Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate Ga0059261_2966 Ga0059261_2966 2-deoxy-D-gluconate 3-dehydrogenase
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__Korea:Ga0059261_2966 Length = 251 Score = 156 bits (395), Expect = 3e-43 Identities = 102/253 (40%), Positives = 138/253 (54%), Gaps = 23/253 (9%) Query: 14 FRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARE----LDGTFERL 69 F L GR A+VTG GIG IA LAQAGA + VG AA E + + Sbjct: 5 FDLTGRVAVVTGANTGIGQGIALALAQAGADIAA------VGRSAATETVEKVRALGRKA 58 Query: 70 NVTDAD---------AVADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDG 120 + AD V + +L +D+LVNNAGI+R A + + ++DW AV+ NL Sbjct: 59 EIVSADLSTIEPVQRVVDETVEKLGGLDILVNNAGIIRRADSVEFTEEDWDAVMDTNLKS 118 Query: 121 VFWCCREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWAS 180 VF+ C+ R M+A G G I++ ASM P +Y ASK+ V LT+ LA EWAS Sbjct: 119 VFFLCQAAARHMIANGGGKIINIASMLTFQGGIRVP--SYTASKSGVGGLTKLLANEWAS 176 Query: 181 RGVRVNAVAPGYTATPLTRRGLETPEWRETWLKE-TPLGRLAEPREIAPAVLYLASDAAS 239 +G+ VNA+APGY AT T L+ E R + E P GR +P ++ A ++LAS A+ Sbjct: 177 KGITVNAIAPGYIATNNT-DALQKDETRNRQIMERIPAGRWGDPADLGGAAVFLASRASD 235 Query: 240 FVTGHTLVVDGGY 252 +V GH L VDGG+ Sbjct: 236 YVQGHILAVDGGW 248 Lambda K H 0.319 0.134 0.408 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: 178 Number of extensions: 7 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: 255 Length of database: 251 Length adjustment: 24 Effective length of query: 231 Effective length of database: 227 Effective search space: 52437 Effective search space used: 52437 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: 46 (22.3 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