Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_900105005.1:WP_090274680.1 Length = 378 Score = 214 bits (544), Expect = 4e-60 Identities = 109/236 (46%), Positives = 161/236 (68%), Gaps = 3/236 (1%) Query: 20 DIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQD 79 D +AV++++L I+ GE L+G SG GKST LR++AG ET +EG + L+ + + + Sbjct: 32 DALAVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGFETPSEGRVLLDGQNITALPPHK 91 Query: 80 RDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPGQ 139 R I M+FQSYAL+PH +V N++FGL++ L + EI +RV E ++ ++ RKP Q Sbjct: 92 RPINMMFQSYALFPHMTVEQNIAFGLKQDK-LSNTEISERVAEMLKLVHMAKYAKRKPHQ 150 Query: 140 LSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTHD 199 LSGGQ+QRVAL R++ + P++ L+DEP+ LD KLR++M+ EL + +GVT + VTHD Sbjct: 151 LSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIERVGVTCIMVTHD 210 Query: 200 QTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGD 255 Q EAMTM R+A++D G + QVGTP+D Y P N VA F+G S+N+F+G + D Sbjct: 211 QEEAMTMAQRIAIMDQGWIVQVGTPMDIYESPVNRHVAEFVG--SVNIFEGEIVAD 264 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: 396 Number of extensions: 14 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: 378 Length adjustment: 30 Effective length of query: 353 Effective length of database: 348 Effective search space: 122844 Effective search space used: 122844 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: 50 (23.9 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