Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_011033083.1 MM_RS05900 UDP-glucose 4-epimerase
Query= BRENDA::O73960 (318 letters) >NCBI__GCF_000007065.1:WP_011033083.1 Length = 316 Score = 335 bits (860), Expect = 7e-97 Identities = 169/316 (53%), Positives = 224/316 (70%), Gaps = 7/316 (2%) Query: 2 RVLVTGGAGFIGSHLVDRLMEEGYKVRVLDDLSAGSLKNIEGWLGNENFEFIKGDMRDVE 61 RVLVTGGAGFIGS+LVDRL+E+ +V V D+LS+G + IE L N +F FIKGD+ D E Sbjct: 6 RVLVTGGAGFIGSNLVDRLLEKESEVIVFDNLSSGKMDFIENHLENPDFSFIKGDLLDPE 65 Query: 62 IVSKAVKDVDAVFHLAANPEVRIGSQSPELLYETNVLITYNLLNAVRNSGVKYLVFTSSS 121 + K KD D V+H+AANP+V++G+ ++ + N+L TYNLL A+R K + FTS+S Sbjct: 66 AIEKVCKDTDMVYHVAANPDVKLGASDTKVHLDQNILATYNLLEAMRKGSAKKIAFTSTS 125 Query: 122 TVYGDAKVIPTPEDYAPLEPISVYGAAKLAAEALISGYAHTFDFRALIIRLANIIGKRSN 181 TVYG+A ++PTPE+Y PL PIS+YGA+KLA EALI+ Y+HTFD +A I R ANI+G RS Sbjct: 126 TVYGEASIMPTPENYGPLIPISLYGASKLACEALITSYSHTFDMQAWIFRFANIVGPRST 185 Query: 182 HGVIYDFINKLKANPNELEILGDGTQRKSYLHISDTIDGIMKLFEHFLNGEERVDFYNLG 241 HG+ DFI KLK NP +LEILGDG Q KSYLH+S+ ++ I+ E +E V+ +N+G Sbjct: 186 HGITVDFIKKLKENPRKLEILGDGKQEKSYLHVSECVNAILFAIE---KSKEEVNIFNIG 242 Query: 242 NEDWITVKEIAEIVSEEMNLNP-RFKFTGGVDGGRGWKGDVKLMLLSIEKAKRTGWKPRM 300 +ED I+ EI +IV EEM L+ F +TG G RGWKGDV M L IEK K GWKP Sbjct: 243 SEDTISATEIGKIVVEEMGLSDVEFTYTG---GSRGWKGDVPRMRLGIEKLKAIGWKPEY 299 Query: 301 NSYEAVRKTVREMLEE 316 S +VR+T R ++++ Sbjct: 300 TSERSVRETARAVIDK 315 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: 312 Number of extensions: 11 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: 318 Length of database: 316 Length adjustment: 27 Effective length of query: 291 Effective length of database: 289 Effective search space: 84099 Effective search space used: 84099 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