Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized)
to candidate SMc02037 SMc02037 oxidoreductase
Query= SwissProt::P0C0Y4 (266 letters) >FitnessBrowser__Smeli:SMc02037 Length = 256 Score = 169 bits (429), Expect = 4e-47 Identities = 100/256 (39%), Positives = 147/256 (57%), Gaps = 7/256 (2%) Query: 13 DLFSLKGKVVIVTGASGPTGIGTEAARGCAEYGADLAITYNSRAEGAEKNAKEMSEKYGV 72 +LF L G+ VTG G GIG A E GA +AI+ SR EG EK +++ +K G+ Sbjct: 4 ELFRLNGRAAFVTG--GSRGIGFACAEALGEAGARVAISARSRDEG-EKAVRQLRQK-GI 59 Query: 73 KVKAYKCQVNEYAQCEKLVQDVIKDFGKVDVFIANAGKTADNGILDATVEQWNEVIQTDL 132 + ++ + +++V+ + G +D+ + NAG L E W+EVI T+L Sbjct: 60 EAIYLPADISNESAAQQVVRQAAAELGGLDILVNNAGIARHCDSLKLEPETWDEVINTNL 119 Query: 133 TGTFNCARAVGLHFRERKTGSLVITSSMSGHIANFPQEQASYNVAKAGCIHLAKSLANEW 192 TG F C RA GS+V S+SG+I+N PQ Q +YN +KAG L KSLA E+ Sbjct: 120 TGLFWCCRAAIETMSAAGRGSIVNIGSISGYISNLPQNQVAYNASKAGVHMLTKSLAGEF 179 Query: 193 -RDFARVNSISPGYIDTGLSDFVPQDIQ--KLWHSMIPMGRDAKATELKGAYVYFASDAS 249 + R+N+++PGYI+T ++ D + K+W M P+GR KA+E+ A ++ ASDA+ Sbjct: 180 AKSNIRINAVAPGYIETAMTQGGLDDPEWSKIWLGMTPLGRAGKASEVAAAVLFLASDAA 239 Query: 250 SYCTGSDLLIDGGYCV 265 SY TGS L IDGGY + Sbjct: 240 SYITGSVLTIDGGYTI 255 Lambda K H 0.316 0.132 0.389 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: 158 Number of extensions: 5 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: 266 Length of database: 256 Length adjustment: 25 Effective length of query: 241 Effective length of database: 231 Effective search space: 55671 Effective search space used: 55671 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 (21.6 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