Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_044410319.1 NA59_RS07300 UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
Query= SwissProt::Q9ZDJ5 (341 letters) >NCBI__GCF_000934765.1:WP_044410319.1 Length = 336 Score = 229 bits (585), Expect = 6e-65 Identities = 131/277 (47%), Positives = 174/277 (62%), Gaps = 16/277 (5%) Query: 1 MFVDKTLMITGGTGSFGN----AVLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALNNS 56 MF +KT+ ITGGTGSFG +L+R+ II IFSRDE KQ +M+ N+S Sbjct: 1 MFDNKTIFITGGTGSFGKKYTQTLLARYKPKKII-------IFSRDELKQFEMQQVFNDS 53 Query: 57 KLKFYIGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAI 116 ++++IGDVR+ +++AM GVD+V HAAALKQVP E+ PME I TN+ GAENV+ AAI Sbjct: 54 CMRYFIGDVRDKNRLEEAMEGVDFVIHAAALKQVPAAEYNPMECIKTNINGAENVIRAAI 113 Query: 117 NNKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRG 176 N+V ++I LSTDKA PIN G +K +KL +A + +T V RYGNV+ SRG Sbjct: 114 KNRVPRIIALSTDKAANPINLYGATKLASDKLFVAANNIAGGKDTRFSVVRYGNVIGSRG 173 Query: 177 SVIPLFIHQIKQG-KELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPASTI 235 SV+P F + QG EL IT P MTRF+++L VD VL FE + G+IFV K P+ + Sbjct: 174 SVVPFFKKLLAQGATELPITHPDMTRFMITLQQGVDFVLKNFERMQGGEIFVPKIPSMNM 233 Query: 236 EVLAKALQEIFGSKNAIRFIGTRHGEKHYESLVSSED 272 LAKA+ K IG R GEK +E + ++D Sbjct: 234 VELAKAMAPTLPQK----IIGIRPGEKMHEIMCPADD 266 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: 304 Number of extensions: 16 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: 336 Length adjustment: 28 Effective length of query: 313 Effective length of database: 308 Effective search space: 96404 Effective search space used: 96404 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