Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_109967995.1 DK846_RS05790 NAD-dependent epimerase/dehydratase family protein
Query= BRENDA::O73960 (318 letters) >NCBI__GCF_003173355.1:WP_109967995.1 Length = 312 Score = 284 bits (726), Expect = 2e-81 Identities = 154/315 (48%), Positives = 206/315 (65%), Gaps = 8/315 (2%) Query: 1 MRVLVTGGAGFIGSHLVDRLMEEGYKVRVLDDLSAGSLKNIEGWLGNENFEFIKGDMRDV 60 MR +VTGGAGFIGSH+VD L+ +G +V V+D L AG L+ I L + +FI+ ++ + Sbjct: 1 MRSIVTGGAGFIGSHIVDHLVAQGDEVVVIDALLAGDLRFISRHLDSGAVKFIRANLLEP 60 Query: 61 EIVSKAVKDVDAVFHLAANPEVRIGSQSPELLYETNVLITYNLLNAVRNSGVKYLVFTSS 120 D V+H+AA+P+VR + +P+ ++ T+ +L A+R + +VFTS+ Sbjct: 61 GW-QDVCAGADRVWHIAADPDVRESAVTPDAQLNNTIIATHRVLEAIRLHKIPEIVFTST 119 Query: 121 STVYGDAKVIPTPEDYAPLEPISVYGAAKLAAEALISGYAHTFDFRALIIRLANIIGKRS 180 STVYG+A VIPTPE Y P+EP+SVYGAAKLA EALIS Y H+F R I R ANIIG RS Sbjct: 120 STVYGEATVIPTPETYTPMEPVSVYGAAKLACEALISAYCHSFGVRGYIFRFANIIGPRS 179 Query: 181 NHGVIYDFINKLKANPNELEILGDGTQRKSYLHISDTIDGIMKLFEHFLNGEERVDFYNL 240 HGVI DFI KL+ANP ELEILGDG Q KSYL ++ + I + H ++V+ YN+ Sbjct: 180 GHGVITDFIKKLRANPKELEILGDGKQTKSYLEVTACVAAISYVIAH---ANDQVNTYNI 236 Query: 241 GNEDWITVKEIAEIVSEEMNL-NPRFKFTGGVDGGRGWKGDVKLMLLSIEKAKRTGWKPR 299 G+EDWI V IA+I+ +E L +K+TG G RGW GDV M LS+EK K G+ P Sbjct: 237 GSEDWIDVTTIADILVKEAGLAGVSYKYTG---GSRGWVGDVPKMQLSVEKLKSLGYTPT 293 Query: 300 MNSYEAVRKTVREML 314 + S+E+VR VR L Sbjct: 294 IGSHESVRLAVRAAL 308 Lambda K H 0.318 0.138 0.397 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: 283 Number of extensions: 15 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: 318 Length of database: 312 Length adjustment: 27 Effective length of query: 291 Effective length of database: 285 Effective search space: 82935 Effective search space used: 82935 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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