Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate PfGW456L13_3262 Short-chain dehydrogenase/reductase SDR
Query= SwissProt::O93868 (262 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3262 Length = 248 Score = 107 bits (266), Expect = 3e-28 Identities = 86/256 (33%), Positives = 127/256 (49%), Gaps = 14/256 (5%) Query: 10 VNKTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRS-AKDAVEVTEKVGKEFGVKTKAYQC 68 ++K I++TGG+RGIG A AA G + + Y++ + A V E+V + G + A + Sbjct: 1 MDKVIVITGGSRGIGAATALLAAAQGYRICINYQADEQSAFGVLEQV-RALGAQAIAVRA 59 Query: 69 DVSNTDIVTKTIQQIDADLGAISGLIANAG-VSVVKPATELTHEDFKFVYDVNVFGVFNT 127 DVS D V ++D++LG ++ L+ NAG V E++ + NV Sbjct: 60 DVSIEDEVIALFNRVDSELGRVTALVNNAGTVGQKSRVDEMSEFRILKIMKTNVLAPM-L 118 Query: 128 CRAVAKLWLQKQ---QKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLA 184 C A L + + Q GSIV SS++S+ L V Y +SK A GL+ Sbjct: 119 CAKHAILRMSPRHGGQGGSIVNVSSVASR------LGSPNEYVDYAASKGALDTFTIGLS 172 Query: 185 AEWASAGIRVNALSPGYVNTDQTAHMDKKIR-DHQASNIPLNRFAQPEEMTGQAILLLSD 243 E A GIRVNA+ PGY+ TD A R S IP+ R +P+E+ + LLSD Sbjct: 173 KEVAGEGIRVNAVRPGYIYTDFHALSGDPDRVSKLESAIPMARGGRPDEVAEAIVWLLSD 232 Query: 244 HATYMTGGEYFIDGGQ 259 A+Y TG + GG+ Sbjct: 233 KASYATGTFVDLGGGR 248 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: 148 Number of extensions: 11 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: 262 Length of database: 248 Length adjustment: 24 Effective length of query: 238 Effective length of database: 224 Effective search space: 53312 Effective search space used: 53312 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