Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_025331514.1 SALWKB2_RS09875 ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_000600005.1:WP_025331514.1 Length = 311 Score = 166 bits (419), Expect = 1e-45 Identities = 87/228 (38%), Positives = 133/228 (58%), Gaps = 1/228 (0%) Query: 9 LTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMN 68 + K+F D V DLSL++ D + + ++G SG GKST L M AGL P SG+I+I +++ Sbjct: 7 INKKFSDKVVAADLSLEVADGQLVAVLGESGSGKSTLLNMAAGLVQPDSGNIFINEENIT 66 Query: 69 YRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLL 128 + +P+ R I ++FQDYAL PH+ V QN+ FGL + + + +++ +G+++ Sbjct: 67 FLLPEQRRIGLMFQDYALLPHLNVWQNVAFGLRMHR-VSKPQAQHQAMQMLAEVGLSEAA 125 Query: 129 DRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTT 188 R+ D LSGG+QQRVAL RA+V P+ L+DEP S LD LRA ++ L Q Sbjct: 126 ARQVDVLSGGEQQRVALARALVLQPQALLLDEPFSALDTTLRASLQQLTVRLLRQQKCPA 185 Query: 189 VYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIG 236 V VTH+ EA +ADRI ++ G Q + + P + + A +G Sbjct: 186 VLVTHSPLEAFALADRICLLRHGRWIQQGTAAQLLARPADAWAARLLG 233 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: 236 Number of extensions: 9 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: 311 Length adjustment: 29 Effective length of query: 354 Effective length of database: 282 Effective search space: 99828 Effective search space used: 99828 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 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