Align UDP-glucose 4-epimerase; UDP-galactose 4-epimerase; Uridine diphosphate galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_013706597.1 DESAC_RS08145 nucleotide sugar epimerase
Query= SwissProt::A0R5C5 (313 letters) >NCBI__GCF_000195295.1:WP_013706597.1 Length = 347 Score = 167 bits (422), Expect = 4e-46 Identities = 111/312 (35%), Positives = 172/312 (55%), Gaps = 9/312 (2%) Query: 4 LVTGAAGFIGSTLVDRLLADGHG-VVGLDDLSSGRAENLHSAENSDKFEFVKADIVD-AD 61 LVTG AG IGS L L G V+ LDDLSS N+ + N FV+ I+D + Sbjct: 14 LVTGGAGAIGSNLTRALGELGARLVIVLDDLSSASRWNVPALPN---VLFVEGSILDEVE 70 Query: 62 LTGLLAEFKPEVIFHLAAQISVKRSVDDPPFDATVNVVGTVRLAEAARLAGVRKVVHTSS 121 L + E +P++++HLAA + + S+D P D VN +GT+++ + ++AGV++ V+ SS Sbjct: 71 LKRVFFE-RPDIVYHLAALFANQNSLDHPETDLLVNGLGTLKILQYCQMAGVQRCVYASS 129 Query: 122 GGSVYGTPPAYPTSED-MPVNPASPYAAGKVAGEVYLNMYRNLYDLDCSHIAPANVYGPR 180 G S+YG+ P +E+ M ++ +SPY K+ GE+Y N + + YDL N YGP Sbjct: 130 GCSIYGSSAPLPLTEEFMSLHLSSPYQITKMLGELYGNFFHHHYDLPVVKARFFNSYGPG 189 Query: 181 QDPHGEAGVVAIFSEALLAGRTTKIFGDGSDTRDYVFVDDVVDAFVRAG-GPAGGGQRFN 239 + P V+ F + G+T I G G +TRD+ +V D+VD +RAG + GQ FN Sbjct: 190 EIPGQYRNVIPNFIYWAMQGQTLPITGTGEETRDFTYVGDIVDGLLRAGYFESAIGQEFN 249 Query: 240 VGTGVETSTRELHTAIAGAVGAPDEPEFHPPRLGDLRRSRLDNT-RAREVLGWQPQVALA 298 + +GVET +L I VG +F R D + L + RA+ ++G+QP Sbjct: 250 LASGVETRIGDLAQMINDQVGNEAGVKFTERRKWDTKPRLLASVDRAQNLIGYQPHTPFE 309 Query: 299 EGIAKTVEFFRN 310 EG+ T+ +F++ Sbjct: 310 EGLKNTIAWFKD 321 Lambda K H 0.317 0.136 0.396 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: 273 Number of extensions: 23 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: 313 Length of database: 347 Length adjustment: 28 Effective length of query: 285 Effective length of database: 319 Effective search space: 90915 Effective search space used: 90915 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 (21.6 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