Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate 350961 BT1433 putative oxidoreductase (NCBI ptt file)
Query= SwissProt::O93868 (262 letters) >FitnessBrowser__Btheta:350961 Length = 270 Score = 106 bits (265), Expect = 4e-28 Identities = 81/265 (30%), Positives = 131/265 (49%), Gaps = 26/265 (9%) Query: 11 NKTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAYQCDV 70 +K +++TGG +G +A GA V V+ RS + + E + E G + DV Sbjct: 9 DKVVVITGGAGILGKGIAAYLAKEGAKVVVLDRSEEAGKALVESIKAE-GNEAMFLYTDV 67 Query: 71 SNTDI-------VTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFG 123 + ++ + K +ID L A G +A A ++ K +L + FK V D+N+FG Sbjct: 68 MDKEVLEGNKVEIMKAYGRIDVLLNAAGGNMAGATIAPDKTFFDLQIDAFKKVVDLNLFG 127 Query: 124 VFNTCRAVAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGL 183 A++ ++ Q+KGSIV ++S+L V Y ++KAA +N K + Sbjct: 128 TVLPTMVFAEIMVE-QKKGSIV-------NFCSESALRPLTRVVGYGAAKAAIANFTKYM 179 Query: 184 AAEWA---SAGIRVNALSPGYVNTDQTAHM----DKKIRDHQAS---NIPLNRFAQPEEM 233 A E A G+RVNA++PG+ TDQ + D + D + + P NRF +PE++ Sbjct: 180 AGELALKFGNGLRVNAIAPGFFLTDQNRALLTNPDGSLTDRSKTILAHTPFNRFGEPEDL 239 Query: 234 TGQAILLLSDHATYMTGGEYFIDGG 258 G L+SD + ++TG IDGG Sbjct: 240 YGTIHYLISDASNFVTGTVAVIDGG 264 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: 156 Number of extensions: 5 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: 270 Length adjustment: 25 Effective length of query: 237 Effective length of database: 245 Effective search space: 58065 Effective search space used: 58065 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