Align UDP-glucose 4-epimerase; UDP-galactose 4-epimerase; Uridine diphosphate galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate 7026960 Shewana3_4089 NAD-dependent epimerase/dehydratase (RefSeq)
Query= SwissProt::A0R5C5 (313 letters) >FitnessBrowser__ANA3:7026960 Length = 335 Score = 159 bits (403), Expect = 7e-44 Identities = 110/334 (32%), Positives = 170/334 (50%), Gaps = 29/334 (8%) Query: 1 MRTLVTGAAGFIGSTLVDRLLADGHGVVGLDDLSSG-----RAENLHSAENSDKFEFVKA 55 M+ LVTGAAGFIG+ + +RL A GH VVG+D+L+ + L E F F+K Sbjct: 1 MKYLVTGAAGFIGAKVSERLCAQGHEVVGIDNLNDYYDVGLKLARLAPLEALSNFRFIKL 60 Query: 56 DIVDAD-LTGLLAEFKPEVIFHLAAQISVKRSVDDPPFDATVNVVGTVRLAEAARLAGVR 114 D+ D D + L AE + HLAAQ V+ S+D+P A N+VG + + E R + Sbjct: 61 DLADRDGIATLFAEQGFRRVIHLAAQAGVRYSLDNPLAYADSNLVGHLTILEGCRHHKIE 120 Query: 115 KVVHTSSGGSVYGTPPAYP-TSEDMPVNPASPYAAGKVAGEVYLNMYRNLYDLDCSHIAP 173 +V+ SS SVYG P ++ED +P S YAA K A E+ + Y +LY L + + Sbjct: 121 HLVYASS-SSVYGLNQKMPFSTEDSVDHPISLYAATKKANELMSHTYSHLYQLPTTGLRF 179 Query: 174 ANVYGPRQDPHGEAGVVAIFSEALLAGRTTKIFGDGSDTRDYVFVDDVVDAFVR------ 227 VYGP P + F++A+LAG ++ G +RD+ ++DD+V+ +R Sbjct: 180 FTVYGPWGRPD---MALFKFTKAILAGDIIDVYNHGDLSRDFTYIDDIVEGIIRVQDKPP 236 Query: 228 ---------AGGPAGGG---QRFNVGTGVETSTRELHTAIAGAVGAPDEPEFHPPRLGDL 275 G PA + FN+G G + TA+ A+G +F P + GD+ Sbjct: 237 RPTPDWRVETGTPANSSAPYRVFNIGNGSPVQLLDFITALESALGIEANKQFLPMQPGDV 296 Query: 276 RRSRLDNTRAREVLGWQPQVALAEGIAKTVEFFR 309 + D + +G++PQV + G+ + VE++R Sbjct: 297 HSTWADTEDLFKAVGYKPQVDINTGVGRFVEWYR 330 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: 265 Number of extensions: 13 Number of successful extensions: 4 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: 335 Length adjustment: 28 Effective length of query: 285 Effective length of database: 307 Effective search space: 87495 Effective search space used: 87495 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: 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