Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 8502259 DvMF_2969 ABC transporter related (RefSeq)
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Miya:8502259 Length = 418 Score = 213 bits (543), Expect = 6e-60 Identities = 119/281 (42%), Positives = 173/281 (61%), Gaps = 23/281 (8%) Query: 23 AVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQDRDI 82 AV ++S +++ G F ++GPSGCGK+T LRM+AG E+ G + + R + G++ R + Sbjct: 43 AVNDVSFEVEQGRFFSILGPSGCGKTTLLRMIAGFESPDSGVIAIRGRDMAGIAPNRRPV 102 Query: 83 AMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPGQLSG 142 ++FQ AL+P SV N++FGL+ G+ EI +RV++ + +G+ + P QLSG Sbjct: 103 NLIFQHLALFPMMSVAENVAFGLKRR-GMAGGEISRRVQDVLERVGLPGYGVKMPAQLSG 161 Query: 143 GQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTHDQTE 202 GQ+QRVA+ R +V +P V L+DEPL LD KLR +M+ EL+ LQ E+G T VY+THDQ+E Sbjct: 162 GQKQRVAIARCLVLEPAVLLLDEPLGALDLKLREQMKVELKTLQAEVGTTFVYITHDQSE 221 Query: 203 AMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGDTFRGDGF 262 A+ M D VAV++ G +QV TP + Y RP + FVAGF+GE N++ G+L T GD Sbjct: 222 ALVMSDHVAVMNAGRFEQVDTPRNLYRRPASAFVAGFVGE--TNVWSGTLEEAT--GD-- 275 Query: 263 DYPLSGATRDQLGG------ASGLTLG------IRPEDVTV 291 +G R G A+GL G IRPE V + Sbjct: 276 ----AGLVRTDEGAVFRARVAAGLAKGTRVDMFIRPEAVLI 312 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: 487 Number of extensions: 32 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: 418 Length adjustment: 31 Effective length of query: 352 Effective length of database: 387 Effective search space: 136224 Effective search space used: 136224 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 17 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