Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_039104322.1 FPB0191_RS04330 UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
Query= curated2:A8GWP0 (341 letters) >NCBI__GCF_000807275.1:WP_039104322.1 Length = 332 Score = 213 bits (542), Expect = 6e-60 Identities = 134/333 (40%), Positives = 199/333 (59%), Gaps = 12/333 (3%) Query: 1 MFVDKTLLITGGTGSFGNAVLSRFLKNDIIK-DIKEIRIFSRDEKKQEDM-RIALNNPKI 58 MF DK +LITGGTGSFG+ +F++ + K + K+I I+SRDE KQ +M ++ N+ +I Sbjct: 1 MFKDKVILITGGTGSFGH----KFVEMTLTKYNPKKIIIYSRDEMKQWEMAKLYANDTRI 56 Query: 59 KFYIGDVRNYNSIDDAMKDVDYVFHAAALKQVPTCEFYPMEAINTNILGAENVLRAATIN 118 +F+IGDVR+ + + A+ VDYV HAAA K VPT E+ P E I TNI GA NV+ A Sbjct: 57 RFFIGDVRDRDRLYRALDGVDYVVHAAATKIVPTAEYNPFECIKTNINGAMNVIDACIDK 116 Query: 119 KVAKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMNVRDKTVFCVTRYGNVMASRGSV 178 V + + LSTDKA P N G +K +K+ +A + DKT F V RYGNVM SRGSV Sbjct: 117 GVKRAVALSTDKASSPANLYGATKLASDKMFVAGNSYSGADKTKFSVVRYGNVMGSRGSV 176 Query: 179 IPLFINQIKQNKDLTITEPSMTRFLMSLVDSVDLVLYAFEYGHQGDIFVQKSPASTIEVL 238 IP F++ IK +L IT+ MTRF+++L V+LV +AFE G+I+V+K P+ + + Sbjct: 177 IPFFLS-IKNKGELPITDARMTRFMITLEQGVELVWHAFEDMIGGEIYVKKIPSMKVTDV 235 Query: 239 AKALQGIFNSKNKIRFIGTRHGEKHYESLVSSEEMAKAEDLGNYYRI-PMDGRDLNYAKY 297 A ++ K+ +G R GEK +E ++S+E+ + +Y+I P N K Sbjct: 236 ALSIL----PDAKLNIVGIRPGEKLHEQMISAEDSYYTYEYPEHYKILPAINGWENCTKR 291 Query: 298 FVEGEKKIALLEDYTSHNTKRLNLEEVKELLLN 330 G+K + +NT+ +++E ++ L N Sbjct: 292 IKNGKKVPEGFIYSSDNNTEWMSIETLQNWLSN 324 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: 305 Number of extensions: 18 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: 332 Length adjustment: 28 Effective length of query: 313 Effective length of database: 304 Effective search space: 95152 Effective search space used: 95152 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