Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized)
to candidate 6938129 Sama_2250 acetoacetyl-CoA reductase (RefSeq)
Query= SwissProt::P0C0Y4 (266 letters) >FitnessBrowser__SB2B:6938129 Length = 243 Score = 105 bits (262), Expect = 9e-28 Identities = 76/244 (31%), Positives = 122/244 (50%), Gaps = 9/244 (3%) Query: 20 KVVIVTGASGPTGIGTEAARGCAEYGADLAITYNSRAEGAEKNAKEMSEKYGVKVKAYKC 79 K V+VTGA+G GIG A + T + + A + EM++K GV +K Y Sbjct: 4 KAVVVTGATG--GIGWTIAEYLMSLEYFVIGTTHRAPQSACEQWIEMADKRGVLIK-YDS 60 Query: 80 QVNEYAQCEKLVQDVIKDFGKVDVFIANAGKTADNGILDATVEQWNEVIQTDLTGTFNCA 139 V+ + + L++ + + + + N G T D+ T EQW +V+ +L F+ Sbjct: 61 NVDNLS-IDTLIE--VANGHSIYGLVNNLGITRDSSFKKMTSEQWKQVMDVNLFSVFSLT 117 Query: 140 RAVGLHFRERKTGSLVITSSMSGHIANFPQEQASYNVAKAGCIHLAKSLANEW-RDFARV 198 + + H +G +V SS++ H F Q +Y AKAG + K+L+ E + V Sbjct: 118 QCIFNHMALSGSGRIVNISSVNAHRGQFGQ--VNYCAAKAGLLGFTKALSLEGAKSGITV 175 Query: 199 NSISPGYIDTGLSDFVPQDIQKLWHSMIPMGRDAKATELKGAYVYFASDASSYCTGSDLL 258 NS+SPGY DT + +P DI + +PM R AK E+ A + D S+Y TG+D+ Sbjct: 176 NSVSPGYTDTKMLSHIPTDILQSIKDSVPMKRLAKPIEIAHAVAFLLDDKSAYITGADIP 235 Query: 259 IDGG 262 ++GG Sbjct: 236 VNGG 239 Lambda K H 0.316 0.132 0.389 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: 178 Number of extensions: 10 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: 266 Length of database: 243 Length adjustment: 24 Effective length of query: 242 Effective length of database: 219 Effective search space: 52998 Effective search space used: 52998 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 (21.6 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