Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate Echvi_0060 Echvi_0060 Predicted nucleoside-diphosphate sugar epimerases
Query= SwissProt::Q9ZDJ5 (341 letters) >FitnessBrowser__Cola:Echvi_0060 Length = 624 Score = 142 bits (359), Expect = 2e-38 Identities = 93/281 (33%), Positives = 151/281 (53%), Gaps = 11/281 (3%) Query: 4 DKTLMITGGTGSFGNAVLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALNNSKLKFYIG 63 D+ +M+TG GS G+ + + ++ I + S +++ R S++K + Sbjct: 279 DRVVMVTGAAGSIGSELCRKIIEHKPALLIMVDKAESALYDVEQEFRSGRWKSQIKPILA 338 Query: 64 DVRNYQSIDDA--MHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAINNKVT 121 D+R+ + +D M+ V+HAAA K VP E YP EA+ +NVL +N+ ++ + V+ Sbjct: 339 DIRDAKKMDRIFKMYKPAIVYHAAAYKHVPMMENYPEEAVTSNVLATKNLADLSVLHNVS 398 Query: 122 KVIVLSTDKAVYPINAMGLSKALMEKLAIAKAR---MRSPGETILCVTRYGNVMASRGSV 178 + + +STDKAV P N MG SK + E A +R + T +TR+GNV+ S GSV Sbjct: 399 QFVFVSTDKAVNPTNVMGASKRIAEIYIQALSRYLDVEKGQVTKFAITRFGNVLGSNGSV 458 Query: 179 IPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLY--AFEHGRQGDIFVQKSPASTIE 236 IPLF QI+QG + +T+P+++R+ M++ ++ L+L A G + IF P ++ Sbjct: 459 IPLFKKQIEQGGPVMVTDPNISRYFMTISEACQLILEAGAMSTGNEIFIFDMGEPVKILD 518 Query: 237 VLAKALQ---EIFGSKNAIRFIGTRHGEK-HYESLVSSEDM 273 + K +Q + G I F G R GEK H E L SE + Sbjct: 519 LAKKMIQLSDKKIGEDIKIVFTGLREGEKLHEELLCHSEQL 559 Lambda K H 0.319 0.135 0.373 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: 445 Number of extensions: 22 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: 341 Length of database: 624 Length adjustment: 33 Effective length of query: 308 Effective length of database: 591 Effective search space: 182028 Effective search space used: 182028 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: 51 (24.3 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