Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate N515DRAFT_2198 N515DRAFT_2198 Tropinone reductase 1
Query= SwissProt::O93868 (262 letters) >FitnessBrowser__Dyella79:N515DRAFT_2198 Length = 280 Score = 121 bits (304), Expect = 1e-32 Identities = 82/252 (32%), Positives = 129/252 (51%), Gaps = 13/252 (5%) Query: 13 TIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFG-VKTKAYQCDVS 71 T ++TG ++GIG A R +A GAN+ ++ R +V ++ +F ++ A+ D+S Sbjct: 34 TALITGASKGIGYAVARELAGLGANLLLVARDDDHLEQVRVELADDFDHIEVLAFAADLS 93 Query: 72 NTDIVTKTIQQIDADLGA-ISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFNTCRA 130 + I ADLGA +S L+ NAG + E + D++ ++++N+F F CR Sbjct: 94 MQEDRLAVFDWI-ADLGAPLSLLVNNAGGNTPAAVLEYSERDYRAIFELNLFSAFEMCR- 151 Query: 131 VAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLAAEWASA 190 +A L + +IV S+S + T Y SKAA L + LAAEWA+ Sbjct: 152 LAHPQLVQHANAAIVNVGSVSG-------ITHVRTGAAYGMSKAALHQLTRNLAAEWATD 204 Query: 191 GIRVNALSPGYVNTDQT--AHMDKKIRDHQASNIPLNRFAQPEEMTGQAILLLSDHATYM 248 GIRVNA++P Y+ T ++ A D + D + PL R +PEE+ L A+Y+ Sbjct: 205 GIRVNAVAPWYIRTQRSEPALADDEYLDEVLDHTPLRRIGEPEEVAAAIAFLCLPAASYI 264 Query: 249 TGGEYFIDGGQL 260 TG +DGG L Sbjct: 265 TGQVLAVDGGFL 276 Lambda K H 0.317 0.130 0.372 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: 168 Number of extensions: 13 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: 262 Length of database: 280 Length adjustment: 25 Effective length of query: 237 Effective length of database: 255 Effective search space: 60435 Effective search space used: 60435 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