Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_010959957.1 MCA_RS03040 NAD-dependent dehydratase
Query= curated2:Q56623 (328 letters) >NCBI__GCF_000008325.1:WP_010959957.1 Length = 324 Score = 229 bits (584), Expect = 7e-65 Identities = 126/311 (40%), Positives = 183/311 (58%), Gaps = 3/311 (0%) Query: 12 ILLTGSTGFVGTNLVKSLTLKSDYIVKSAVRHAVNKDDGL--LFEVGDINASTDFELPLK 69 IL+TG+ GFVG +L L + ++ + R + + VGDI TD++ L+ Sbjct: 3 ILVTGANGFVGRHLTALLVDQGHWVTAAVRREGAAPPTSIAEMRVVGDIGPDTDWDGLLE 62 Query: 70 NTTVVVHCAARAHVMDDKEAEPLTLYREVNTAGTVNLAKQAIDSGVKRFIFISSIKVNGE 129 V+H AAR HVM + PL+ +R+VN GT LA+ A +GV+ +++SS+KV+GE Sbjct: 63 GVDAVIHLAARVHVMRETGPAPLSRFRQVNVLGTERLARAAARTGVRHLVYLSSVKVHGE 122 Query: 130 GTLVGCPFKTEDNHAPEDDYGLSKSEAEKQLVALAKDSSMEVVIIRPTIVYGPGVKANFA 189 + G PF APED YG+SK EAE+ L +A ++ + V + RP +VYGPGV+ANF Sbjct: 123 TSPSGAPFTEAMAPAPEDAYGISKWEAERALAEIAAETGLGVTVFRPPLVYGPGVRANFG 182 Query: 190 SLMRLVSKGIPLPFGSITQNKRSLVSINNLVDLIVTCIDHPKAANQVFLVSDGHDVSTAE 249 L+ V +G+PLPFG++ QN+RSLV + NL D + T + A Q FLVSDG +STAE Sbjct: 183 RLVEAVRRGVPLPFGAV-QNRRSLVYVGNLADAVATSLLRADAIGQTFLVSDGPPLSTAE 241 Query: 250 MVRELAIALDKPTWQLPVPIWCYKLFGKLFGKSDIVDRLTGTLQVDISHTKETLGWKPPQ 309 +VR +A A+ + L +P ++ G L GK + RL G L VD S + L W+P Sbjct: 242 LVRSIARAMHRKPRLLSIPPALLRVTGALTGKRAEIGRLLGDLAVDDSLLRSRLAWQPAY 301 Query: 310 TLQEGFKQTAQ 320 L+EG T + Sbjct: 302 GLEEGLAATVR 312 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: 245 Number of extensions: 9 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: 328 Length of database: 324 Length adjustment: 28 Effective length of query: 300 Effective length of database: 296 Effective search space: 88800 Effective search space used: 88800 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