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_2630 Ga0059261_2630 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= SwissProt::Q6CEE9 (278 letters) >FitnessBrowser__Korea:Ga0059261_2630 Length = 254 Score = 128 bits (322), Expect = 1e-34 Identities = 93/251 (37%), Positives = 133/251 (52%), Gaps = 13/251 (5%) Query: 31 LKGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLS---KTYGVRSKAY 87 L+GK +TG S+GIG A A A+ GA+VAI Y S SD+KA + G R A Sbjct: 4 LEGKTVLVTGGSTGIGRAAAIGAARHGANVAINYAS--SDDKAASCVAEIEALGKRGLAV 61 Query: 88 KCAVTNAKQVETTIQTIEKDFGKIDIFIANAGI-PWTAGPMIDVPNNEEWDKVVDLDLNG 146 K V + + FG++D+ ++NAGI P+ A +D+P E D+ ++L+G Sbjct: 62 KGDVALPETATDFVSKAVAAFGRVDVMVSNAGICPFHA--FLDMPV-ETVDRTFRVNLHG 118 Query: 147 AYYCAKYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLHLSRSLAVEWAG 206 AYY + A KQG G I S +V + Q Y K V L +S A+ Sbjct: 119 AYYMVQAAANQMVKQGEGGAIVAVSSISALVG-GEYQTHYTPTKAGVHSLMQSAAIALGK 177 Query: 207 FA-RCNTVSPGYMATEIS--DFIPRDTKEKWWQLIPMGREGDPSELAGAYIYLASDASTY 263 RCN+V PG + TEI+ D +D +++ IP+GR G+ +LAG ++LASD + Y Sbjct: 178 HGIRCNSVLPGTILTEINKDDLADQDKRDRMTARIPLGRLGESEDLAGPIVFLASDMAAY 237 Query: 264 TTGADILVDGG 274 TGA +LVDGG Sbjct: 238 VTGAALLVDGG 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: 142 Number of extensions: 12 Number of successful extensions: 5 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: 254 Length adjustment: 25 Effective length of query: 253 Effective length of database: 229 Effective search space: 57937 Effective search space used: 57937 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