Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate AO356_21080 AO356_21080 sugar dehydrogenase
Query= SwissProt::Q8NK50 (266 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_21080 Length = 266 Score = 121 bits (303), Expect = 2e-32 Identities = 87/255 (34%), Positives = 131/255 (51%), Gaps = 11/255 (4%) Query: 16 SLKGKVVVVTGASGPRGMGIEAARGCAEMGADLAITYSSRKEGAEKNAEELTKEYGVKVK 75 SL +V +VTGAS G+G +AR A+ GA + + Y S A+ A E+ G + Sbjct: 4 SLARQVALVTGASS--GIGAGSARALADAGAAVVLNYHSSAGPAQDLAREINANGGRAIA 61 Query: 76 VYKVNQSDYNDVERFVNQVVSDFGKIDAFIANAGATANSGVVDGSASDWDHVIQVDLSGT 135 V + S ++VE+ Q + FG +D +AN+G ++ VD S +DW+ VI +L+G Sbjct: 62 V-GADVSKEHEVEQLFAQTLEAFGTLDILVANSGLQKDAAAVDMSLADWNTVIGTNLTGQ 120 Query: 136 AYCAKAVGAHFKKQG-HGSLVITASMSGHVANYPQE-----QTSYNVAKAGCIHLARSLA 189 CA+A F +QG + A H+++ Q +Y +K G L +SLA Sbjct: 121 FLCARAALRVFNRQGIRQGVSRAAGKIIHMSSVHQRIPWAGHVNYAASKGGVDLLMQSLA 180 Query: 190 NEW-RDFARVNSISPGYIDTGLSDFIDEKTQE-LWRSMIPMGRNGDAKELKGAYVYLVSD 247 E R+NSI+PG I T ++ E QE ++IP GR GD +++ A V+L SD Sbjct: 181 QETSHQRIRINSIAPGAIRTAINREATEGEQEQKLLALIPYGRVGDVEDVANAVVWLASD 240 Query: 248 ASSYTTGADIVIDGG 262 S Y G + IDGG Sbjct: 241 LSDYVVGTTLFIDGG 255 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: 177 Number of extensions: 17 Number of successful extensions: 3 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: 266 Length adjustment: 25 Effective length of query: 241 Effective length of database: 241 Effective search space: 58081 Effective search space used: 58081 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 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