Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized)
to candidate Ac3H11_1578 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= SwissProt::P0C0Y4 (266 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1578 Length = 236 Score = 108 bits (269), Expect = 1e-28 Identities = 74/240 (30%), Positives = 123/240 (51%), Gaps = 8/240 (3%) Query: 24 VTGASGPTGIGTEAARGCAEYGADLAITYNSRAEGAEKNAKEMSEKYGVKVKAYKCQVNE 83 VTGAS GIG A A G + T + EGA + ++ ++ G + VN+ Sbjct: 1 VTGAS--RGIGAAIALELAVRGYQVVGTATTD-EGAARISQALAAYPGCR--GANLNVND 55 Query: 84 YAQCEKLVQDVIKDFGKVDVFIANAGKTADNGILDATVEQWNEVIQTDLTGTFNCARAVG 143 A E L+ ++K G + V + NAG T D + + W+ V+ T+L F +RA Sbjct: 56 VAAVEALMDSIVKQQGGLHVLVNNAGITRDTLAMRMKDDDWDAVMDTNLKAVFRVSRAAI 115 Query: 144 LHFRERKTGSLVITSSMSGHIANFPQEQASYNVAKAGCIHLAKSLANEWRDFA-RVNSIS 202 +++ G ++ +S+ G N QA+Y AKAG + ++LA E + VN ++ Sbjct: 116 RPMMKQRFGRIISITSVVGASGN--PGQANYAAAKAGVAGMTRALARELGSRSITVNCVA 173 Query: 203 PGYIDTGLSDFVPQDIQKLWHSMIPMGRDAKATELKGAYVYFASDASSYCTGSDLLIDGG 262 PG+I+T ++ +P+D QK ++ IP+G K ++ A Y AS + Y TG +L ++GG Sbjct: 174 PGFIETDMTSVLPEDQQKALNAQIPLGHMGKPADVAHAVAYLASREAGYVTGQELHVNGG 233 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: 139 Number of extensions: 7 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: 236 Length adjustment: 24 Effective length of query: 242 Effective length of database: 212 Effective search space: 51304 Effective search space used: 51304 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: 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