Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate 206645 3-oxoacyl-(acyl-carrier-protein) reductase
Query= SwissProt::O93868 (262 letters) >MicrobesOnline__882:206645 Length = 259 Score = 130 bits (327), Expect = 3e-35 Identities = 82/254 (32%), Positives = 128/254 (50%), Gaps = 8/254 (3%) Query: 5 FTISFVNKTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTK 64 F +S + T IVTGG+RGIG A +A AG V + Y S D E ++ G Sbjct: 11 FVMSELTPTAIVTGGSRGIGKAVAETLARAGLQVFLTYVSKPDEAEAVAAGIRDAGGSAT 70 Query: 65 AYQCDVSNTDIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGV 124 A++ DVS+ V Q D + L+ NAG++ + EDF+ V DVN+ G Sbjct: 71 AFRLDVSDAAAVAAFFQSEIKDKVRLDVLVNNAGITKDGLIMRMKDEDFERVLDVNLCGA 130 Query: 125 FNTCRAVAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLA 184 F R +KL + +Q+ G I+ +S+ Q+ G+ Q Y ++KA L K A Sbjct: 131 FTCLREASKL-MTRQRLGRIINITSVVGQM-------GNAGQANYCAAKAGLIGLTKSAA 182 Query: 185 AEWASAGIRVNALSPGYVNTDQTAHMDKKIRDHQASNIPLNRFAQPEEMTGQAILLLSDH 244 E A+ + VNA++PG++ TD TA + +++R IPL R +++ L S+ Sbjct: 183 KELAARNVTVNAVAPGFIETDMTAGLPEEVRKAYVEAIPLRRLGSAQDIADAVAFLASER 242 Query: 245 ATYMTGGEYFIDGG 258 A+Y+TG ++GG Sbjct: 243 ASYITGQVLAVNGG 256 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: 164 Number of extensions: 8 Number of successful extensions: 2 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: 259 Length adjustment: 25 Effective length of query: 237 Effective length of database: 234 Effective search space: 55458 Effective search space used: 55458 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