Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_026608426.1 METAC_RS0120285 UDP-glucuronate 5-epimerase
Query= BRENDA::A3MUJ4 (312 letters) >NCBI__GCF_000427445.1:WP_026608426.1 Length = 336 Score = 124 bits (312), Expect = 2e-33 Identities = 101/330 (30%), Positives = 147/330 (44%), Gaps = 38/330 (11%) Query: 1 MRIVVTGGAGFIGSHLVDKLVELGYEVVVVDN--------LSSGRREFVNPS-----AEL 47 MRI+VTG AGFIG HL +L+E G++VV VD L R E + S E Sbjct: 1 MRILVTGSAGFIGFHLARRLLEAGHDVVGVDGFTPYYDRTLKLKRHEILAQSQSFTGCEA 60 Query: 48 HVRDLKDYSWGAGIKGDVVFHFAANPEVRLSTTEPIVHFNENVVATFNVLEWARQTGVRT 107 + DL G D V+HFAA VR S P + + N+V TFN+LE R Sbjct: 61 MLEDLPALQDIYGEGYDAVYHFAAQAGVRYSLENPRAYVDANLVGTFNLLELMRHKPPAH 120 Query: 108 VVFASSSTVYGDADVIPTPE-EEPYKPISVYGAAKAAGEVMCATYARLFGVRCLAVRYAN 166 + AS+S+VYG +P E + P++ Y A+K A E M Y LFG+ +R+ Sbjct: 121 ALMASTSSVYGANASVPFREIDRADHPLTFYAASKKANEEMAHAYGHLFGIPITMLRFFT 180 Query: 167 VVGPRLRHGV-IYDFIMKLRRNPNVLEVLGDGTQRKSYLYVRDAVEATLAAWKKF----- 220 V GP R + ++ F L L++ G R+ + Y+ D VEA + +K Sbjct: 181 VYGPWGRPDMALFKFAAALFEG-RPLDIYNRGDMRRDFTYIDDLVEAMILLLEKVPPAPS 239 Query: 221 ------EEMD-----APFLALNVGNVDAVRVLDIAQIVAEVLGLRPEIRLVPSTPDGRGW 269 E+D AP+ +N+G + ++D + GLR + Sbjct: 240 RRQSAPSEIDSLSPTAPWRVVNIGAQTPIALMDFVAAIEAATGLRAACNFMDMQ------ 293 Query: 270 PGDVKYMTLAVTKLMKLTGWRPTMTSAEAV 299 GDV L++LTG+ P T + V Sbjct: 294 EGDVPLTHADTRLLIQLTGFTPRTTLQDGV 323 Lambda K H 0.320 0.137 0.409 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: 255 Number of extensions: 9 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: 312 Length of database: 336 Length adjustment: 28 Effective length of query: 284 Effective length of database: 308 Effective search space: 87472 Effective search space used: 87472 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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