Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate Ga0059261_2966 Ga0059261_2966 2-deoxy-D-gluconate 3-dehydrogenase
Query= reanno::Korea:Ga0059261_1894 (259 letters) >FitnessBrowser__Korea:Ga0059261_2966 Length = 251 Score = 128 bits (322), Expect = 1e-34 Identities = 84/244 (34%), Positives = 115/244 (47%), Gaps = 3/244 (1%) Query: 16 LKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERVD 75 L G+ +VTG +GIG GI A+ GAD+ + A VE++ A G KA D Sbjct: 7 LTGRVAVVTGANTGIGQGIALALAQAGADIAAVGRSAATET--VEKVRALGRKAEIVSAD 64 Query: 76 LTDVASLQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIFFCAQ 135 L+ + +Q V+ ++ GG DILVNNA R E TE WD + NLK +FF Q Sbjct: 65 LSTIEPVQRVVDETVEKLGGLDILVNNAGIIRRADSVEFTEEDWDAVMDTNLKSVFFLCQ 124 Query: 136 AVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRATCV 195 A M A GGG I+N+ S+ G + Y K+ + GLT+ LA + GI + Sbjct: 125 AAARHMIANGGGKIINIASMLTFQGGIRVPSYTASKSGVGGLTKLLANEWASKGITVNAI 184 Query: 196 IPGNVRTPRQLKWYSPEGEAEIVAAQCLDGRLA-PEDVAAMVLFLASDDARLVTGHSYFV 254 PG + T E + + GR P D+ +FLAS + V GH V Sbjct: 185 APGYIATNNTDALQKDETRNRQIMERIPAGRWGDPADLGGAAVFLASRASDYVQGHILAV 244 Query: 255 DAGW 258 D GW Sbjct: 245 DGGW 248 Lambda K H 0.321 0.137 0.409 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: 159 Number of extensions: 9 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: 259 Length of database: 251 Length adjustment: 24 Effective length of query: 235 Effective length of database: 227 Effective search space: 53345 Effective search space used: 53345 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 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