Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_111394018.1 CLV31_RS16420 glucose 1-dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >NCBI__GCF_003253485.1:WP_111394018.1 Length = 264 Score = 147 bits (370), Expect = 3e-40 Identities = 88/248 (35%), Positives = 137/248 (55%), Gaps = 5/248 (2%) Query: 19 LKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRER-GADVHALKA 77 LK K ++TG +G+G A+ A AS A +++ +A + AA E+ G A Sbjct: 17 LKGKSAIITGGTKGLGLAMAAGLASAGANVLLVSRKASDGDQAAAEIAEKFGVKALTFSA 76 Query: 78 DVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137 DV++Q + AMA+ A E G ID+L+N AG+N+ E+T ED+ + ++++G W C Sbjct: 77 DVADQAGMEAMAKFAHEAFGSIDILINSAGINIRGAIDELTHEDFTKVMEVNVNGTWLAC 136 Query: 138 KAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNA 197 +AV P M EQ G+IIN+AST + PY +K ++ +TRAL +E AP + VNA Sbjct: 137 RAVTPFMKEQKKGAIINLASTLGLVGLANRTPYTASKGAVVQMTRALALELAPWNINVNA 196 Query: 198 IAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINA 257 I PG T++N+ AD ++ + R G+ E+ A+FLAS A ++ Sbjct: 197 ICPGPFLTEMNLP----IADTEEGKKFVVGATALGRWGELKEIQGAAIFLASYAATYMVG 252 Query: 258 SCITIDGG 265 S +T+DGG Sbjct: 253 SMVTVDGG 260 Lambda K H 0.321 0.137 0.419 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: 151 Number of extensions: 9 Number of successful extensions: 4 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: 272 Length of database: 264 Length adjustment: 25 Effective length of query: 247 Effective length of database: 239 Effective search space: 59033 Effective search space used: 59033 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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