Align Putative UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_012969466.1 ALVIN_RS01120 epimerase
Query= curated2:Q57664 (305 letters) >NCBI__GCF_000025485.1:WP_012969466.1 Length = 328 Score = 184 bits (466), Expect = 3e-51 Identities = 118/325 (36%), Positives = 176/325 (54%), Gaps = 34/325 (10%) Query: 2 ILVTGGAGFIGSHIVDKLIEN--NYDVIILDNLTTGNKNNINPKAEF------------- 46 +L+TGG GFIG+ ++ KL+ + I+DN TG+ ++ F Sbjct: 5 VLITGGCGFIGTSLIHKLLARYPTAHIRIVDNFVTGSPADLAEVCVFQSTQAADLAQATL 64 Query: 47 ------VNADIRDKDLDEKINFKDVEVVIHQAAQINVRNSVENPVYDGDINVLGTINILE 100 + DIRD D + + V+ ++H AA V SVE+P D D NV+GT N LE Sbjct: 65 TAGVFLLEGDIRDADFLLQCA-QGVDCIVHLAANTGVGPSVEDPRLDMDCNVVGTFNALE 123 Query: 101 MMRKYDIDKIVFASSGG-AVYGEPNYLPVDENHPINPLSPYGLSKYVGEEYIKLYNRLYG 159 R + + +FASSG A EP P+ E P +P+SPYG SK GE Y Y R +G Sbjct: 124 AARLNGVKRFIFASSGAPAGEVEP---PIHEELPPHPVSPYGASKLAGEGYCSAYYRTFG 180 Query: 160 IEYAILRYSNVYGERQDPKGEAGVISIFIDKMLKNQSPIIFGDGNQTRDFVYVGDVAKAN 219 IE LR+ NVYG R K ++ V++ FI + L+ + II+GDG QTRDF+Y+ D+ +A Sbjct: 181 IETICLRFGNVYGPRS--KKKSSVVAKFIRQALQGEPCIIYGDGTQTRDFLYIDDLVRAV 238 Query: 220 LMALNWK--NEIVNIGTGKETSVNELFDIIKHEIGFRG---EAIYDKPREGEVYRIYLDI 274 ++A+ E I TG E +V E+ ++ + RG + +D PR G+V R + D Sbjct: 239 MLAMEQPVGGETFQIATGMERTVGEVATLLAKALEKRGTHMDIQHDSPRLGDVRRNFSDT 298 Query: 275 KK-AESLGWKPEIDLKEGIKRVVNW 298 K A L W+ E+++ EGI+R ++W Sbjct: 299 SKAARLLEWRTEVEVPEGIERTLDW 323 Lambda K H 0.317 0.140 0.405 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: 264 Number of extensions: 17 Number of successful extensions: 6 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: 305 Length of database: 328 Length adjustment: 27 Effective length of query: 278 Effective length of database: 301 Effective search space: 83678 Effective search space used: 83678 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: 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