Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate 5208820 Shew_1322 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= SwissProt::O93868 (262 letters) >FitnessBrowser__PV4:5208820 Length = 242 Score = 115 bits (289), Expect = 7e-31 Identities = 76/249 (30%), Positives = 126/249 (50%), Gaps = 13/249 (5%) Query: 12 KTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAYQCDVS 71 K IIVTGG+RG+GLA + A G V+ R+ +E E+ F K + C++ Sbjct: 2 KHIIVTGGSRGLGLAIVTHLLAQGYKVSTCSRATTSTIEALEQSNPNF----KWFPCEIG 57 Query: 72 NTDIVTKTIQQ--IDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFNTCR 129 N + ++ +++ I A+ + GLI NAG++ + + + VN+ G T R Sbjct: 58 NAEQTSQFVKEACIWANESPLWGLINNAGIAKEGVLATFPNIESDALIQVNLNGALYTAR 117 Query: 130 AVAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLAAEWAS 189 V +++L++ G I+ SS II G Y++SKA L + LA E Sbjct: 118 EVLRVFLRQNSAGRIINISS----IIGSRGYTGLAA---YSASKAGLDGLTRALARENGR 170 Query: 190 AGIRVNALSPGYVNTDQTAHMDKKIRDHQASNIPLNRFAQPEEMTGQAILLLSDHATYMT 249 I VN+++PGY++T+ ++ + K RD P++R + +++T LLSD A ++T Sbjct: 171 RNITVNSIAPGYLDTEMSSTLSDKKRDQIIRRTPMHRLGKVDDITPAISFLLSDGAAFIT 230 Query: 250 GGEYFIDGG 258 G IDGG Sbjct: 231 GQTLTIDGG 239 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: 128 Number of extensions: 4 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: 242 Length adjustment: 24 Effective length of query: 238 Effective length of database: 218 Effective search space: 51884 Effective search space used: 51884 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: 46 (22.3 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