Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_043458116.1 H537_RS0103160 ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_000430725.1:WP_043458116.1 Length = 331 Score = 206 bits (524), Expect = 8e-58 Identities = 112/241 (46%), Positives = 155/241 (64%), Gaps = 5/241 (2%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 +A L L ++K Y G AV+ I L + G + L+GPSGCGK+TTLRM+AG E Sbjct: 5 LAHLELVALSKRY----GPGTPAVDAIDLQVRAGSYCCLLGPSGCGKTTTLRMIAGHEVA 60 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 TEG++ L R + + A R AM+FQSYAL+PH + N++FGL+ G+ R R Sbjct: 61 TEGDILLGARNITDLDATQRGTAMMFQSYALFPHLNALDNVAFGLK-MRGVDAATRRARA 119 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 E D++ + RKPG+LSGGQQQRVAL RA++ +P+V L+DEPLS LD LR +MR Sbjct: 120 AELLDLVAMGAYAQRKPGELSGGQQQRVALARALITNPKVLLLDEPLSALDPFLRVKMRA 179 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 EL+R Q +LG + V+VTH Q EAM + D+V V++ G ++Q GTP ++ P FVA F+ Sbjct: 180 ELKRWQKDLGFSFVHVTHSQEEAMALADQVVVMNAGRIEQQGTPHQIFNAPRTEFVARFM 239 Query: 241 G 241 G Sbjct: 240 G 240 Lambda K H 0.316 0.136 0.384 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: 295 Number of extensions: 10 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: 331 Length adjustment: 29 Effective length of query: 354 Effective length of database: 302 Effective search space: 106908 Effective search space used: 106908 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: 42 (22.0 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