Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate Ga0059261_2966 Ga0059261_2966 2-deoxy-D-gluconate 3-dehydrogenase
Query= SwissProt::Q6CEE9 (278 letters) >FitnessBrowser__Korea:Ga0059261_2966 Length = 251 Score = 123 bits (308), Expect = 5e-33 Identities = 83/252 (32%), Positives = 132/252 (52%), Gaps = 13/252 (5%) Query: 29 FSLKGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLSKTYGVRSKAYK 88 F L G+VA +TG+++GIG +A A AQAGAD+A S ++ + + G +++ Sbjct: 5 FDLTGRVAVVTGANTGIGQGIALALAQAGADIAAVGRSAATETVEKV--RALGRKAEIVS 62 Query: 89 CAVTNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWDKVVDLDLNGAY 148 ++ + V+ + + G +DI + NAGI A + E+WD V+D +L + Sbjct: 63 ADLSTIEPVQRVVDETVEKLGGLDILVNNAGIIRRADSVEFT--EEDWDAVMDTNLKSVF 120 Query: 149 YCAKYAGQIFKKQGYGSFIFTASMSGHI--VNIPQMQACYNAAKCAVLHLSRSLAVEWAG 206 + + A + G G I ASM + +P Y A+K V L++ LA EWA Sbjct: 121 FLCQAAARHMIANGGGKIINIASMLTFQGGIRVPS----YTASKSGVGGLTKLLANEWAS 176 Query: 207 FA-RCNTVSPGYMATEISDFIPRDT--KEKWWQLIPMGREGDPSELAGAYIYLASDASTY 263 N ++PGY+AT +D + +D + + IP GR GDP++L GA ++LAS AS Y Sbjct: 177 KGITVNAIAPGYIATNNTDALQKDETRNRQIMERIPAGRWGDPADLGGAAVFLASRASDY 236 Query: 264 TTGADILVDGGY 275 G + VDGG+ Sbjct: 237 VQGHILAVDGGW 248 Lambda K H 0.317 0.132 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: 155 Number of extensions: 11 Number of successful extensions: 6 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: 278 Length of database: 251 Length adjustment: 25 Effective length of query: 253 Effective length of database: 226 Effective search space: 57178 Effective search space used: 57178 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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