114 RVVEVAETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEM 173 +V +AE L I+ L P +LSGGQQQRVA+ RA++ DP++ L DEP NLD+K E+ Sbjct: 121 KVAAIAERLNISHRLKHYPQQLSGGQQQRVAVARALINDPKIILADEPTGNLDSKNGNEV 180 Query: 174 RTELQNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDG 211 L +L Q T V VTH+ +A + + R +M DG Sbjct: 181 MELLTDLHAQ-GATIVMVTHSDYDA-SFSQRTILMKDG 216 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: 168 Number of extensions: 10 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: 233 Length adjustment: 26 Effective length of query: 357 Effective length of database: 207 Effective search space: 73899 Effective search space used: 73899 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 24 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