Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_014264878.1 ACIX8_RS08235 glucose 1-dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >NCBI__GCF_000178955.2:WP_014264878.1 Length = 258 Score = 133 bits (335), Expect = 3e-36 Identities = 79/248 (31%), Positives = 127/248 (51%), Gaps = 6/248 (2%) Query: 19 LKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKAD 78 L K ++ G GIG A+ A A +V S +AE+V+ A G L +D Sbjct: 8 LTGKTAVIVGGTSGIGLAMAIGLAEAGADVVASSRRAEQVDEAAKKIESTGRKSLRLTSD 67 Query: 79 VSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCK 138 V+++ L A+ ++ G++D+L+NCAG ++ E++W+ ++ G C+ Sbjct: 68 VADRASLEALCAGTIKEFGKVDILINCAGKIKRAPTVDFPEDEWQSIMDTNVTGTLRACQ 127 Query: 139 AVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAI 198 M+E+G G IINIAS ++ + Y +K + LTR+L +E++ +GV VNAI Sbjct: 128 IFGRHMLERGYGRIINIASLNTFVALKEVAAYAASKAAIGSLTRSLAVEWSSQGVTVNAI 187 Query: 199 APGYIETQLNVDYWNGFADPYAERQRALDLHPPR-RIGQPIEVAMTAVFLASDEAPFINA 257 APG T LN + + +ER + L + P R G E+ A++LASD A F+ Sbjct: 188 APGVFRTALNAELLD-----KSERGKELRMRTPMGRFGATEELVGGAIYLASDSAAFVTG 242 Query: 258 SCITIDGG 265 + IDGG Sbjct: 243 EILVIDGG 250 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: 7 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: 272 Length of database: 258 Length adjustment: 25 Effective length of query: 247 Effective length of database: 233 Effective search space: 57551 Effective search space used: 57551 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