Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_011767305.1 AZO_RS17995 NAD-dependent dehydratase
Query= curated2:Q56623 (328 letters) >NCBI__GCF_000061505.1:WP_011767305.1 Length = 327 Score = 270 bits (689), Expect = 5e-77 Identities = 141/305 (46%), Positives = 196/305 (64%), Gaps = 3/305 (0%) Query: 13 LLTGSTGFVGTNLVKSLTLKSDYIVKSAVRHAVNKDDGLLFEVGDINASTDFELPLKNTT 72 ++TG++GFVG LV +L + ++ A V + +GD T F L+ Sbjct: 19 VVTGASGFVGQALVAALRARGRDVIPLARGEDVGRGFRAAPALGDSACWTPF---LEGAG 75 Query: 73 VVVHCAARAHVMDDKEAEPLTLYREVNTAGTVNLAKQAIDSGVKRFIFISSIKVNGEGTL 132 VVH AAR HVM D+E +PL +R VN GT+ LA+QA ++ V+RF+F+S++KV+GE + Sbjct: 76 QVVHLAARVHVMKDEEIDPLAAFRAVNVTGTLELARQAAEAKVRRFVFVSTVKVHGENSP 135 Query: 133 VGCPFKTEDNHAPEDDYGLSKSEAEKQLVALAKDSSMEVVIIRPTIVYGPGVKANFASLM 192 G P + D AP D Y SK+EAE+ L L S ME+V+IRP +VYG GVKANF S++ Sbjct: 136 AGRPLRETDALAPVDPYARSKAEAEEGLRNLCARSGMELVVIRPPLVYGAGVKANFRSIV 195 Query: 193 RLVSKGIPLPFGSITQNKRSLVSINNLVDLIVTCIDHPKAANQVFLVSDGHDVSTAEMVR 252 R V+ G+PLP G N+RSLV+++NLVDLI+TC+DHP AA F +DG D+STA +VR Sbjct: 196 RWVASGMPLPLGGCNANRRSLVALDNLVDLIITCLDHPGAAGGCFFAADGEDLSTAALVR 255 Query: 253 ELAIALDKPTWQLPVPIWCYKLFGKLFGKSDIVDRLTGTLQVDISHTKETLGWKPPQTLQ 312 LA A+ +P PVP+W +L G D++ RL G+LQVDIS +ETLGW PP + Sbjct: 256 RLARAMGRPARLWPVPLWMLRLAAAGTGHHDVLQRLCGSLQVDISSARETLGWTPPVGVD 315 Query: 313 EGFKQ 317 EG ++ Sbjct: 316 EGLRR 320 Lambda K H 0.318 0.134 0.388 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: 262 Number of extensions: 6 Number of successful extensions: 2 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: 328 Length of database: 327 Length adjustment: 28 Effective length of query: 300 Effective length of database: 299 Effective search space: 89700 Effective search space used: 89700 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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