Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_013706824.1 DESAC_RS09365 UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
Query= SwissProt::Q9ZDJ5 (341 letters) >NCBI__GCF_000195295.1:WP_013706824.1 Length = 326 Score = 218 bits (555), Expect = 2e-61 Identities = 142/340 (41%), Positives = 197/340 (57%), Gaps = 23/340 (6%) Query: 1 MFVDKTLMITGGTGSFGNA----VLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALNNS 56 MF DK ++ITGGTGSFG +L R+ II IFSRDE KQ +M ++ Sbjct: 1 MFDDKAILITGGTGSFGRKCAQILLERYAPRKII-------IFSRDEYKQFEMGRIFSHE 53 Query: 57 K---LKFYIGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLS 113 K +++++GDVR+ + + A H VDY+ HAAALKQ+P E+ P EA+ TN+LGA+NV++ Sbjct: 54 KYPNMRYFLGDVRDKERLYRAFHEVDYIIHAAALKQIPAAEYNPFEAVKTNILGAQNVIN 113 Query: 114 AAINNKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMA 173 AI+ KV KVI LSTDKA P+N G +K +KL IA TI V RYGNV+ Sbjct: 114 VAIDQKVKKVIALSTDKAANPVNLYGATKLCSDKLFIAGNAYVGRDHTIFSVVRYGNVVG 173 Query: 174 SRGSVIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPAS 233 SRGSVIPLF+ + +G L IT+P MTRF ++L +V VL E G++FV K P+ Sbjct: 174 SRGSVIPLFLRERAKG-VLPITDPRMTRFWITLEQAVLFVLDCLERMVGGELFVPKLPSM 232 Query: 234 TIEVLAKALQEIFGSKNAIRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRIPMDGRDLN 293 I LA A+ G + + IG R GEK +E +++ +D + YY I D R Sbjct: 233 NIMDLAAAI----GPECQTKIIGIRPGEKLHELMITKDDARNTIEFKDYYVIKPDFR--Y 286 Query: 294 YAKYFVTGEKKVALLD-DYTS-HNTKRLNLKEVKELLLTL 331 +A+ F D +Y S +N RL +E++EL+ L Sbjct: 287 FARRFQEEAGTPTPPDFEYDSLNNPWRLQPEELRELIQDL 326 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: 288 Number of extensions: 9 Number of successful extensions: 5 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: 326 Length adjustment: 28 Effective length of query: 313 Effective length of database: 298 Effective search space: 93274 Effective search space used: 93274 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: 49 (23.5 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