Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_051181742.1 G579_RS17890 UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
Query= curated2:A8GWP0 (341 letters) >NCBI__GCF_000423825.1:WP_051181742.1 Length = 345 Score = 215 bits (547), Expect = 2e-60 Identities = 136/338 (40%), Positives = 195/338 (57%), Gaps = 23/338 (6%) Query: 1 MFVDKTLLITGGTGSFGNAVLSRFLKNDIIKDIKEIRIFSRDEKKQEDMRIALNNPKIKF 60 MF DK +LITGGTGSFG + L+ + + ++SRDE KQ +M+ N+P +++ Sbjct: 1 MFNDKAILITGGTGSFGRLYVQTLLER---YRPRRVVVYSRDELKQFEMQQEFNSPVMRY 57 Query: 61 YIGDVRNYNSIDDAMKDVDYVFHAAALKQVPTCEFYPMEAINTNILGAENVLRAATINKV 120 +IGDVR+ + AMK +DYV HAAALKQVP E+ PME I TN+ GAENV+ AA +V Sbjct: 58 FIGDVRDGPRLKQAMKGIDYVIHAAALKQVPAAEYNPMECIKTNVHGAENVINAALECEV 117 Query: 121 AKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMNVRDKTVFCVTRYGNVMASRGSVIP 180 KVI LSTDKA P+N G +K +KL +A + KT F V RYGNV+ SRGSV+P Sbjct: 118 EKVIALSTDKAANPVNLYGATKLASDKLFVAANNITGGSKTRFAVVRYGNVVGSRGSVVP 177 Query: 181 LFINQIKQN-KDLTITEPSMTRFLMSLVDSVDLVLYAFEYGHQGDIFVQKSPASTIEVLA 239 F + + +L IT+P MTRF ++L VD VL FE G++FV K P++ I LA Sbjct: 178 FFKKLLAEGAAELPITDPRMTRFWITLQQGVDFVLKNFERMWGGELFVPKIPSARITDLA 237 Query: 240 KAL-QGIFNSKNKIRFIGTRHGEKHYESLVSSEEMAKAEDLGNYYRIPMDGRDLNYAKYF 298 ++L G+ R +G R GEK +E + ++ + ++Y I R Y Sbjct: 238 ESLAPGL-----PTRIVGIRPGEKLHEIMCPRDDSHLTLEFHDHYVI----RPTITFTYK 288 Query: 299 VE------GEKKIALLEDY---TSHNTKRLNLEEVKEL 327 V+ GE+ + + E + + N L +E+++EL Sbjct: 289 VDYELNALGERGVPVAEGFEYNSGTNPHFLTVEQLREL 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: 277 Number of extensions: 12 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: 345 Length adjustment: 29 Effective length of query: 312 Effective length of database: 316 Effective search space: 98592 Effective search space used: 98592 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