Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate H281DRAFT_04849 H281DRAFT_04849 UDP-glucose 4-epimerase
Query= curated2:Q56623 (328 letters) >FitnessBrowser__Burk376:H281DRAFT_04849 Length = 318 Score = 219 bits (557), Expect = 9e-62 Identities = 134/314 (42%), Positives = 179/314 (57%), Gaps = 12/314 (3%) Query: 12 ILLTGSTGFVGTNLVKSLTLKSDYIVKSAVRHAVNKDDGLLFEVGDINASTDFELPLKN- 70 ++++G+ GFVG L ++L L + + V VR + N DG+ V +ASTD+ N Sbjct: 4 VVVSGANGFVGRALCRAL-LGAGHCVTGLVRRSGNCVDGVTEWV---DASTDYHGIAHNW 59 Query: 71 -----TTVVVHCAARAHVMDDKEAEPLTLYREVNTAGTVNLAKQAIDSGVKRFIFISSIK 125 VVH AAR HVM D A+P T +R N GT+ LA A GV RF+F+SSIK Sbjct: 60 PANMKADCVVHLAARVHVMHDTAADPETAFRATNVDGTLRLAATARRHGVPRFVFVSSIK 119 Query: 126 VNGEGTLVGCPFKTEDNHAPEDDYGLSKSEAEKQLVALAKDSSMEVVIIRPTIVYGPGVK 185 E + G D+ PED YG SK AE L+ + D+ +EVVI+RP +VYGP V+ Sbjct: 120 AVAEQSR-GQSLCENDSPRPEDAYGRSKRAAEDALIRMGDDTGLEVVIVRPPLVYGPHVR 178 Query: 186 ANFASLMRLVSKGIPLPFGSITQNKRSLVSINNLVDLIVTCIDHPKAANQVFLVSDGHDV 245 ANF LM V +G+PLP G +RS+V + NL D +V C +AA Q F V+D Sbjct: 179 ANFLRLMDAVWRGVPLPLGG-ADARRSMVYVGNLADALVHCATDARAARQCFHVADSDAP 237 Query: 246 STAEMVRELAIALDKPTWQLPVPIWCYKLFGKLFGKSDIVDRLTGTLQVDISHTKETLGW 305 + AE+VR L L KP LPVP ++ +L G+S VDRL G+LQVD SH ++ LGW Sbjct: 238 TVAELVRSLGRHLGKPVRLLPVPAAWLRMAARLTGQSSRVDRLLGSLQVDTSHIRDVLGW 297 Query: 306 KPPQTLQEGFKQTA 319 PP + EG TA Sbjct: 298 HPPFSTDEGLAATA 311 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: 252 Number of extensions: 11 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: 318 Length adjustment: 28 Effective length of query: 300 Effective length of database: 290 Effective search space: 87000 Effective search space used: 87000 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 17 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