Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 209225 DVU0291 ABC transporter, ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >MicrobesOnline__882:209225 Length = 354 Score = 152 bits (384), Expect = 1e-41 Identities = 95/234 (40%), Positives = 131/234 (55%), Gaps = 16/234 (6%) Query: 21 DLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMNYRVPQNRD--IA 78 D++L E + LVGPSG GK+T LR +AGL+ P G I + PQ + Sbjct: 20 DVNLTAAAGEVVCLVGPSGVGKTTLLRCIAGLDAPDEGTIRV-------TPPQGHGGGVV 72 Query: 79 MVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA-----ETLGIADLLDRKPD 133 +VFQDY L+PH++V +N+ FG G A ERV + +T +A + R P Sbjct: 73 LVFQDYLLFPHLSVFENVAFG-PRARGVRGAALKERVHTMLRAFRLDTDDLAHMASRYPA 131 Query: 134 ELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTVYVTH 193 +LS GQ+QRVAL RA+V DP V L+DEP +NLD LR EM ++++ + V TV VTH Sbjct: 132 QLSAGQRQRVALARALVCDPAVLLLDEPFANLDRGLRGEMAAFVRDVVRRFGVATVTVTH 191 Query: 194 NQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINLVRGTR 247 + EA + DR+ VM G L Q+A P + Y P + A F+G P+ L TR Sbjct: 192 DLEEAFAIGDRLGVMLGGTLAQLAPPLDVYRHPADEATARFLG-PVTVLDETTR 244 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: 330 Number of extensions: 19 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: 354 Length adjustment: 30 Effective length of query: 353 Effective length of database: 324 Effective search space: 114372 Effective search space used: 114372 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 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