Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_102999338.1 C1M55_RS10010 glucose 1-dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2119 (272 letters) >NCBI__GCF_002893965.1:WP_102999338.1 Length = 256 Score = 144 bits (363), Expect = 2e-39 Identities = 86/250 (34%), Positives = 133/250 (53%), Gaps = 7/250 (2%) Query: 19 LKNKVVLLTGAAQGIGEAIVATFASQQARLIISDIQGEKVEKVAAHWRDQGADVVAIKAD 78 L NKV ++TGA GIG AI F ++ AR+++SDI G + VA D +A+ D Sbjct: 5 LANKVAIVTGAGAGIGAAIARAFGAEGARVVVSDINGGAAQAVA----DSIDGAIAVTTD 60 Query: 79 VSRQQDLHAMARLAIDLHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCK 138 V+ +Q + + A++ G ++V+V AG+ +E + EDWR+ +++L+G + + Sbjct: 61 VTDEQQVKDLVARAVEEFGGLNVVVPNAGIATTTPLIETSFEDWRKVMSVNLNGVFLTVR 120 Query: 139 AVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAI 198 LP ++ G GSI+NI+S ST P Y AK + LT L E G+R NA+ Sbjct: 121 HSLPALVASGGGSIVNISSISSTTGSPLIGSYAAAKAAVRNLTETLSAELRFHGIRANAL 180 Query: 199 APGYIETQLNVDYWNGFADPHAERQRAFD---LHPPRRIGQPIEVAMTAVFLASDEAPFI 255 PG+I+T L + F + FD + R G+ EVA AVF ASD++ + Sbjct: 181 LPGFIDTDLVKSHQQDFENALGLESGGFDDLMVTKQTRYGRTEEVAAAAVFFASDQSSWC 240 Query: 256 NASCITIDGG 265 N S + +DGG Sbjct: 241 NGSSLVLDGG 250 Lambda K H 0.322 0.138 0.426 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: 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: 272 Length of database: 256 Length adjustment: 25 Effective length of query: 247 Effective length of database: 231 Effective search space: 57057 Effective search space used: 57057 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 (21.9 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