Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized)
to candidate 201911 SO2776 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI ptt file)
Query= SwissProt::P0C0Y4 (266 letters) >FitnessBrowser__MR1:201911 Length = 248 Score = 130 bits (328), Expect = 2e-35 Identities = 87/248 (35%), Positives = 130/248 (52%), Gaps = 10/248 (4%) Query: 16 SLKGKVVIVTGASGPTGIGTEAARGCAEYGADLAITYNSRAEGAEKNAKEMSEKYGVKVK 75 SL GKV +VTGAS GIG A E GA + T S EK A + E G K Sbjct: 6 SLAGKVALVTGAS--RGIGRAIAETLVEAGAVVIGTATS-----EKGAAAIQEYLGDKGF 58 Query: 76 AYKCQVNEYAQCEKLVQDVIKDFGKVDVFIANAGKTADNGILDATVEQWNEVIQTDLTGT 135 V + L + + G VD+ + NAG T DN ++ ++WN++I T+LT Sbjct: 59 GLVLNVTDSQSVTDLFDSIKEKAGDVDILVNNAGITRDNLLMRMKDDEWNDIIDTNLTSL 118 Query: 136 FNCARAVGLHFRERKTGSLVITSSMSGHIANFPQEQASYNVAKAGCIHLAKSLANEWRDF 195 F ++ V +++ G ++ S+ G + N Q +Y+ AKAG I KSLA E Sbjct: 119 FRLSKPVMRTMMKKRFGRIINIGSVVGTMGN--AGQVNYSAAKAGLIGFTKSLAREVASR 176 Query: 196 A-RVNSISPGYIDTGLSDFVPQDIQKLWHSMIPMGRDAKATELKGAYVYFASDASSYCTG 254 VN+I+PG+I T ++D + +D QK S +PM R +A E+ A ++ ASD+++Y TG Sbjct: 177 QITVNAIAPGFIQTDMTDELTEDQQKAIMSQVPMERLGQAQEIANAVLFLASDSAAYITG 236 Query: 255 SDLLIDGG 262 L ++GG Sbjct: 237 ETLHVNGG 244 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: 134 Number of extensions: 7 Number of successful extensions: 4 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: 248 Length adjustment: 24 Effective length of query: 242 Effective length of database: 224 Effective search space: 54208 Effective search space used: 54208 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