Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_109969581.1 DK846_RS13945 SDR family NAD(P)-dependent oxidoreductase
Query= curated2:A8GWP0 (341 letters) >NCBI__GCF_003173355.1:WP_109969581.1 Length = 343 Score = 204 bits (518), Expect = 3e-57 Identities = 129/342 (37%), Positives = 189/342 (55%), Gaps = 23/342 (6%) Query: 5 KTLLITGGTGSFGNAVLSRFLKNDIIKDIKEIRIFSRDEKKQEDMRIALNNPKIKFYIGD 64 K +LITGG GS G+ ++ ++ D + IR+F +E D+ LN+ K++ IGD Sbjct: 10 KRVLITGGVGSIGSVLVREIIQ----LDPEFIRVFDNNETALFDLEQDLNSQKLRPLIGD 65 Query: 65 VRNYNSIDDAMKDVDYVFHAAALKQVPTCEFYPMEAINTNILGAENVLRAATINKVAKVI 124 +R+ + AM+ VD VFHAAALK VP CEF P +AI TN+LG +NVL A I V K+I Sbjct: 66 IRDKARLVMAMEHVDIVFHAAALKHVPICEFNPFDAIKTNVLGTQNVLEAGLIQGVGKII 125 Query: 125 VLSTDKAVYPINAMGLSKALMEKLAIAKARMNVRDKTVFCVTRYGNVMASRGSVIPLFIN 184 +STDKAV P N MG +K L E+L I+ KT F R+GNV+ SRGSVIP F+ Sbjct: 126 TVSTDKAVNPSNVMGATKLLAERLTISANSYRGHKKTAFSCVRFGNVLNSRGSVIPTFLK 185 Query: 185 QIKQNKDLTITEPSMTRFLMSLVDSVDLVLYAFEYGHQGDIFVQKSPASTIEVLAKALQG 244 QI++ ++IT P M RF+M + + L+L A +IF+ K P I+ L + ++ Sbjct: 186 QIRKGGPISITHPDMRRFIMDIPSAAKLILIAGILAEGKEIFILKMPVIRIQDLGEVMKE 245 Query: 245 IFNSKN-------KIRFIGTRHGEKHYESLVSSEEMAKAEDLGNYYRI-----PMDGRDL 292 +F S + + IG R GEK E L++++E A + + Y I P + + Sbjct: 246 MFASHYGYTPNDIETQIIGLRGGEKIDEVLMTTDETIAAYESDSMYLILPKERPYGNKTI 305 Query: 293 --NYAKYFVEGEKKIALLEDYTSHNTKRLNLEEVKELLLNLD 332 N F E + I Y+S + L+ EE++ LL L+ Sbjct: 306 KPNIPAGFRELSEGI-----YSSRDLPLLSKEEIRHLLAELE 342 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: 270 Number of extensions: 13 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: 341 Length of database: 343 Length adjustment: 29 Effective length of query: 312 Effective length of database: 314 Effective search space: 97968 Effective search space used: 97968 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