Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate WP_004289114.1 BUB52_RS00875 SDR family oxidoreductase
Query= SwissProt::Q8NK50 (266 letters) >NCBI__GCF_900129655.1:WP_004289114.1 Length = 271 Score = 108 bits (271), Expect = 9e-29 Identities = 88/268 (32%), Positives = 130/268 (48%), Gaps = 24/268 (8%) Query: 15 FSLKGKVVVVTGASGPRGMGIEAARGCAEMGADLAITYSSRKEGAEKNAEELTKEYGVKV 74 FS+ GKV V+TGA G G I A+ + GA + + R+E +K EEL K YG V Sbjct: 5 FSIAGKVAVITGAGGVLGGSI--AKCFMQQGAKV-VAVDIRQEQLDKRVEEL-KTYGEDV 60 Query: 75 KVYKVNQSDYNDVERFVNQVVSDFGKIDAFIANAGATANSGVV-------DGSASDWDHV 127 N D +E+ + +V+ +G+ID + AG + D S W+ V Sbjct: 61 IGIVGNVLDIASLEKLADDIVAKWGRIDILLNIAGGNMPGATLAPDQHFYDMDISCWEKV 120 Query: 128 IQVDLSGTAYCAKAVGAHFKKQGHGSLVITASMSGHVANYPQEQTSYNVAKAGCIH---- 183 ++++GT Y + KQG G +V +SM+ + A Y+ AK + Sbjct: 121 TNLNMNGTVYPSLVFSKVMAKQGKGCIVNVSSMAAYSAI--TRVPGYSAAKTAVANFTQW 178 Query: 184 LARSLANEWRDFARVNSISPGYI--DTGLSDFIDEKTQELWRSM-----IPMGRNGDAKE 236 LA LA ++ D RVN+I+PG+ D + I+ RS PM R GD E Sbjct: 179 LASELALKYGDGIRVNAIAPGFFIGDQNRAVLINPDGSLTDRSKKVLAKTPMKRFGDINE 238 Query: 237 LKGAYVYLVSDASSYTTGADIVIDGGYT 264 L GA +L SDA+S+ TGA + IDGG++ Sbjct: 239 LNGAVQFLCSDAASFVTGALLPIDGGFS 266 Lambda K H 0.314 0.131 0.379 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: 148 Number of extensions: 11 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: 271 Length adjustment: 25 Effective length of query: 241 Effective length of database: 246 Effective search space: 59286 Effective search space used: 59286 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: 42 (22.0 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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