Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate Dsui_0400 Dsui_0400 putative nucleoside-diphosphate sugar epimerase
Query= SwissProt::Q9ZDJ5 (341 letters) >FitnessBrowser__PS:Dsui_0400 Length = 620 Score = 136 bits (343), Expect = 1e-36 Identities = 97/284 (34%), Positives = 152/284 (53%), Gaps = 17/284 (5%) Query: 1 MFVDKTLMITGGTGSFGNAV---LSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALNNSK 57 + ++T+++TG GS G+ + ++RF ++ + E+ F+ + +QE R Sbjct: 289 LIAERTILVTGAGGSIGSELARQIARFAPRQLV--LFEVSEFALYQIEQE-FRRTFPGLD 345 Query: 58 LKFYIGDVRNYQSIDD--AMHGVDYVFHAAALKQVPTCEFY-PMEAINTNVLGAENVLSA 114 + +GDV++ + A + VFHAAA K VP E EA+ NVLG V A Sbjct: 346 VVCVVGDVKDEARLQQVFAAYRPALVFHAAAYKHVPLMESANAWEAVRNNVLGTWRVAMA 405 Query: 115 AINNKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMAS 174 A V K++++STDKAV P N MG +K + E+ + ++ ++ G T V R+GNV+ S Sbjct: 406 ARQAGVEKMVLISTDKAVNPTNVMGTTKRMAER--VVQSLEQAGGGTQFIVVRFGNVLGS 463 Query: 175 RGSVIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFV--QKSPA 232 GSVIP F QI +G +T+T P + R+ M + ++ LVL A G G+IFV P Sbjct: 464 NGSVIPTFREQIARGGPVTVTHPDIIRYFMLIPEAAQLVLQAGLMGNGGEIFVLDMGEPV 523 Query: 233 STIEVLAKALQEIFG---SKNAIRFIGTRHGEKHYESLVSSEDM 273 ++ LA+ L + G + I F G R GEK YE L++ +M Sbjct: 524 KIVD-LARDLIRLSGFTEEEIPIEFTGLRPGEKLYEELLADNEM 566 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: 393 Number of extensions: 19 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: 341 Length of database: 620 Length adjustment: 33 Effective length of query: 308 Effective length of database: 587 Effective search space: 180796 Effective search space used: 180796 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